Oxidative stress in mollusks Biomphalaria Glabrata exposed to gamma radiation

International Nuclear Information System (INIS)

Silva, Luanna R.S.; Augusto, Ricielle L.; Siqueira, Williams N.; Luna Filho, Ricardo L.C.; Pereira, Dewson R.; França, Elvis J.; Silva, Edvane B.; Melo, Ana M.M.A.

2017-01-01

Ionizing radiation can cause biological changes in different organisms such as mollusks from Biomphalaria glabrata species, in which alterations could be observed in the reproductive system of the specimens, prejudicing fertility and fecundity. As the changes may occur due to the lipid peroxidation caused by the action of free radicals on the gonads, the objective of this work was to evaluate the oxidative damage caused by the exposure of B. glabrata mollusks to different doses of gamma radiation. In addition, efforts were carried out to standardize a sensitive and low-cost technique for detecting negative effects caused by high doses of ionizing radiation. For this, each mollusk group (n = 10) was submitted to 0 (control), 10, 15, 20 and 25 Gy (Gammacell- "6"0Co, dose rate 3.532 kGy/h). The TBARS method was applied for the quantification of lipid peroxidation of the gonads of the mollusks after 24 and 48 h. ANOVA, followed by the mean comparison (Tukey) at the 5% of significance level, indicated high concentrations of TBARS in the gonads after 24 h. Otherwise, after 48 h, differences for TBARS concentrations were not significant at the 95% confidence level, determining that the action of free radicals from ionizing radiation on cell membranes mainly occurred within 24 h after irradiation. (author)

Oxidative stress in mollusks Biomphalaria Glabrata exposed to gamma radiation

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Silva, Luanna R.S.; Augusto, Ricielle L.; Siqueira, Williams N.; Luna Filho, Ricardo L.C.; Pereira, Dewson R.; França, Elvis J.; Silva, Edvane B.; Melo, Ana M.M.A., E-mail: luannaribeiro_lua@hotmail.com, E-mail: williams.wns@gmail.com, E-mail: ejfranca@gmail.com, E-mail: edvborges@yahoo.com, E-mail: luannaribeiro_lua@hotmail.com, E-mail: williams.wns@gmail.com, E-mail: ricardolclf@hotmail.com, E-mail: dewson.rocha@gmail.com, E-mail: s, E-mail: amdemelo@hotmail.com, E-mail: ricielleaugusto@gmail.com, E-mail: williams.wns@gmail.com, E-mail: ejfranca@gmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil); Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil)

2017-11-01

Ionizing radiation can cause biological changes in different organisms such as mollusks from Biomphalaria glabrata species, in which alterations could be observed in the reproductive system of the specimens, prejudicing fertility and fecundity. As the changes may occur due to the lipid peroxidation caused by the action of free radicals on the gonads, the objective of this work was to evaluate the oxidative damage caused by the exposure of B. glabrata mollusks to different doses of gamma radiation. In addition, efforts were carried out to standardize a sensitive and low-cost technique for detecting negative effects caused by high doses of ionizing radiation. For this, each mollusk group (n = 10) was submitted to 0 (control), 10, 15, 20 and 25 Gy (Gammacell- {sup 60}Co, dose rate 3.532 kGy/h). The TBARS method was applied for the quantification of lipid peroxidation of the gonads of the mollusks after 24 and 48 h. ANOVA, followed by the mean comparison (Tukey) at the 5% of significance level, indicated high concentrations of TBARS in the gonads after 24 h. Otherwise, after 48 h, differences for TBARS concentrations were not significant at the 95% confidence level, determining that the action of free radicals from ionizing radiation on cell membranes mainly occurred within 24 h after irradiation. (author)

Estudo quantitativo de metais presentes na hemolinfa de Biomphalaria glabrata (Gastropoda, infectadas e não infectadas com Schistosoma mansoni Quantitative study of metal present in the hemolymph of Biomphalaria glabrata (Gastropoda, infected and uninfected with Schistosoma mansoni

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Marco Antonio Vasconcelos Santos

2005-04-01

Full Text Available Inicialmente, desenvolveu-se um estudo para quantificar e comparar as concentrações de alguns metais presentes em duas amostras de hemolinfa do caramujo Biomphalaria glabrata (infectados e não-infectados com Schistosoma mansoni. A espectrometria de emissão óptica com fonte de plasma induzido (ICP-OES, foi utilizada para analisar os metais nas duas amostras. Os metais estudados foram: alumínio, cálcio, cádmio, cobalto, cromo, cobre, ferro, potássio, magnésio, manganês, chumbo e zinco. Os resultados mostram que, a princípio, os metais não são fatores determinantes no processo de defesa desses organismos contra este parasita, quando presente nos seus tecidos.We conducted a preliminary study to quantify and compare two concentrations of the same metals present in the hemolymph of snail Biomphalaria glabrata. In this context, we used Induction Coupled Plasma Optical Emission Spectroscopy technique (ICP-OES, to analyze the metals in the two samples (snails infected and not infected with Schistosoma mansoni. The metals studied were: aluminum, calcium, cadmium, cobalt, chromium, copper, iron, potassium, magnesium, manganese, lead and zinc. Preliminary results showed that such metals are not involved in the defense of these organisms against the parasite, when present in their tissues.

The Compatibility Between Biomphalaria glabrata Snails and Schistosoma mansoni: An Increasingly Complex Puzzle.

Science.gov (United States)

Mitta, G; Gourbal, B; Grunau, C; Knight, M; Bridger, J M; Théron, A

2017-01-01

This review reexamines the results obtained in recent decades regarding the compatibility polymorphism between the snail, Biomphalaria glabrata, and the pathogen, Schistosoma mansoni, which is one of the agents responsible for human schistosomiasis. Some results point to the snail's resistance as explaining the incompatibility, while others support a "matching hypothesis" between the snail's immune receptors and the schistosome's antigens. We propose here that the two hypotheses are not exclusive, and that the compatible/incompatible status of a particular host/parasite couple probably reflects the balance of multiple molecular determinants that support one hypothesis or the other. Because these genes are involved in a coevolutionary arms race, we also propose that the underlying mechanisms can vary. Finally, some recent results show that environmental factors could influence compatibility. Together, these results make the compatibility between B. glabrata and S. mansoni an increasingly complex puzzle. We need to develop more integrative approaches in order to find targets that could potentially be manipulated to control the transmission of schistosomiasis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Potential use of glycogen level as biomarker of chemical stress in Biomphalaria glabrata

International Nuclear Information System (INIS)

Ansaldo, Martin; Nahabedian, Daniel E.; Holmes-Brown, Eduardo; Agote, Marcos; Ansay, Cristina V.; Guerrero, Noemi R. Verrengia; Wider, Eva A.

2006-01-01

Biomphalaria glabrata, a freshwater gastropod mollusc, was tested as biondicator organism to assess cadmium, lead and arsenic exposure using acute laboratory bioassays. Modifications of glycogen levels were measured in different anatomical regions of B. glabrata in order to test the usefulness of this parameter as a general biomarker of chemical stress. The snails were exposed 96 h to different concentrations of the following contaminants: 0.1 and 0.05 mg Cd/L; 0.5, 0.1 and 0.05 mg Pb/L; 0.5, 0.1 and 0.05 mg As/L. Significant decreases in the polysaccharide content were observed in gonadal region for all treated animals. Arsenic and lead at 0.1 and 0.5 mg/L level of exposure were also able to decrease the levels of glycogen in the pulmonary and digestive gland region. Glycogen content in the cephalopedal region of treated animals presented a significant decrease (p < 0.05) when compared with control organisms only for arsenic at the highest level of exposure. To establish possible correlations between glycogen and contaminants accumulated by snails, analyses of the elements bioaccumulated in the different anatomical regions of B. glabrata were also performed. Cadmium and lead followed a similar pattern of bioaccumulation with highest values in the digestive gland region. Arsenic bioaccumulation, however, was highest in the gonadal region

Avaliação da bioatividade dos extratos de cúrcuma (Curcuma longa L., Zingiberaceae em Artemia salina e Biomphalaria glabrata

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Carlos R. M. da Silva Filho

Full Text Available A cúrcuma é o rizoma limpo, em boas condições, seco e moído da Curcuma longa L., uma planta herbácea da família Zingiberaceae. Visando novas alternativas para o controle da esquistossomose, os extratos de Curcuma longa L. foram testados para a avaliação da atividade moluscicida contra caramujos adultos da espécie Biomphalaria glabrata, e toxicidade (ensaio de letalidade com Artemia salina. A oleoresina e o óleo essencial de cúrcuma foram ativos contra Artemia salina (CL50 = 80,43 e CL50 = 319,82 μg/mL, respectivamente e também ativos contra os indivíduos adultos de Biomphalaria glabrata (CL50 = 58,3 e CL50 = 46,73 μg/mL, respectivamente. A partir dos resultados obtidos pôde ser concluído que ambos os extratos podem constituir uma alternativa no controle da população desses caramujos e na redução da esquistossomose.

Effects of 60Co gamma radiation on Biomphalaria glabrata (Say, 1818) Embryo, I. Mortality

International Nuclear Information System (INIS)

Okazaki, K.; Kawano, T.

1990-01-01

A study was conducted on the radiosensitivity of Biomphalaria glabrata embryos submitted to doses of 5, 10,15,20 and 25 Gy of 60 Co during the cleavage, blastula, gastrula, young trochophore and trochophore stages. Mortality was the parameter used to evaluated the damage induced by ionizing radiation. Susceptibility decreased with increasing embryo age and with decreased radiation dose. Estimated LD 50 values (15 days) showed that the cleavage stage (4.3 Gy) was approximately four times more radiosensitive than the trochophore stage (17.0 Gy). The survival curves obtained for each embryo stage are discussed on the basis of the multitarget theory. (author) [pt

Aspectos ultraestruturais de hemócitos de Biomphalaria glabrata Say (1818 (Gastropoda: Planorbidae analisados sob microscopia eletrônica de transmissão Ultrastructural aspects of hemocytes from Biomphalaria glabrata Say (1818 (Gastropoda: Planorbidae analysed with transmission eletronic microscopy

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Marco Antonio Vasconcelos Santos

2009-09-01

Full Text Available Os hemócitos do caramujo Biomphalaria glabrata, um importante transmissor do trematódeo Schistosoma mansoni no Brasil, foram coletados de especimens na região Bragantina, localizada a oeste do estado do Pará. Os hemócitos foram examinados por meio de microscopia eletrônica de transmissão. As células foram fixadas pelo método de rotina com o uso do tampão PHEM (PIPES, HEPES, EGTA e Magnésio. Foram descritos os aspectos ultra-estruturais celulares como inclusões citoplasmáticas limitadas por membranas, mitocôndrias, retículos endoplasmáticos e outros. As observações mostram que esse tampão possui a propriedade de preservação do citoesqueleto celular, apresentando bons resultados na preservação das estruturas dos hemócitos e suas organelas.The blood cells of the pulmonate snail Biomphalaria glabrata from the region of Bragantina in the state of Pará, an important vector of the trematode Schistosoma mansoni in Brazil, were collected and fixed by routine method with PHEM buffer and examined with transmission electron microscopy. Ultrastructural cellular aspects like cytoplasmic inclusions, mitochondrion, vesicles and others organelles are described. The buffer used resulted in good preservations of the hemocytes and their organelles.

Effects of high dose rate gamma radiation on survival and reproduction of Biomphalaria glabrata

Energy Technology Data Exchange (ETDEWEB)

Cantinha, Rebeca S.; Nakano, Eliana [Instituto Butantan, Sao Paulo, SP (Brazil). Lab. de Parasitologia], e-mail: rebecanuclear@gmail.com, e-mail: eliananakano@butantan.gov.br; Borrely, Sueli I. [Instituto de Pesquisas Energeticas e Nucleares (IPEN-CNEN/SP), Sao Paulo, SP (Brazil). Centro de Tecnologia das Radiacoes], e-mail: sborrely@ipen.br; Amaral, Ademir; Melo, Ana M.M.A. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear. Grupo de Estudos em Radioprotecao e Radioecologia (GERAR)], e-mail: amaral@ufpe.br; Silva, Luanna R.S. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Biofisica e Radiobiologia. Lab. de Radiobiologia], e-mail: amdemelo@hotmail.com, e-mail: luannaribeiro_lua@hotmail.com

2009-07-01

Ionizing radiations are known as mutagenic agents, causing lethality and infertility. This characteristic has motivated its application on animal biological control. In this context, the freshwater snail Biomphalaria glabrata can be considered an excellent experimental model to study effects of ionizing radiations on lethality and reproduction. This work was designed to evaluate effects of {sup 60}Co gamma radiation at high dose rate (10.04 kGy/h) on B. glabrata. For this purpose, adult snails were selected and exposed to doses ranging from 20 to 100 Gy, with 10 Gy intervals; one group was kept as control. There was not effect of dose rate in the lethality of gamma radiation; the value of 64,3 Gy of LD{sub 50} obtained in our study was similar to that obtained by other authors with low dose rates. Nevertheless, our data suggest that there was a dose rate effect in the reproduction. On all dose levels, radiation improved the production of embryos for all exposed individuals. However, viability indexes were below 6% and, even 65 days after irradiation, fertility was not recovered. These results are not in agreement with other studies using low dose rates. Lethality was obtained in all groups irradiated, and the highest doses presented percentiles of dead animals above 50%. The results demonstrated that doses of 20 and 30 Gy were ideal for population control of B. glabrata. Further studies are needed; nevertheless, this research evidenced great potential of high dose rate gamma radiation on B. glabrata reproductive control. (author)

Effects of high dose rate gamma radiation on survival and reproduction of Biomphalaria glabrata

International Nuclear Information System (INIS)

Cantinha, Rebeca S.; Nakano, Eliana; Silva, Luanna R.S.

2009-01-01

Ionizing radiations are known as mutagenic agents, causing lethality and infertility. This characteristic has motivated its application on animal biological control. In this context, the freshwater snail Biomphalaria glabrata can be considered an excellent experimental model to study effects of ionizing radiations on lethality and reproduction. This work was designed to evaluate effects of 60 Co gamma radiation at high dose rate (10.04 kGy/h) on B. glabrata. For this purpose, adult snails were selected and exposed to doses ranging from 20 to 100 Gy, with 10 Gy intervals; one group was kept as control. There was not effect of dose rate in the lethality of gamma radiation; the value of 64,3 Gy of LD 50 obtained in our study was similar to that obtained by other authors with low dose rates. Nevertheless, our data suggest that there was a dose rate effect in the reproduction. On all dose levels, radiation improved the production of embryos for all exposed individuals. However, viability indexes were below 6% and, even 65 days after irradiation, fertility was not recovered. These results are not in agreement with other studies using low dose rates. Lethality was obtained in all groups irradiated, and the highest doses presented percentiles of dead animals above 50%. The results demonstrated that doses of 20 and 30 Gy were ideal for population control of B. glabrata. Further studies are needed; nevertheless, this research evidenced great potential of high dose rate gamma radiation on B. glabrata reproductive control. (author)

Molluscicidal activity of Manilkara subsericea (Mart.) dubard on Biomphalaria glabrata (Say, 1818).

Science.gov (United States)

Faria, Robson Xavier; Rocha, Leandro Machado; Souza, Eloísa Portugal Barros Silva Soares; Almeida, Fernanda Borges; Fernandes, Caio Pinho; Santos, José Augusto Albuquerque

2018-02-01

Schistosomiasis is promoted for species from Schistosoma genus affecting over 200 million people worldwide. Molluscicides are an efficient method to control this disease, being able to reduce intermediate host snail Biomphalaria glabrata number. In function of resistance cases using niclosamide, natural products are promisors to discover new drugs. Manilkara subsericea is endemic to Brazilian sandbanks of Rio de Janeiro State and wide ranges of biological activities. However, there is no studies evaluating its effects as molluscicidal agent. We tested crude extract from leaves of M. subsericea molluscicidal action, as well it ethyl-acetate fraction and isolated substances against B. glabrata. M. subsericea leaves crude extract and ethyl acetate fraction induced 80±4.13% and 86.66±4.59% mortality of adult snails at concentrations of 250ppm after 96h, and their LD 50 values were 118.7±1.62 and 23.41±1.15ppm respectively. Isolated substances from M. subsericea were also considered active. Quercetin, myricetin and ursolic acid, at concentration of 100ppm (96h), were able to induce mortality levels of 100%, 80% and 53.33%, respectively. Our results suggest that M. subsericea can be considered promising as a molluscicide agent. Copyright © 2017. Published by Elsevier B.V.

Molluscicidal effect of Euphorbia umbellata (Pax Bruyns latex on Biomphalaria glabrata, Schistosoma mansoni host snail

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Luciana Patrícia Lima Alves Pereira

2017-12-01

Full Text Available ABSTRACT Euphorbia umbellata (Pax Bruyns is an easily cultivated shrub, with occurrence in the tropical regions of the American and African continents. Chemical studies have revealed that the latex of this plant is rich in terpene compounds, which are highly toxic to snails Biomphalaria glabrata (Basommatophora: Planorbidae. The aim of this study was to evaluate the chemical composition and molluscicidal activity of the latex produced by E. umbellata, as well as the safety of its application in aquatic environments. The concentration of latex that killed 90% of the exposed snails after 24 h exposure (LC90 was 3.69 mg/L. Toxicity bioassays using Danio rerio (zebrafish revealed that these animals were less susceptible to latex than planorbids. However, it is important to perform other toxicity tests to ensure the feasibility of using latex to control populations of mollusks that contribute to schistosomiasis transmission. A phytochemical screening performed with the E. umbellata latex identified the triterpenoid and coumarin class. Further studies are warranted to isolate, identify, and test the active compounds of E. umbellata latex in B. glabrata.

Analysis of toxicity of Anacardium occidentale L. extract submitted to ionizing radiation on embryos of Biomphalaria glabrata and Artemia salina

International Nuclear Information System (INIS)

Silva, Hianna A.M.F.; Sa, Jose L.F.; Lima, Claudia S.A.; Amancio, Francisco F.; Melo, Ana M.M.A.; Ribeiro, Luanna R.S.; Santos, Gustavo H.F.; Silva, Edvane B.

2013-01-01

The use of gamma radiation as a sterilization method for herbs, herbal medicines and foods, shows positive results regarding the retention of such products, economy and safety of the method. However, it is known that this method of processing plant material can cause chemical changes in these products related to the type of material, its components and the dose received. Evaluated, in the present study, the action of gamma radiation as a modifier of toxicity extract of Anacardium occidentale Linn. To evaluate the toxicity of the extract irradiated at doses of 5.0, 7.5 and 10.0 kGy and concentrations of 250, 500 and 1000 mg/L was used bioassays with Artemia salina and Biomphalaria glabrata. For the test to A. salina, 520 specimens were used divided into groups of 10 larvae. For the bioassay with B. glabrata, 3900 specimens were used divided into groups of, approximately, 100 embryos. Larvae of A. salina and embryos were subjected to extracts irradiated and unirradiated for 24 hours. The bioassay with A. salina, showed a decrease, compared to extract unirradiated and irradiated at doses of 5.0 and 7.5 kGy, of extract irradiated with 10 kGy, where the mortality did not differ from the control group. In tests with embryos was observed an increase in the toxicity of the extract at a dose of 7.5 kGy and a decrease in the dose of 10.0 kGy. The radiation promoted changes in the toxicity of leaves extracts of Anacardium occidentale Linn. on embryos of Biomphalaria glabrata and Artemia salina. (author)

Analysis of toxicity of Anacardium occidentale L. extract submitted to ionizing radiation on embryos of Biomphalaria glabrata and Artemia salina

Energy Technology Data Exchange (ETDEWEB)

Silva, Hianna A.M.F.; Sa, Jose L.F.; Lima, Claudia S.A.; Amancio, Francisco F.; Melo, Ana M.M.A., E-mail: hiannaamfs@gmail.com, E-mail: luismuma6@gmail.com, E-mail: claudia.salima@gmail.com, E-mail: amancioff@bol.com.br, E-mail: amdemelo@hotmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Biofisica e Radiobiologia; Ribeiro, Luanna R.S.; Santos, Gustavo H.F.; Silva, Edvane B., E-mail: luannaribeiro_lua@hotmail.com, E-mail: santosghf@hotmail.com, E-mail: edvborges@yahoo.com.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Energia Nuclear. Grupo de Estudos em Radioprotecao e Radioecologia

2013-07-01

The use of gamma radiation as a sterilization method for herbs, herbal medicines and foods, shows positive results regarding the retention of such products, economy and safety of the method. However, it is known that this method of processing plant material can cause chemical changes in these products related to the type of material, its components and the dose received. Evaluated, in the present study, the action of gamma radiation as a modifier of toxicity extract of Anacardium occidentale Linn. To evaluate the toxicity of the extract irradiated at doses of 5.0, 7.5 and 10.0 kGy and concentrations of 250, 500 and 1000 mg/L was used bioassays with Artemia salina and Biomphalaria glabrata. For the test to A. salina, 520 specimens were used divided into groups of 10 larvae. For the bioassay with B. glabrata, 3900 specimens were used divided into groups of, approximately, 100 embryos. Larvae of A. salina and embryos were subjected to extracts irradiated and unirradiated for 24 hours. The bioassay with A. salina, showed a decrease, compared to extract unirradiated and irradiated at doses of 5.0 and 7.5 kGy, of extract irradiated with 10 kGy, where the mortality did not differ from the control group. In tests with embryos was observed an increase in the toxicity of the extract at a dose of 7.5 kGy and a decrease in the dose of 10.0 kGy. The radiation promoted changes in the toxicity of leaves extracts of Anacardium occidentale Linn. on embryos of Biomphalaria glabrata and Artemia salina. (author)

Radioprotective effect of the extract of Ziziphus joazeiro and Anacardium occidentale on embryos of Biomphalaria glabrata submitted to ionizing radiation

International Nuclear Information System (INIS)

Siqueira, Williams N.; Silva, Luanna R.S.; Silva, Edvane B.; Silva, Ronaldo C.; Lacerda, Laila B.N.; Silva, Hianna A.M.F.; Santos, Mariana L.O.; Sa, Jose L.F.; Melo, Ana M.M.A.

2011-01-01

Electromagnetic radiations are energies that can be classified as non-ionizing and ionizing. This type of energy is propagated by a material medium and the vacuum. The important characteristic of ionizing radiation is the localized release of large amounts of energy. The biological effects of radiation result principally from damage to DNA, which is the critical target. Given these harmful effects caused by radiation highlights the importance of acquiring knowledge about the radioprotective substance, because they act to protect the living tissue, decreasing the damage he caused by the effects of radiation. In this study we investigated the radioprotective effect of extract hydroalcoholic of Ziziphus joazeiro and Anacardium occidentale on embryos of Biomphalaria glabrata. The embryos of Biomphalaria glabrata pigmented were divided into 18 groups of 100 specimens. The experimental groups were exposed to the extracts at a concentration of 200 ppm and then irradiated. For irradiation, we used a source of 60 Co (Gammacell of Radionics Labs. Dose rate = 4.359 Gy/h). The viability of the embryos was examined using a stereoscopic microscope and statistical analysis was performed using the test Student-Newman-Keuls and χ 2 . Our results showed that the extracts of hydroalcoholic Ziziphus joazeiro showed radioprotective effect and that the aqueous extract of the bark of Anacardium occidentale exhibited a reduction in its embryotoxic effect. (author)

Radioprotective effect of the extract of Ziziphus joazeiro and Anacardium occidentale on embryos of Biomphalaria glabrata submitted to ionizing radiation

Energy Technology Data Exchange (ETDEWEB)

Siqueira, Williams N.; Silva, Luanna R.S.; Silva, Edvane B. [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear. Grupo de Estudos em Radioprotecao e Radioecologia; Silva, Ronaldo C. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Genetica; Lacerda, Laila B.N.; Silva, Hianna A.M.F.; Santos, Mariana L.O.; Sa, Jose L.F.; Melo, Ana M.M.A. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de de Biofisica e Radiobiologia. Lab. de Radiobiologia

2011-07-01

Electromagnetic radiations are energies that can be classified as non-ionizing and ionizing. This type of energy is propagated by a material medium and the vacuum. The important characteristic of ionizing radiation is the localized release of large amounts of energy. The biological effects of radiation result principally from damage to DNA, which is the critical target. Given these harmful effects caused by radiation highlights the importance of acquiring knowledge about the radioprotective substance, because they act to protect the living tissue, decreasing the damage he caused by the effects of radiation. In this study we investigated the radioprotective effect of extract hydroalcoholic of Ziziphus joazeiro and Anacardium occidentale on embryos of Biomphalaria glabrata. The embryos of Biomphalaria glabrata pigmented were divided into 18 groups of 100 specimens. The experimental groups were exposed to the extracts at a concentration of 200 ppm and then irradiated. For irradiation, we used a source of {sup 60}Co (Gammacell of Radionics Labs. Dose rate = 4.359 Gy/h). The viability of the embryos was examined using a stereoscopic microscope and statistical analysis was performed using the test Student-Newman-Keuls and {chi}{sup 2}. Our results showed that the extracts of hydroalcoholic Ziziphus joazeiro showed radioprotective effect and that the aqueous extract of the bark of Anacardium occidentale exhibited a reduction in its embryotoxic effect. (author)

Molluscicidal and ovicidal activities of plant extracts of the Piperaceae on Biomphalaria glabrata (Say, 1818).

Science.gov (United States)

Rapado, L N; Nakano, E; Ohlweiler, F P; Kato, M J; Yamaguchi, L F; Pereira, C A B; Kawano, T

2011-03-01

Schistosomiasis is a tropical disease caused by Schistosoma and occurs in 54 countries, mainly in South America, the Caribbean region, Africa and the eastern Mediterranean. Currently, 5 to 6 million Brazilian people are infected and 30,000 are under infection risk. Typical of poor regions, this disease is associated with the lack of basic sanitation and very frequently to the use of contaminated water in agriculture, housework and leisure. One of the most efficient methods of controlling the disease is application of molluscicides to eliminate or to reduce the population of the intermediate host snail Biomphalaria glabrata. Studies on molluscicidal activity of plant extracts have been stimulated by issues such as environmental preservation, high cost and recurrent resistance of snails to synthetic molluscicides. The aim of this study was to determine the molluscicide action of extracts from Piperaceae species on adult and embryonic stages of B. glabrata. Fifteen extracts from 13 Piperaceae species were obtained from stems, leaves and roots. Toxicity of extracts was evaluated against snails at two different concentrations (500 and 100 ppm) and those causing 100% mortality at 100 ppm concentration were selected to obtain the LC₉₀ (lethal concentration of 90% mortality). Piper aduncum, P. crassinervium, P. cuyabanum, P. diospyrifolium and P. hostmannianum gave 100% mortality of adult snails at concentrations ranging from 10 to 60 ppm. These extracts were also assayed on embryonic stages of B. glabrata and those from P. cuyabanum and P. hostmannianum showed 100% ovicidal action at 20 ppm.

Growth of Biomphalaria glabrata populations in the presence of the ampullariid snails Pila ovata, Lanistes carinatus and Marisa cornuarietis.

Science.gov (United States)

Stryker, G A; Koech, D K; Loker, E S

1991-06-01

Adults of three ampullariid species were examined for their ability to affect the population growth of Biomphalaria glabrata (M line strain) under laboratory conditions in which food (lettuce) was supplied ad libitum over an eleven week interval. Lanistes carinatus and Pila ovata were obtained from Kenya, and Marisa cornuarietis originated from the Dominican Republic. The presence of either 3 or 9 L. carinatus or 3 M. cornuarietis per 40 l aquarium did not reduce the population size of B. glabrata below levels attained in control aquaria lacking ampullariids. The presence of 9 M. cornuarietis adults significantly reduced B. glabrata populations by week 10 of the experiment. Presence of 3 or 9 P. ovata per aquarium significantly reduced B. glabrata numbers below control levels starting at week four of the experiment. Aquaria with 9 P. ovata were observed to have fewer B. glabrata egg masses than control aquaria, but the number of egg masses observed was not significantly reduced in aquaria with 3 P. ovata or with 3 or 9 L. carinatus or M. cornuarietis. However, the presence of 3 or 9 adults of each ampullariid species resulted in a significant increase in the percentage of such egg masses that disappeared prior to expected hatching date and that were presumed to have been consumed. The results of his laboratory study suggest that further investigation of the role of ampullariids as biological control agents for pulmonate snails in sub-Saharan Africa should focus on P. ovata.

New insights into the amphibious life of Biomphalaria glabrata and susceptibility of its egg masses to fungal infection.

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Duarte, Glennyha F; Rodrigues, Juscelino; Fernandes, Éverton K K; Humber, Richard A; Luz, Christian

2015-02-01

The air-breathing snail Biomphalaria glabrata proliferates in stagnant freshwater, and nothing is known about the survival of eggs in intermittently (rather than perpetually) wet habitats. In the present study their egg masses matured, and juveniles subsequently eclosed and were mobile in a stable water film of transitory habitats simulated by two different simple test devices described here. The viability of eggs maintained in an unstable film however, was diminished. The maturation of egg masses in a water film or in water was significantly prevented by the entomopathogenic fungi Beauveria bassiana and Metarhizium anisopliae. The efficiency depended on the fungal propagule and test environment. Hyphal bodies were more effective against egg masses than conidia. This appears to be a first report of activity of either entomopathogen against a mollusc. Both devices offer accurate and reproducible conditions to test both biological questions and the effects of substances or pathogens against B. glabrata egg masses in water films. Copyright © 2015 Elsevier Inc. All rights reserved.

Suscetibilidade de biomphalaria glabrata, B. straminea e B. tenagophila a diferentes cepas de schistosoma mansoni

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Luiz Candido de Souza Dias

1987-08-01

Full Text Available Em condições experimentais foi estudada a suscetibilidade de Biomphalaria glabrata, B. straminea e B. tenagophila a quatro linhagens humanas (MAP, PTH, UPH, e OuH e duas de roedores silvestres (PTR e VPR do Schistosoma mansoni. Grupos de 50 moluscos foram expostos individualmente a 10 miracídios e observados durante 70 dias. Avaliou-se a suscetibilidade dos moluscos ao parasito por meio da % de animais com esporocistos, % de moluscos que eliminavam cercárias e mortalidade conjunta dos animais expostos e infectados. Exemplares de B. glabrata mineira infectaram-se com cepa simpátrica (MAP e com 5 alopátricas do Estado de São Paulo (PTH, VPH, OuH, PTR e VPR. B. glabrata paulista mostrou altas taxas de infecção com as cepas MAP, VPR e OuH do trematódeo. Quatro % dos exemplares B. straminea de São Paulo eliminavam cercárias de cepas simpátricas; com cepa mineira apenas 4% apresentaram esporocistos na vigência de 20 miracídios por molusco; as menores taxas de mortalidade foram registradas com essa espécie de molusco, não sendo maior do que 20%. B. tenagophila paulista foi suscetível apenas às linhagens simpáticas sendo 6% a maior taxa de moluscos que eliminaram cercárias. Os resultados indicam que os movimentos populacionais humanos dentro do território paulista e para fora dele são importantes na disseminação da esquistossomose mansônica.

A low stringency polymerase chain reaction approach to the identification of Biomphalaria glabrata and B. tenagophila, intermediate snail hosts of Schistosoma mansoni in Brazil

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Teofânia HDA Vidigal

1996-12-01

Full Text Available The low stringency-polymerase chain reaction (LS-PCR with a pair of specific primers for the amplification of the 18S rRNA gene was evaluated as a means of differentiating between the two Schistosoma mansoni intermediate host species in Brazil: Biomphalaria glabrata and B. tenagophila. Individual snails obtained from different states of Brazil were used and the amplification patterns obtained showed a high degree of genetic variability in these species. Nevertheless, 4 and 3 clearly defined specific diagnostic bands was observed in individuals from B. glabrata and B. tenagophila respectively. The detection of snail specific diagnostic bands suggests the possibility of reliable species differentiation at the DNA level using LS-PCR.

Padronização da técnica de marcação de caramujos Biomphalaria glabrata com radioestroncio Standardization of the technic of labeling Biomphalaria glabrata snails with radiostrontium

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Miguel Archanjo Muniz Leal

1982-06-01

Full Text Available Caramujos Biomphalaria glabrata vetor da esquistossomose mansônica, utilizados em experiências de campo, nas quais se faz necessário sua identificação e/ou localização, devem ser marcados com radioestrôncio 85,89 ou 90. Sua marcação em laboratório deve ser procedida em aquários de vidro sem fundo de areia, temperatura de 26,5 ± 1ºC, pH ajustado ao valor encontrado no "habitat", aeração artificial, alimentação diária com pequenas porções de alface fresca e 25 ml de água desionizada por caramujo. O nível de atividade no caramujo pode ser estimado sabendo-se que para o tempo de marcação de 5 dias e atividades iniciais de 0,036 a 0,362 µCi/ml, a captação global para grupos de 10 caramujos está em torno de 84 ± 2% e que a marcação em água contendo cálcio, praticamente não se altera até concentrações de 50ppm. A sobrevida ao longo de nove semanas não foi influenciada pela presença de radioestrôncio no caramujo.The vector snail of schistosomiasis mansoni, Biomphalaria glabrata, when used in field experiments in which it is to be recovered and/or located, should be labeled with radiostrontium 85,89 or 90. The labeling in laboratory should be carried out in an artificially aerated aquarium with 25 ml of deionized water per snail, without sand at the bottom, at a temperature of 26.5 ± 1ºC, pH adjusted to the value found in the natural habitat, and the snails should be fed with small pieces of fresh lettuce. The level of snail activity can be estimated taking into account that, for a labeling time of 5 days and initial activities of 0.036 to 0.362 µCi/ml, the global uptake for groups of 10 snails is about 84 ± 2% and that labeling in calcium-containing water parctically does not change till a 50 ppm concentration. Survival along 9 weeks was not influenced by the presence of radiostrontium in the snail.

Effect of cadmium, lead and arsenic on the oviposition, hatching and embryonic survival of Biomphalaria glabrata

International Nuclear Information System (INIS)

Ansaldo, Martin; Nahabedian, Daniel E.; Di Fonzo, Carla; Wider, Eva A.

2009-01-01

Biomphalaria glabrata is a widespread freshwater gastropod mollusc. The easy aquaculture of these organisms allow its use as an accessible tool for contamination bioassays. B. glabrata showed marked metabolic responses when exposed to cadmium, lead and arsenic. Those responses could also affect the reproduction of the snails. Taking into account this hypothesis, B. glabrata were exposed for 96 h (acute laboratory bioassays) to different concentrations of cadmium (0.1, 0.05 and 0 mg/L), lead (0.5, 0.1, 0.05 and 0 mg/L) and arsenic (0.5, 0.1, 0.05 and 0 mg/L). Snails were removed from the aquaria while eggs were left in the same contaminant concentrations. The effect of the assayed toxicants on snail reproduction was registered as the alterations of the total number of laid eggs (TNLE), hatching time and embryonic survival. At 0.10 mg/L cadmium significantly decreased the TNLE (p < 0.05) and no embryos survived. The lowest assayed level (0.05 mg/L) of cadmium, delayed the hatching time twice when it was compared with the control group (p < 0.01). Lead decreased the TNLE at 0.5 mg/L level (p < 0.01). The other assayed doses (0.05 and 0.10 mg/L) also decreased embryonic survival significantly (p < 0.05 and p < 0.01 respectively) and extended twice the time to hatching (p < 0.01). The 0.50 mg/L level killed all embryos. Arsenic at all studied concentrations decreased the TNLE (p < 0.05) while the hatching time was increased by 50%. Embryo survival only decreased at the highest level (0.5 mg/L) of arsenic assayed. In summary, the acute exposure (96 h) to cadmium lead and arsenic, altered the reproduction of B. glabrata, modifying the TNLE, hatching time and embryonic survival

Effects of Co60 gamma radiation on Biomphalaria glabrata (Say, 1818) Embryo. II. Malformations

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Okazaki, K.; Kawano, T.

1990-01-01

The morphogenetic effects of ionizing radiation were investigated in Biomphalaria glabrata embryos irradiated in the cleavage, blastula, gastrula, young trochophore and trochophore stages with 5 to 25 Gy doses of 60 CO gamma radiation. The number of malformed embryos rapidly increased with increasing radiation dose, reaching a maximum between 5th to 8th day after irradiation in all stages analyzed. Susceptibility to malformation induction was higher the younger than the age of the irradiated embryo. However, for the cleavage stage the frequency of malformed embryos was inversely proportional to radiation dose for the same radiation dose. Several types of morphogenetic malformations were obtained, among then cephalic malformations, exogastrula, shell malformations and embryos with everted stomodeum, unspecific malformations being the most frequent. The results show that the types of malformation induced by radiation probably are not radiation-specific and do not depend on the dose applied [pt

BgTEP: An Antiprotease Involved in Innate Immune Sensing in Biomphalaria glabrata

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Anaïs Portet

2018-05-01

Full Text Available Insect thioester-containing protein (iTEP is the most recently defined group among the thioester-containing protein (TEP superfamily. TEPs are key components of the immune system, and iTEPs from flies and mosquitoes were shown to be major immune weapons. Initially characterized from insects, TEP genes homologous to iTEP were further described from several other invertebrates including arthropods, cniderians, and mollusks albeit with few functional characterizations. In the freshwater snail Biomphalaria glabrata, a vector of the schistosomiasis disease, the presence of a TEP protein (BgTEP was previously described in a well-defined immune complex involving snail lectins (fibrinogen-related proteins and schistosome parasite mucins (SmPoMuc. To investigate the potential role of BgTEP in the immune response of the snail, we first characterized its genomic organization and its predicted protein structure. A phylogenetic analysis clustered BgTEP in a well-conserved subgroup of mollusk TEP. We then investigated the BgTEP expression profile in different snail tissues and followed immune challenges using different kinds of intruders during infection kinetics. Results revealed that BgTEP is particularly expressed in hemocytes, the immune-specialized cells in invertebrates, and is secreted into the hemolymph. Transcriptomic results further evidenced an intruder-dependent differential expression pattern of BgTEP, while interactome experiments showed that BgTEP is capable of binding to the surface of different microbes and parasite either in its full length form or in processed forms. An immunolocalization approach during snail infection by the Schistosoma mansoni parasite revealed that BgTEP is solely expressed by a subtype of hemocytes, the blast-like cells. This hemocyte subtype is present in the hemocytic capsule surrounding the parasite, suggesting a potential role in the parasite clearance by encapsulation. Through this work, we report the first

Female biased sex-ratio in Schistosoma mansoni after exposure to an allopatric intermediate host strain of Biomphalaria glabrata.

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Lepesant, Julie M J; Boissier, Jérôme; Climent, Déborah; Cosseau, Céline; Grunau, Christoph

2013-10-01

For parasites that require multiple hosts to complete their development, the interaction with the intermediate host may have an impact on parasite transmission and development in the definitive host. The human parasite Schistosoma mansoni needs two different hosts to complete its life cycle: the freshwater snail Biomphalaria glabrata (in South America) as intermediate host and a human or rodents as final host. To investigate the influence of the host environment on life history traits in the absence of selection, we performed experimental infections of two B. glabrata strains of different geographic origin with the same clonal population of S. mansoni. One B. glabrata strain is the sympatric host and the other one the allopatric host. We measured prevalence in the snail, the cercarial infectivity, sex-ratio, immunopathology in the final host and microsatellite frequencies of individual larvae in three successive generations. We show that, even if the parasite population is clonal based on neutral markers, S. mansoni keeps the capacity of generating phenotypic plasticity and/or variability for different life history traits when confront to an unusual environment, in this study the intermediate host. The most dramatic change was observed in sex-ratio: in average 1.7 times more female cercariae were produced when the parasite developed in an allopatric intermediate host. Copyright © 2013 Elsevier Inc. All rights reserved.

Consumption of Biomphalaria glabrata egg masses and juveniles by the ampullariid snails Pila ovata, Lanistes carinatus and Marisa cornuarietis.

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Hofkin, B V; Stryker, G A; Koech, D K; Loker, E S

1991-04-01

Lanistes carinatus and Pila ovata from Kenya and Marisa cornuarietis from the Dominican Republic were examined for their ability to consume egg masses and juveniles of Biomphalaria glabrata (M line strain) under laboratory conditions. Adults of all three ampullariid species consumed all egg masses presented to them over a five day period of observation. Juvenile P. ovata consumed significantly more egg masses than juveniles of M. cornuarietis or L. carinatus. Both adult and juvenile ampullariids generally ate more egg masses when maintained under a temperature regime (25-32 degrees C) approximating conditions in coastal Kenya than at 13-25 degrees C which approximates the temperature regime near Nairobi, Kenya. Egg masses attached to floating 'refugia' were not attacked, apparently reflecting the difficulty experienced by ampullariids in reaching free-floating objects. Adults of each ampullariid species ate approximately 25% of all lariids in reaching free-floating objects. Adults of each ampullariid species ate approximately 25% of all 1.5 +/- 0.5 mm B. glabrata juvenile snails presented to them. P. ovata adults consumed significantly more 3.0 +/- 0.5 mm juveniles than adults of the other two species. B. glabrata egg masses and juveniles were consumed even though lettuce was continually present in experimental aquaria. Implications of these results for biological control studies in East Africa are discussed.

Changes in energetic metabolism of Biomphalaria glabrata (Mollusca, Planorbidae in response to exogenous calcium

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L. D. Silva

Full Text Available Abstract Calcium is considered an essential element for the metabolism of aquatic snail Biomphalaria glabrata (Say, 1818, intermediate host of Schistosoma mansoni Sambon, 1907 in Brazil, and represents a limiting factor to its distribution and adaptation to the environment. This study investigated the effect of different concentrations of exogenous CaCO3 on the energetic metabolism of B. glabrata for better understanding the physiological interference of chemical elements dissolved in the environment with the physiology of this species. Sixty-day-old snails were distributed into six groups, five exposed to different concentrations of CaCO3 (20, 40, 60, 80 and 100 mg/L and a control group. The exposure to CaCO3 was assessed over time, with analysis of 15 snails of each group in the following intervals: 1, 14, 21 or 30 days for hemolymph extraction. Concentrations of calcium and glucose in the hemolymph were determined by commercial kits, and organic acids were extracted using an ion exchange column and analyzed by high-performance liquid chromatography. Concentration of calcium in the hemolymph showed no significant difference (p>0.05 from the control group and between the concentrations tested. Concentration of glucose decreased (p<0.05 in the treatments of exposure to 20 and 40 mg/L and increased when exposed to 80 and 100 mg/L CaCO3 compared to control and to other concentrations tested over 30 days. The organic acids pyruvate, oxaloacetate, citrate, succinate, fumarate, beta-hydroxybutyrate and lactate presented increased concentrations, while propionate and acetoacetate, decreased concentrations, when exposed to CaCO3 compared to control. Considering the influence of different periods of exposure to CaCO3, on the 14th day, there were stronger alterations in the metabolism of B. glabrata. In conclusion, exposure to CaCO3 reduced the concentration of glucose, which is metabolized into pyruvate, the final product of glycolysis, and also

A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

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Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

2017-07-05

The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

Controlled chaos of polymorphic mucins in a metazoan parasite (Schistosoma mansoni interacting with its invertebrate host (Biomphalaria glabrata.

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Emmanuel Roger

Full Text Available Invertebrates were long thought to possess only a simple, effective and hence non-adaptive defence system against microbial and parasitic attacks. However, recent studies have shown that invertebrate immunity also relies on immune receptors that diversify (e.g. in echinoderms, insects and mollusks (Biomphalaria glabrata. Apparently, individual or population-based polymorphism-generating mechanisms exists that permit the survival of invertebrate species exposed to parasites. Consequently, the generally accepted arms race hypothesis predicts that molecular diversity and polymorphism also exist in parasites of invertebrates. We investigated the diversity and polymorphism of parasite molecules (Schistosoma mansoni Polymorphic Mucins, SmPoMucs that are key factors for the compatibility of schistosomes interacting with their host, the mollusc Biomphalaria glabrata. We have elucidated the complex cascade of mechanisms acting both at the genomic level and during expression that confer polymorphism to SmPoMuc. We show that SmPoMuc is coded by a multi-gene family whose members frequently recombine. We show that these genes are transcribed in an individual-specific manner, and that for each gene, multiple splice variants exist. Finally, we reveal the impact of this polymorphism on the SmPoMuc glycosylation status. Our data support the view that S. mansoni has evolved a complex hierarchical system that efficiently generates a high degree of polymorphism-a "controlled chaos"-based on a relatively low number of genes. This contrasts with protozoan parasites that generate antigenic variation from large sets of genes such as Trypanosoma cruzi, Trypanosoma brucei and Plasmodium falciparum. Our data support the view that the interaction between parasites and their invertebrate hosts are far more complex than previously thought. While most studies in this matter have focused on invertebrate host diversification, we clearly show that diversifying mechanisms also

Controlled Chaos of Polymorphic Mucins in a Metazoan Parasite (Schistosoma mansoni) Interacting with Its Invertebrate Host (Biomphalaria glabrata)

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Roger, Emmanuel; Grunau, Christoph; Pierce, Raymond J.; Hirai, Hirohisa; Gourbal, Benjamin; Galinier, Richard; Emans, Rémi; Cesari, Italo M.; Cosseau, Céline; Mitta, Guillaume

2008-01-01

Invertebrates were long thought to possess only a simple, effective and hence non-adaptive defence system against microbial and parasitic attacks. However, recent studies have shown that invertebrate immunity also relies on immune receptors that diversify (e.g. in echinoderms, insects and mollusks (Biomphalaria glabrata)). Apparently, individual or population-based polymorphism-generating mechanisms exists that permit the survival of invertebrate species exposed to parasites. Consequently, the generally accepted arms race hypothesis predicts that molecular diversity and polymorphism also exist in parasites of invertebrates. We investigated the diversity and polymorphism of parasite molecules (Schistosoma mansoni Polymorphic Mucins, SmPoMucs) that are key factors for the compatibility of schistosomes interacting with their host, the mollusc Biomphalaria glabrata. We have elucidated the complex cascade of mechanisms acting both at the genomic level and during expression that confer polymorphism to SmPoMuc. We show that SmPoMuc is coded by a multi-gene family whose members frequently recombine. We show that these genes are transcribed in an individual-specific manner, and that for each gene, multiple splice variants exist. Finally, we reveal the impact of this polymorphism on the SmPoMuc glycosylation status. Our data support the view that S. mansoni has evolved a complex hierarchical system that efficiently generates a high degree of polymorphism—a “controlled chaos”—based on a relatively low number of genes. This contrasts with protozoan parasites that generate antigenic variation from large sets of genes such as Trypanosoma cruzi, Trypanosoma brucei and Plasmodium falciparum. Our data support the view that the interaction between parasites and their invertebrate hosts are far more complex than previously thought. While most studies in this matter have focused on invertebrate host diversification, we clearly show that diversifying mechanisms also exist on

The subunit structure of the extracellular hemoglobin of Biomphalaria glabrata

International Nuclear Information System (INIS)

Arndt, Marcio H.L.; Naves, Cristiani F.; Xavier, Luciana P.; Santoro, Marcelo M.

1997-01-01

Full text. The hemoglobin of Biomphalaria glabrata was purified to homogeneity by a two step purification protocol using a gel filtration column (Superose 6 HR/Pharmacia ) followed by an anion exchange chromatography (MONO-Q Sepharose/Pharmacia). The dissociation products were analysed by a 5 - 15 % Polyacrylamide gel electrophoresis containing Sodium Dodecyl Sulfate (SDS-PAGE) giving a band of 270 K Daltons and a band of 180 K Daltons after reduction with β-mercaptoethanol. The same profile was obtained in a 3.5 % Agarose gel electrophoresis containing SDS (SDS-AGE) showing additional bands of higher molecular weight. These bands were proposed to be monomers, dimers and trimers and, after reduction in a Bidimensional SDS-AGE, the proposed monomers and dimers were decomposed in two and four bands that were interpreted as 1 - 4 chains. The hemoglobin was digested by four different proteases ( Thrombin, Trypsin, Chymotrypsin and Subtilisin ) showing several equivalent fragments with molecular weights multiples of its minimum molecular weight ( 17.7 K Daltons). The circular dichroism spectrum of the protein showed a characteristic high α-helix content. We proposed that this hemoglobin is a pentamer of approx. 360 K Daltons subunits each formed by two 180 K Daltons chains linked in pairs by disulfide bridges and each of these chains comprises ten Heme binding domains. These data were compared to other Planorbidae extracellular hemoglobins. Up to now, the quaternary structure of this hemoglobin (shape and disposition of the subunits) is unknown. It is intended to elucidate its structure by Small Angle X-Ray Scattering in Brazilian National Laboratory of Synchrotron Light (LNLS). (author)

Nitric oxide production by Biomphalaria glabrata haemocytes: effects of Schistosoma mansoni ESPs and regulation through the extracellular signal-regulated kinase pathway

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Kirk Ruth S

2009-04-01

Full Text Available Abstract Background Schistosoma mansoni uses Biomphalaria glabrata as an intermediate host during its complex life cycle. In the snail, the parasite initially transforms from a miracidium into a mother sporocyst and during this process excretory-secretory products (ESPs are released. Nitric oxide (NO and its reactive intermediates play an important role in host defence responses against pathogens. This study therefore aimed to determine the effects of S. mansoni ESPs on NO production in defence cells (haemocytes from schistosome-susceptible and schistosome-resistant B. glabrata strains. As S. mansoni ESPs have previously been shown to inhibit extracellular signal-regulated kinase (ERK phosphorylation (activation in haemocytes from susceptible, but not resistant, B. glabrata the regulation of NO output by ERK in these cells was also investigated. Results Haemocytes from resistant snails challenged with S. mansoni ESPs (20 μg/ml over 5 h displayed an increase in NO production that was 3.3 times greater than that observed for unchallenged haemocytes; lower concentrations of ESPs (0.1–10 μg/ml did not significantly increase NO output. In contrast, haemocytes from susceptible snails showed no significant change in NO output following challenge with ESPs at any concentration used (0.1–20 μg/ml. Western blotting revealed that U0126 (1 μM or 10 μM blocked the phosphorylation (activation status of ERK in haemocytes from both snail strains. Inhibition of ERK signalling by U0126 attenuated considerably intracellular NO production in haemocytes from both susceptible and resistant B. glabrata strains, identifying ERK as a key regulator of NO output in these cells. Conclusion S. mansoni ESPs differentially influence intracellular NO levels in susceptible and resistant B. glabrata haemocytes, possibly through modulation of the ERK signalling pathway. Such effects might facilitate survival of S. mansoni in its intermediate host.

Implications of water hardness in ecotoxicological assessments for water quality regulatory purposes: a case study with the aquatic snail Biomphalaria glabrata (Say, 1818

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EC Oliveira-Filho

Full Text Available Water hardness is a property depending on the presence of alkaline earth metals, mainly calcium and magnesium. Among the strategies for water quality monitoring, ecotoxicological assays are performed to minimize impacts and classify water bodies. For these laboratory evaluations parameters are previously defined in the guidelines, including water hardness for both cultivation and testing medium. The present work was performed to evaluate the effects of different levels of water hardness on the survival and reproduction of the freshwater snail Biomphalaria glabrata and discuss the influence of natural water hardness on the results of ecotoxicological tests with these environmental samples. Comparing the groups it was possible to observe that those maintained in waters with least hardness had lower reproductive success, while the groups maintained in highest hardness showed better reproduction. These data show that waters with low hardness make the reproduction of the snail B. glabrata unfeasible, and this reveal a problem for ecotoxicity assays using natural water samples.

Distribution and Schistosoma mansoni infection of Biomphalaria glabrata in different habitats in a rural area in the Jequitinhonha Valley, Minas Gerais, Brazil: environmental and epidemiological aspects

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Helmut Kloos

2004-11-01

Full Text Available This paper examines the distribution and infection of Biomphalaria glabrata with Schistosoma mansoni in all aquatic snail habitats in a rural area in the state of Minas Gerais, Brazil, in relation to physico/biotic and behavioral factors. Snail and environmental surveys were carried out semi-annually between July 2001 and November 2002 at 106 sites. Collected snails were examined in the laboratory for infection. B. glabrata densities were highest in overflow ponds, irrigation ponds, springs, canals and wells, and lowest in fishponds and water tanks. Snail densities were higher during the hot, rainy season except for streams and canals and were statistically associated with the presence of fish, pollution, and vegetation density. Tilapia fish and an unidentified Diptera larva were found to be predators of B. glabrata but ducks were not. Twenty-four of the 25 infected snails were collected in 2001(1.4% infection rate and only one in 2002, after mass chemotherapy. The occurrence of B. glabrata in all 11 snail habitats both at and away from water contact sites studied indicates widespread risk of human infection in the study area. In spite of the strong association between B. glabrata and tilapia in fishponds we do not recommend its use in schistosomiasis control for ecological reasons and its relative inefficiency in streams and dams.

The effect of gamma radiation and caffeine during the embrionic development of Biomphalaria glabrata

International Nuclear Information System (INIS)

Kawano, T.

1982-01-01

Some experiments have been carried out, dealing with the interations of caffeine and gamma radiation in the embryonic development of Biomphalaria glabrata. Gamma radiation was used in a dosis of 1000r (exposure time of 1/2 hour) and caffeine concentration was 0.1% (Exposure time of 24 hours). Experiment I. The embryos were irradiated before treatment with caffeine. In this experiment we have observed a synergistic effect between caffeine and gamma radiation. Experiment II. The embryos in the caffeine solution were irradiated 8 hours after the beginning of the experiment. The synergistic effect observed in this experiment was reduced when compared with the first one. Experiment III. In this experiment we made the pre-treatment with caffeine. We have not observed any synergistic effect between the drug and gamma radiation. Experiment IV. Embryos were irradiated, and after 24 hours treated with caffeine during another 24 hours. As in the previous experiment, we have not observed any synergism between the radiation and the drug. According to the above results, we conclude that the synergistic effect between caffeine and gamma radiation in the embryos was more effective when the embryos have been treated with caffeine after irradiation. (Author) [pt

Dominant lethal effect of gamma radiation of 60Co in Biomphalaria glabrata (SAY, 1818)

International Nuclear Information System (INIS)

Tallarico, Lenita de Freitas

2003-01-01

Germ cell mutations are used in ecotoxicological studies as biomarkers of population effects and indicators of ecological changes. Biomphalaria glabrata, a freshwater mollusk, is a good experimental model for biomonitoring studies due to its biological characteristics and the ecological importance of this invertebrate group. The dominant lethal test was established in B. glabrata for the detection of germ cell mutations. Results with chemical mutagens showed that this system is efficient, specific and sensitive in the evaluation of germ cell mutations induced by reference mutagens. In this work, the dominant lethal effects of gamma radiation of 60 Co were studied. A preliminary experiment was done to establish the dose range and to estimate the chronology of spermatogenesis in B. glabrata. This estimate is possible because of the uniformity in response to ionizing radiation between germ cells at homologous stages of spermatogenesis in widely different species. In general, pre-meiotic germ cells are less sensitive to the induction of lethal dominant mutations than post-meiotic cells. This effect can be attributed to: young gametogenic cells - mitotically active - have greater repair ability from sub-lethal DNA damage and there is a selective elimination of the damaged cells. In our system: induction of lethal dominant mutations causes an increase in the frequency of malformations and, cytotoxic effect is displayed as a reduction in the crossing rates. Total duration of spermatogenesis was estimated in approximately 36 days, with the following distribution of stages: 1 to 13 days - spermatogonia, 14 to 20 days - spermatocytes, 21 to 36 days - spermatids and spermatozoa. Based on this chronology, irradiated wild-type snails with 2,5; 10 and 20Gy and crossed with non-irradiated albino snails after 7, 17, 23, 30 and 36 days. The frequencies of malformations in the heterozygous wild-type offspring of the nonirradiated albino snails were used as indicator of germ cell

Evaluation of a linear spectral mixture model and vegetation indices (NDVI and EVI) in a study of schistosomiasis mansoni and Biomphalaria glabrata distribution in the state of Minas Gerais, Brazil.

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Guimarães, Ricardo J P S; Freitas, Corina C; Dutra, Luciano V; Scholte, Ronaldo G C; Amaral, Ronaldo S; Drummond, Sandra C; Shimabukuro, Yosio E; Oliveira, Guilherme C; Carvalho, Omar S

2010-07-01

This paper analyses the associations between Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) on the prevalence of schistosomiasis and the presence of Biomphalaria glabrata in the state of Minas Gerais (MG), Brazil. Additionally, vegetation, soil and shade fraction images were created using a Linear Spectral Mixture Model (LSMM) from the blue, red and infrared channels of the Moderate Resolution Imaging Spectroradiometer spaceborne sensor and the relationship between these images and the prevalence of schistosomiasis and the presence of B. glabrata was analysed. First, we found a high correlation between the vegetation fraction image and EVI and second, a high correlation between soil fraction image and NDVI. The results also indicate that there was a positive correlation between prevalence and the vegetation fraction image (July 2002), a negative correlation between prevalence and the soil fraction image (July 2002) and a positive correlation between B. glabrata and the shade fraction image (July 2002). This paper demonstrates that the LSMM variables can be used as a substitute for the standard vegetation indices (EVI and NDVI) to determine and delimit risk areas for B. glabrata and schistosomiasis in MG, which can be used to improve the allocation of resources for disease control.

Differences in the gene expression profiles of haemocytes from schistosome-susceptible and -resistant biomphalaria glabrata exposed to Schistosoma mansoni excretory-secretory products.

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Zahida Zahoor

Full Text Available During its life cycle, the helminth parasite Schistosoma mansoni uses the freshwater snail Biomphalaria glabrata as an intermediate host to reproduce asexually generating cercariae for infection of the human definitive host. Following invasion of the snail, the parasite develops from a miracidium to a mother sporocyst and releases excretory-secretory products (ESPs that likely influence the outcome of host infection. To better understand molecular interactions between these ESPs and the host snail defence system, we determined gene expression profiles of haemocytes from S. mansoni-resistant or -susceptible strains of B. glabrata exposed in vitro to S. mansoni ESPs (20 μg/ml for 1 h, using a 5K B. glabrata cDNA microarray. Ninety-eight genes were found differentially expressed between haemocytes from the two snail strains, 57 resistant specific and 41 susceptible specific, 60 of which had no known homologue in GenBank. Known differentially expressed resistant-snail genes included the nuclear factor kappa B subunit Relish, elongation factor 1α, 40S ribosomal protein S9, and matrilin; known susceptible-snail specific genes included cathepsins D and L, and theromacin. Comparative analysis with other gene expression studies revealed 38 of the 98 identified genes to be uniquely differentially expressed in haemocytes in the presence of ESPs, thus identifying for the first time schistosome ESPs as important molecules that influence global snail host-defence cell gene expression profiles. Such immunomodulation may benefit the schistosome, enabling its survival and successful development in the snail host.

The introduction of Melanoides tuberculata (Mollusca: Thiaridae) to the island of Saint Lucia (West Indies) and its role in the decline of Biomphalaria glabrata, the snail intermediate host of Schistosoma mansoni.

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Pointier, J P

1993-06-01

A malacological survey was carried out in May 1992 in the whole hydrographic system of Saint Lucia 11 years after the end of a biological control programme to eliminate Biomphalaria glabrata, the snail intermediate host of Schistosoma mansoni. A competitor snail, Melanoides tuberculata, was introduced to Saint Lucia in 1978 and field experiments in several habitats were conducted by Prentice between 1978 and 1986. At the present time M. tuberculata is the most common freshwater snail in Saint Lucia. The results of the survey, undertaken in sites where B. glabrata occurred in large populations in the past showed (i) the absence of the snail hosts from seven sites now extensively colonized by the competitor (ii) the presence of B. glabrata in low or very low densities in 17 sites together with the competitor and (iii) the presence of the intermediate hosts in large populations in only two sites where M. tuberculata was absent. These results confirm the positive results observed by Prentice. The presence of another planorbid snail, B. straminea, is reported for the first time in Saint Lucia.

Resistência de Biomphalaria peregrina de Santa Rita do Sapucaí, Minas Gerais, a infecção com três cepas de Schistosoma mansoni Resistance of Biomphalaria peregrina from Santa Rita do Sapucaí, State of Minas Gerais, Brazil, to infection with strain of Schistosoma mansoni

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Cecília Pereira de Souza

1988-12-01

Full Text Available Descendentes do planorbídeo Biomphalaria peregrina, coletados em Santa Rita do Sapucaí, Minas Gerais, Brasil, foram expostos a miracídios de três cepas de Schistosoma mansoni: "LE" de Belo Horizonte, MG; "SJ" de São José dos Campos, SP e "AL" do Estado de Alagoas. Dentre 300 exemplares expostos, nenhum se infectou com as três cepas do trematódeo. Por outro lado, 300 exemplares de B. glabrata, dos grupos de controle, apresentaram taxas de infecção de 61,1 a 95,3% com as três cepas do trematódeo. As taxas de mortalidade de B. peregrina e de B. glabrata foram de 20,0 e de 28,0%, respectivamente.The descendants of the planorbid snail Biomphalaria peregrina, collected in the region of Santa rita do Sapucaí, Minas Gerais, Brazil, were exposed to miracidia of three strains of Schistosoma mansoni: "LE" strain from Belo Horizonte, State of Minas Gerais; "SJ", strain from São José dos Campos, State of São Paulo and "AL" strain from State of Alagoas. Of 300 snails exposed to miracidia of the three strains, none was infected. On the other hand, 300 Biomphalaria glabrata of the control groups showed infection rates of 61.1 to 95.3% with three strains. The mortality rates of B. peregrina and B. glabrata were 20% and 28%, respectively.

Evaluation of molluscicidal activity of three mangrove species (Avicennia schaueriana, Laguncularia racemosa and Rhizophora mangle) and their effects on the bioactivity of Biomphalaria glabrata Say, 1818

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Mendes, Renato Juvino de Aragão; Pereira, Adalberto Alves; Nogueira, Aline de Jesus Lustosa; Araújo, Karla Regina Freitas; França, Clícia Rosane Costa; de Carvalho, Iramar Borba; da Silva, Natale Maria Lindoso; Azevedo, Alexandre Santana; Rosa, Ivone Garros

2018-01-01

ABSTRACT Schistosomiasis is a disease of global extent reaching populations in social vulnerability. One of the control measures of this parasitosis is the use of molluscicidal substances that can fight snails of the genus Biomphalaria, intermediate hosts of Schistosoma mansoni. The aim of this work was to study the toxic activity of three mangrove species (Avicennia schaueriana Stapf. & Leech, ex Moldenke, 1939, Laguncularia racemosa (L.) CF Gaertn, 1807 and Rhizophora mangle L. 1753) on the biological activities of snails Biomphalaria glabrata. Hydroalcoholic extracts were prepared from the stem and leaves of each of the three plant species to which mollusks were exposed. The phytochemical analysis of plants showed the presence of important metabolites in the leaves and stems of L. racemosa and R. mangle, such as tannins and saponins, but the absence of these metabolites in A. schaueriana. Leaf and stem extracts of the three plant species showed low molluscicidal activity, not reaching the standards determined by the World Health Organization (WHO, 1983). L. racemosa and R. mangle has interfered with motility, feeding and oviposition of snails, unlike the extracts of A. schaueriana, which had no effect on these activities. PMID:29451595

Steroid Androgen Exposure during Development Has No Effect on Reproductive Physiology of Biomphalaria glabrata.

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Satwant Kaur

Full Text Available Gastropod mollusks have been proposed as alternative models for male reproductive toxicity testing, due to similarities in their reproductive anatomy compared to mammals, together with evidence that endocrine disrupting chemicals can cause effects in some mollusks analogous to those seen in mammals. To test this hypothesis, we used the freshwater pulmonate snail, Biomphalaria glabrata, for which various genetic tools and a draft genome have recently become available, to investigate the effects of two steroid androgens on the development of mollusk secondary sexual organs. Here we present the results of exposures to two potent androgens, the vertebrate steroid; 5α-dihydrotestosterone (DHT and the pharmaceutical anabolic steroid; 17α-methyltestosterone (MT, under continuous flow-through conditions throughout embryonic development and up to sexual maturity. Secondary sexual gland morphology, histopathology and differential gene expression analysis were used to determine whether steroid androgens stimulated or inhibited organ development. No significant differences between tissues from control and exposed snails were identified, suggesting that these androgens elicited no biologically detectable response normally associated with exposure to androgens in vertebrate model systems. Identifying no effect of androgens in this mollusk is significant, not only in the context of the suitability of mollusks as alternative model organisms for testing vertebrate androgen receptor agonists but also, if applicable to other similar mollusks, in terms of the likely impacts of androgens and anti-androgenic pollutants present in the aquatic environment.

Estratégia competitiva entre Biomphalaria glabrata e Biomphalaria tenagophila: estudos de laboratório

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Mairy Barbosa Loureiro dos Santos

1989-01-01

Full Text Available Observation about conhabitation among B. glabrata and B. tenagophila revealed a greater vulnerability of B. tenagophila population during the process of competition when its density was severaly decreased in 12 trials, moderate in 2 trials. It was higher than B. glabrata in only one trial. Some snail water chemical parameters analysed such as pH, alkalinity, conductivity and oxygen dissolve, an the viability rate of batch of eggs didn't give subsidy to explain the competition mechanism. The newly-born survival, in the situation of cohabitation, was low for both species. This reveals the existence of intra and interspecific competitive interacition. The fertility rate reduction of B. tenagophila during the cohabitation was considered as a cause of its exlusion. One of the factors that seems to have influenced the fertility rate was a possible wrong crossing.

Size Polymorphism in Alleles of the Myoglobin Gene from Biomphalaria Mollusks

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Marcelo M. Santoro

2010-10-01

Full Text Available Introns are common among all eukaryotes, while only a limited number of introns are found in prokaryotes. Globin and globin-like proteins are widely distributed in nature, being found even in prokaryotes and a wide range of patterns of intron-exon have been reported in several eukaryotic globin genes. Globin genes in invertebrates show considerable variation in the positions of introns; globins can be found without introns, with only one intron or with three introns in different positions. In this work we analyzed the introns in the myoglobin gene from Biomphalaria glabrata, B. straminea and B. tenagophila. In the Biomphalaria genus, the myoglobin gene has three introns; these were amplified by PCR and analyzed by PCR-RFLP. Results showed that the size (number or nucleotides and the nucleotide sequence of the coding gene of the myoglobin are variable in the three species. We observed the presence of size polymorphisms in intron 2 and 3; this characterizes a homozygous/heterozygous profile and it indicates the existence of two alleles which are different in size in each species of Biomphalaria. This polymorphism could be explored for specific identification of Biomphalaria individuals.

Bioactivity Evaluation of Plant Extracts Used in Indigenous Medicine against the Snail, Biomphalaria glabrata, and the Larvae of Aedes aegypti.

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Dos Santos, Edilson Alves; de Carvalho, Cenira M; Costa, Ana L S; Conceição, Adilva S; Moura, Flávia de B Prado; Santana, Antônio Euzébio Goulart

2012-01-01

This investigation examined the molluscicidal and larvicidal activity of eight plants that are used in the traditional medicine of the Pankararé indigenous people in the Raso da Catarina region, Bahia state, Brazil. The tested plants were chosen based on the results of previous studies. Only those plants that were used either as insect repellents or to treat intestinal parasitic infections were included in the study. Crude extracts (CEs) of these plants were tested for their larvicidal activity (against Aedes aegypti larvae in the fourth instar) and molluscicidal activity (against the snail Biomphalaria glabrata). The plant species Scoparia dulcis and Helicteres velutina exhibited the best larvicidal activities (LC(50) 83.426 mg/L and LC(50) 138.896 mg/L, resp.), and Poincianella pyramidalis, Chenopodium ambrosoides, and Mimosa tenuiflora presented the best molluscicidal activities (LC(50) 0.94 mg/L, LC(50) 13.51 mg/L, and LC(50) 20.22 mg/L, resp.). As we used crude extracts as the tested materials, further study is warranted to isolate and purify the most active compounds.

Bioactivity Evaluation of Plant Extracts Used in Indigenous Medicine against the Snail, Biomphalaria glabrata, and the Larvae of Aedes aegypti

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Edilson Alves dos Santos

2012-01-01

Full Text Available This investigation examined the molluscicidal and larvicidal activity of eight plants that are used in the traditional medicine of the Pankararé indigenous people in the Raso da Catarina region, Bahia state, Brazil. The tested plants were chosen based on the results of previous studies. Only those plants that were used either as insect repellents or to treat intestinal parasitic infections were included in the study. Crude extracts (CEs of these plants were tested for their larvicidal activity (against Aedes aegypti larvae in the fourth instar and molluscicidal activity (against the snail Biomphalaria glabrata. The plant species Scoparia dulcis and Helicteres velutina exhibited the best larvicidal activities (LC50 83.426 mg/L and LC50 138.896 mg/L, resp., and Poincianella pyramidalis, Chenopodium ambrosoides, and Mimosa tenuiflora presented the best molluscicidal activities (LC50 0.94 mg/L, LC50 13.51 mg/L, and LC50 20.22 mg/L, resp.. As we used crude extracts as the tested materials, further study is warranted to isolate and purify the most active compounds.

Reduction in transmission of Schistosoma mansoni by a four-year focal mollusciciding programme against Biomphalaria glabrata in Saint Lucia.

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Prentice, M A; Jordan, P; Bartholomew, R K; Grist, E

1981-01-01

The effect of transmission of Schistosoma mansoni of a focal snail control programme was investigated over four years amongst approximately 1250 people living in five communities in the steep-sided Soufriere river valley, St. Lucia, West Indies. Bayer 6076 was applied from constant flow drip cans to 12 stream sections at a target dose of 8 mg/litre clonitralide every four weeks. Only proven and potential transmission sites were treated; marsh habitats, where Biomphalaria glabrata were widespread, were ignored. In the stream snail numbers were reduced by 94% in the first year and by 100% thereafter. Incidence of new S. mansoni infections amongst children fell from 18% in the last year before control to 6% and 9% after three and four years respectively. Amongst children and adults in the four years of control the conversion/reversion ratio declined leading to a lowering of the over-all prevalence from 40% to 22%. Parasitologically the results were similar to those of a previously evaluated area-wide mollusciciding programme. The mean annual cost per person protected was US $2.60. This figure is atypically high because the topography of the area severely limited the population size.

Susceptibility of Biomphalaria tenagophila and Biomphalaria straminea to Schistosoma mansoni infection detected by low stringency polymerase chain reaction

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JANNOTTI-PASSOS Liana Konovaloff

2000-01-01

Full Text Available In order to determine Schistosoma mansoni infection rates in Biomphalaria tenagophila and B. straminea, low stringency polymerase chain reaction (LS-PCR technique was used as a complementary method to light exposure technique. LS-PCR has already been standardized in our laboratory to detect the trematode DNA in B. glabrata. Higher S. mansoni infection rates were detected using conventional method and LS-PCR. The parasite DNA profile was detected in both species after 7-day exposure to miracidia, using LS-PCR. This technique enables early detection of schistosomiasis transmission focuses, in endemic areas, before the beginning of cercariae shedding.

Proteomics of drug resistance in Candida glabrata biofilms.

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Seneviratne, C Jayampath; Wang, Yu; Jin, Lijian; Abiko, Y; Samaranayake, Lakshman P

2010-04-01

Candida glabrata is a fungal pathogen that causes a variety of mucosal and systemic infections among compromised patient populations with higher mortality rates. Previous studies have shown that biofilm mode of the growth of the fungus is highly resistant to antifungal agents compared with the free-floating or planktonic mode of growth. Therefore, in the present study, we used 2-D DIGE to evaluate the differential proteomic profiles of C. glabrata under planktonic and biofilm modes of growth. Candida glabrata biofilms were developed on polystyrene surfaces and age-matched planktonic cultures were obtained in parallel. Initially, biofilm architecture, viability, and antifungal susceptibility were evaluated. Differentially expressed proteins more than 1.5-fold in DIGE analysis were subjected to MS/MS. The transcriptomic regulation of these biomarkers was evaluated by quantitative real-time PCR. Candida glabrata biofilms were highly resistant to the antifungals and biocides compared with the planktonic mode of growth. Candida glabrata biofilm proteome when compared with its planktonic proteome showed upregulation of stress response proteins, while glycolysis enzymes were downregulated. Similar trend could be observed at transcriptomic level. In conclusion, C. glabrata biofilms possess higher amount of stress response proteins, which may potentially contribute to the higher antifungal resistance seen in C. glabrata biofilms.

Studies on survival, biological activities and behavior of Biomphalaria glabrata, the host snail of Schistosomiasis, submitted to increased hydrostatic pressure: a technique Estudos sobre a sobrevivência, atividades biológicas e comportamento de Biomphalaria glabrata, hospedeiro intermediário da esquistossomose, submetido a aumento da pressão hidrostática: uma técnica

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P. Jurberg

1988-03-01

Full Text Available To study changes in survival, in biological activities and behavior of planorbids submitted to increased hydrostatic pressure, we developed a technique using two transparent chambers and a hydraulic piston. The apparatus permitted renewal of the liquid medium without substantial variations in pressure, thus eliminating excretion products and maintaining the desired O2 level and thereby permitting us to evaluate the effects of pressure independently of the occurrence of anoxia. Pressure was maintained without any contact of the liquid medium with compressed air, a situation which reproduced with relative fidelity what occurs in nature and assured the presence of the same amounts of gases in the two observation chambers (Control and Experimental. Biomphalaria glabrata was found to be able to survive at least 48 hours when submitted to 49.02 x 10**4 Pa (equivalent to a water depth of 48.8 m, continuing to day egg masses and showing few behavioral changes when compared with the control group.Para estudar mudanças na sobrevivência, atividades biológicas e comportamento de planorbídeos submetidos a aumento de pressão hidrostática, desenvolvemos uma técnica que utiliza duas câmaras transparentes e um pistão hidráulico. O aparelho permitiu a renovação do meio líquido sem variações substanciais na pressão, eliminando assim os produtos de excreção e mantendo o nível de O2 disseolvido desejado, e desse modo permitido-nos avaliar o efeito da pressão independente da ocorrência de anoxia. A pressão foi mantida sem nenhum contato do meio líquido com o ar comprimido, situação que produziu com relativa fidelildade o que ocorre na natureza, e assegurou a presença da mesma quantidade de gases nas duas câmaras de observação. Biomphalaria glabrata foi capaz de sobreviver pelo menos 48 horas quando submetida a 49,02 x 10 Pa (equivalente a 48 m de profundidade continuando a pôr massas ovíferas, e mostrando poucas modifica

Estudo da potencialidade de populações de Biomphalaria straminea do Estado de Minas Gerais, como hospedeiras do Schistosoma mansoni Potentiality of the Biomphalaria straminea populations of the State of Minas Gerais, as hosts of Schistosoma mansoni

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Cecília Pereira de Souza

1983-09-01

Full Text Available Caramujos de Biomphalaria straminea, descendentes de exemplares coletados em nove municípios do Estado de Minas Gerais, foram infectados experimentalmente com três cepas de Schistosoma mansoni: "LE", procedente de Belo Horizonte (MG; "SJ", procedente de São José dos Campos (SP e "AL" procedente do Nordeste (AL. As taxas de infeção variaram de 0,0 a 24,0% com a cepa "LE"; de 0,0 a 16% com a cepa "SJ" e de 2,0 a 9,0% com a cepa "AL". Os índices de infecção experimental obtidos foram semelhantes aos registrados por outros autores, para B. straminea dessa região. Comparou-se o número de cercárias de cepa "LE", eliminadas por oito exemplares de B. straminea de Baldim e oito Biomphalaria glabrata do controle, após 30 minutos de exposição à luz. O número de cercárias eliminadas por B. straminea foi de 4.550, aproximadamente cinco vezes menor que o de B. glabrata, 22.679. Discute-se a potencialidade desses moluscos como hospedeiros do S. mansoni nessa região.The decendents of Biomphalaria straminea snails collected in nine regions from the State of Minas Gerais were experimentally infected with three strains of Schistosoma mansoni: "LE", from Belo Horizonte, Minas Gerais; "SJ", from São José dos Campos, State of São Paulo and "AL", from State of Alagoas. The infection rates obtained were of 0 to 24% (LE strain, 0 to 16% (SJ strain and 2 to 9% (AL strain. These infection rates were similar to those obtained by other authors for B. straminea from this region. Comparation were made between the numbers of cercariae (LE strain shed by eight specimens of B. straminea from Baldim and eight B. glabrata of the control group, after 30 minutes of exposure to light. B. straminea shed 4,550 cercariae, about five times less than B. glabrata (22,679. The authors discuss the potentiality of theses molluscs as hosts of S. mansoni in this region.

Effects of Different Levels of Echinostoma caproni Miracidial Dose on Glucose and Maltose Composition of Biomphalaria glabrata Snails as Determined by High Performance Thin-Layer Chromatography-Densitometry

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Dolcie DeGrandchamp

2015-04-01

Full Text Available The effects of 5, 25, and 40 Echinostoma caproni miracidia on the sugar content of young adult and mature adult Biomphalaria glabrata were studied using high performance thin layer chromatography (HPTLC-densitometry. Analysis was done on the snail’s digestive gland gonad complex (DGG at two and four weeks postmiracidial exposure. The sugars were extracted from the DGG using 70% ethanol and analyzed on silica gel HPTLC plates with a preadsorbent zone using 1-butanol-glacial acetic acid-diethyl ether-deionized water (27:18:5:3 mobile phase. The separated bands were then detected using alpha-naphthol-sulfuric reagent and quantified by densitometry at 515 nm. Significant differences were found in the maltose content between two and four weeks post exposure for both age groups. Additionally, significantly lower maltose and glucose levels were observed in the high exposure groups of both ages.

Schistosoma mansoni control in Cul de Sac Valley, Saint Lucia. I. A two-year focal surveillance-mollusciciding programme for the control of Biomphalaria glabrata.

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Barnish, G; Christie, J D; Prentice, M A

1980-01-01

An area-wide mollusciciding campaign in Cul de Sac valley, St. Lucia reduced incidence of Schistosoma mansoni from 22% to 4.3% between 1970 and 1975. Following this, a two-year focal surveillance-mollusciciding programme was introduced. Sites of potential transmission of S. mansoni were identified and routinely searched for Biomphalaria glabrata. If found, the site was treated with clonitralide 25% emulsifiable concentrate. Two chemotherapy campaigns supplemented the snail control programme. As a result of the combined measures, incidence of the infection dropped from 4.3% to 1.0% and from 2.2% to 0.6% in areas originally of high and low transmission respectively. The cost of protecting the 7,000 population was US $20,362: of these costs, labour absorbed 68%, transport 24%, equipment 4% and molluscicide 4%. The cost per person per year protected was US $1.45 which compares favourably with the $3.24 of the previous scheme. Although effective and relatively cheap, this programme was still dependent on a high standard of supervision for maximum benefit.

Avaliação da atividade tóxica em Artemia salina e Biomphalaria glabrata de extratos de quatro espécies do gênero Eleocharis (Cyperaceae

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A.L.T.G. Ruiz

Full Text Available O gênero Eleocharis R. Br. compreende cerca de 200 espécies, ocorrendo em ambientes úmidos tais como brejos e margens de rios e lagos. Procurando novos agentes moluscicidas, os extratos de Eleocharis acutangula (Roxb. Schult., Eleocharis interstincta (Vahl Roem. & Schult., Eleocharis maculosa (Vahl Roem. & Schult. e Eleocharis sellowiana Kunth foram testados para atividade moluscicida, contra caramujos adultos e desovas, e toxicidade (ensaio de letalidade com Artemia salina. O extrato hexânico de Eleocharis acutangula (parte subterrânea fresca foi ativo contra Artemia salina (CL50 = 476,00 mg/mL, enquanto os demais extratos apresentaram CL50 >> 10³ mg/mL, sugerindo baixa toxicidade. O extrato hidro-etanólico de Eleocharis sellowiana (parte subterrânea fresca foi ativo contra desovas de Biomphalaria glabrata (CL50 = 24,27 mg/mL mas inativo contra indivíduos adultos. Os demais extratos testados não apresentaram atividade moluscicida.

The role of behavior in the survival of Biomphalaria glabrata in biossays with the plant molluscicide Phytolacca dodecandra O papel do comportamento na sobrevivência de Biomphalaria glabrata submetida a bioensaios com o moluscicida vegetal Phytolacca dodecandra

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P. Jurberg

1988-03-01

Full Text Available This work examines the role of behavior in the survival of Biomphalaria glabrata exposed to 25, 50 75 and 100 mgl-1 of Phytolacca dodecandra. Time-lapse cinematography was used to quantify accurately the following parameters: (a frequency of exits from the solution, (b time spent out of the solution and (c time elapsed until the first exit from the solution. These behavior patterns were statistically compared between surviving snails and those which later died. The proportion of surviving snails leaving the liquid medium was significantly higher than that of dying snails. In addition, the surviving group spent significantly more time out of the solution than the group which died, except for the 100 mgl-1 concentration. However, no significant difference was detected in the time elapsed until the first exit from the solution. It can be concluded that both the tendency to leave the P. dodecandra solutions, and the time spent out of them, contributed significantly to snail survival. Molluscicide bioassays should take into account the possibility that some behavior patterns of planorbids might contribute to the protection of the snails.Este trabalho investiga o papel do comportamento na sobrevivência de Biomphalaria glabarta exposta a 25, 50, 75 e 100 mgI-1 de Phytolacca dodecandra. Foi utilizada a técnica de cinematografia com lapso de tempo para quantificar acuradamente os seguintes parâmetros (a freqüência de saídas da solução, (b tempo de permanência fora da solução e (e tempo decorrido até a primeira saída da soluçao. Estes padrões comportamentais foram estatisticamente comparados no que se refere aos caramujos sobreviventes e aos que vieram a morrer. Dentre os camundongos que abandonaram o meio líquido, a proporção de sobreviventes foi significativamente maior que a de mortos. Além disso, um tempo significativamente maior de permanência fora da solução foi observado no grupo que sobreviveu, em relação ao grupo que veio

Esquistossomose: nova ocorrência de Biomphalaria straminea em Belo Horizonte, Minas Gerais Schistosomiasis: new occurrence of Biomphalaria straminea in Belo Horizonte, Minas Gerais

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Cecília Pereira de Souza

1996-12-01

Full Text Available Em Belo Horizonte, Minas Gerais, Brasil, a Biomphalaria straminea é encontrada na região da Pampulha. Recentemente, o molusco foi encontrado em valas da antiga Barragem de Santa Lúcia, foco extinto de esquistossomose transmitida por B. glabrata. Os moluscos foram coletados e examinados para verificar se estavam naturalmente infectados com Schistosoma mansoni. Os exemplares negativos foram usados para criação ou infecção com a cepa LE de S. mansoni, mantida no laboratório, e outra cepa VGS, obtida de ovos de fezes de escolar de Belo Horizonte. Dentre 1.890 moluscos capturados em 1994 e 1995, nenhum estava infectado com S. mansoni. Dentre 87 exemplares coletados no criadouro e expostos à cepa LE, nove (10,3% eliminaram cercárias; dentre 83 moluscos da F1, dez (12,0% eliminaram cercárias e dentre 88 exemplares coletados e expostos à cepa VGS, dez (11,3% eliminaram cercárias. Em Belo Horizonte, a esquistossomose é transmitida por B. glabrata e B. tenagophila. Entretanto, atualmente existe o risco de aparecimento de novo foco, no qual a B. straminea poderá vir a ser a transmissora, se medidas profiláticas adequadas não forem tomadas pelas autoridades responsáveis pela construção de um parque e lago no local.In Belo Horizonte, Minas Gerais, Brazil, the snail Biomphalaria straminea was found in the Pampulha region. Recently the snail was found in ditches in the old Santa Lúcia Reservoir, a now-extinct focus of schistosomiasis transmission by B. glabrata. The snails were collected and examined to verify whether they were naturally infected with Schistosoma mansoni. Negative specimens were used for breeding or infection with the LE strain of S. mansoni from the laboratory and another strain obtained from eggs found in the feces of a schoolchild (VGS from Belo Horizonte. Among the 1890 snails collected from 1994 to 1995, none were infected with S. mansoni. Among 87 snails collected and exposed to the LE strain, 9 (10.3% shed cercariae

Malacological survey of Biomphalaria snails in municipalities along the Estrada Real in the southeast of the State of Minas Gerais, Brazil.

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Tibiriçá, Sandra Helena Cerrato; Mitterofhe, Adalberto; Castro, Milton Ferreira de; Lima, Adilson da Costa; Gonçalves, Murilo; Pinheiro, Izabella de Oliveira; Freitas, Corina da Costa; Guimarães, Ricardo José Paula de Souza e; Carvalho, Omar dos Santos; Coimbra, Elaine Soares

2011-01-01

The increasing practice of ecotourism and rural tourism in the State of Minas Gerais, Brazil, highlights the importance of studies concerning the occurrence of potential intermediate hosts of Schistosoma mansoni. This study aimed to identify species of Biomphalaria snails in municipalities along the Estrada Real, an important Brazilian tourism project. The specimens were collected in different water collections of 36 municipalities along the Estrada Real in the southeast of the State of Minas Gerais. Biomphalaria species were characterized using both morphological and molecular approaches. The research was conducted between August 2005 and September 2009 and all the sites visited were georeferenced using GPS. Six Biomphalaria species were found in 30 of the 36 municipalities studied: glabrata, tenagophila, straminea, peregrina, occidentalis and schrammi. The first three species of Biomphalaria, recognized as intermediate hosts of S. mansoni, were present in 33.3%, 47.2% and 8.3% of the municipalities studied, respectively. The mollusks were found in different types of water collections and no infection by S. mansoni was detected. The highest occurrence of Biomphalaria concentration was verified in the area covered by the Caminho Novo route (Diamantina/MG to Rio de Janeiro/RJ). Considering the occurrence of schistosomiasis in the State of Minas Gerais and the socioeconomic repercussions involved in the Estrada Real Project, this work focuses on the vulnerability of water collections due to the presence of Biomphalaria mollusks and emphasizes the need for epidemiological surveillance and sanitary and educational measures integrated with the local community and tourism sectors.

Malacological survey of Biomphalaria snails in municipalities along the Estrada Real in the southeast of the State of Minas Gerais, Brazil

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Sandra Helena Cerrato Tibiriçá

2011-04-01

Full Text Available INTRODUCTION: The increasing practice of ecotourism and rural tourism in the State of Minas Gerais, Brazil, highlights the importance of studies concerning the occurrence of potential intermediate hosts of Schistosoma mansoni. This study aimed to identify species of Biomphalaria snails in municipalities along the Estrada Real, an important Brazilian tourism project. METHODS: The specimens were collected in different water collections of 36 municipalities along the Estrada Real in the southeast of the State of Minas Gerais. Biomphalaria species were characterized using both morphological and molecular approaches. The research was conducted between August 2005 and September 2009 and all the sites visited were georeferenced using GPS. RESULTS: Six Biomphalaria species were found in 30 of the 36 municipalities studied: glabrata, tenagophila, straminea, peregrina, occidentalis and schrammi. The first three species of Biomphalaria, recognized as intermediate hosts of S. mansoni, were present in 33.3%, 47.2% and 8.3% of the municipalities studied, respectively. The mollusks were found in different types of water collections and no infection by S. mansoni was detected. The highest occurrence of Biomphalaria concentration was verified in the area covered by the Caminho Novo route (Diamantina/MG to Rio de Janeiro/RJ. CONCLUSIONS: Considering the occurrence of schistosomiasis in the State of Minas Gerais and the socioeconomic repercussions involved in the Estrada Real Project, this work focuses on the vulnerability of water collections due to the presence of Biomphalaria mollusks and emphasizes the need for epidemiological surveillance and sanitary and educational measures integrated with the local community and tourism sectors.

Characterization of South American Snails of the Genus Biomphalaria (Basommatophora: Planorbidae and Schistosoma mansoni (Platyhelminthes: Trematoda in Molluscs by PCR-RFLP

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Roberta Lima Caldeira

2016-01-01

Full Text Available The identification of snails of the genus Biomphalaria can be done using morphological characteristics which depends on the size of the snails and skill and knowledge of researcher. These methods sometimes are not adequate for identification of species. The PCR-RFLP, using the ITS region of the rDNA, has been used to identify Brazilian species of the genus Biomphalaria. Nevertheless, there is a lack of information about snails from other Latin American countries. In addition, some snails may be infected by Schistosoma mansoni and when submitted to PCR-RFLP they show molecular profiles different from those previously standardized for the other mollusc species. In this work the molecular profiles of 15 species and the subspecies were established by PCR-RFLP of ITS-rDNA with the enzyme DdeI. Moreover, the molecular profiles of host species, B. glabrata, B. straminea, B. tenagophila, and B. prona, infected by S. mansoni were also established. The molluscs were dissected to permit morphological identification. These results contribute to a correct identification of snails of the genus Biomphalaria and detection of these snails infected by S. mansoni.

Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni.

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Jacob A Tennessen

Full Text Available New strategies to combat the global scourge of schistosomiasis may be revealed by increased understanding of the mechanisms by which the obligate snail host can resist the schistosome parasite. However, few molecular markers linked to resistance have been identified and characterized in snails.Here we test six independent genetic loci for their influence on resistance to Schistosoma mansoni strain PR1 in the 13-16-R1 strain of the snail Biomphalaria glabrata. We first identify a genomic region, RADres, showing the highest differentiation between susceptible and resistant inbred lines among 1611 informative restriction-site associated DNA (RAD markers, and show that it significantly influences resistance in an independent set of 439 outbred snails. The additive effect of each RADres resistance allele is 2-fold, similar to that of the previously identified resistance gene sod1. The data fit a model in which both loci contribute independently and additively to resistance, such that the odds of infection in homozygotes for the resistance alleles at both loci (13% infected is 16-fold lower than the odds of infection in snails without any resistance alleles (70% infected. Genome-wide linkage disequilibrium is high, with both sod1 and RADres residing on haplotype blocks >2 Mb, and with other markers in each block also showing significant effects on resistance; thus the causal genes within these blocks remain to be demonstrated. Other candidate loci had no effect on resistance, including the Guadeloupe Resistance Complex and three genes (aif, infPhox, and prx1 with immunological roles and expression patterns tied to resistance, which must therefore be trans-regulated.The loci RADres and sod1 both have strong effects on resistance to S. mansoni. Future approaches to control schistosomiasis may benefit from further efforts to characterize and harness this natural genetic variation.

Comportamento de Biomphalaria glabrata (Say, 1818 como critério de toxicidade em ensaios biológicos com moluscicidas Behavior of Biomphalaria glabrata (Say, 1818 as a parameter of toxicity in biological assays with molluscicides

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Otávio S. Pieri

1981-06-01

Full Text Available Visando à aplicação sistemática de parâmetros comportamentais como indicadores da ação tóxica de moluscicidas empregados no combate aos hospedeiros intermediários do Schistosoma mansoni, um procedimento para avaliação quantitativa do efeito de dose sobre o comprotamento de Biomphalaria glabrata foi desenvolvido, com base no paradigma recomendado pela O.M.S. para ensaios biológicos e envolvendo registro comportamental por cenematografia ocm lapso de tempo: caramujos com 5 7/8 ± 1/8 giros eram subemtidos a diferentes concentrações subletais de sulfato de cobre durante 24 horas e em seguida transferidos para recuperação em água destilada desionizada; a partir da análise dos registros foram computados (a a freqüência total de subidas à superfície por indivíduo, (b a frqüência total de saídas da água por indivíduo e (c a proporção média de indivíduos no terço superior do recipiente de teste. O método Litchfield-Wilcoxon foi empregaod para determinação de índices de referência (denominados "concentrações de efieto comportamental de 50%" ou CEC50 em relação a cada parâmetro, e os valores obtidos - (a 0,010, (b 0,006 e (c 0,029 ppm de cobre - não só evidenciaram a exeqüibilidade da aplicação sistemática de critérios comportamentais de toxidade, como se revelaram capazes de detectar o efieto tóxico do produto em concentrações muito infereiores às obtidas nas determinações convencionais de letalidade. Os dados também mostraram alterações na atividade dos caramujos em decorrência do ciclo de iluminação dia-noite. Embora o esclarecimento dos aspectos etológicos envolvidos no problema do controle químico do vetor dependa da análise das relações entre o indivíduo e seu ambiente natural, estudos de laboratório com mensurações acuradas de parâmetros relacionados a comportamentos de proteção podem fornecer subsídios relevantes a respeito.The possibility of using reliable behavioural

Defense response of susceptible and resistant Biomphalaria alexandrina snails against Schistosoma mansoni infection

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Iman F. Abou-El-Naga

2012-09-01

Full Text Available In Egypt, Biomphalaria alexandrina is the intermediate host for Schistosoma mansoni. The fates of Schistosoma miracidia in the snails varies between different species of Biomphalaria. The internal defense system is one of the factors that influence the susceptibility pattern of the snails. The interaction between Biomphalaria snails and S. mansoni needs to be identified for each species, and even between the members of the same species with different degrees of susceptibility. In the present study, the first generation of susceptible and resistant parents of B. alexandrina was examined histologically at the 30th day post exposure. The study includes the characterization of the immune response, as expressed by tissue reactions, of susceptible and resistant B. alexandrina snails against S. mansoni. It was also designed to determine the impact of the resistance increase in parent snails, on the mechanisms of interaction of their offspring against infection. The results showed that the infection rate of the offspring from the susceptible parents was 92%. No susceptible offspring was produced from the resistant parents. When the parents were of equal number of susceptible and resistant snails, they gave an offspring with an infection rate of 20%. Susceptible snails that had susceptible parents showed a higher degree of susceptibility than those that had both susceptible and resistant parents. A common feature of the resistant snails was the absence of any viable parasites. The tissue reactions of the resistant snails having only resistant parents occurred at the site of miracidial penetration. In resistant snails for which susceptible ones were included in their parents, the reactions occurred in the deep tissues. These results characterized the immune response of B. alexandrina snails against Schistosoma infection which was found to occur by two different mechanisms. One type of defense occurs in highly resistant snails, and employs direct

Biomphalaria species distribution and its effect on human Schistosoma mansoni infection in an irrigated area used for rice cultivation in northeast Brazil

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Delmany Moitinho Barboza

2012-09-01

Full Text Available The role of irrigated areas for the spread of schistosomiasis is of worldwide concern. The aim of the present study was to investigate the spatial distribution of the intermediate snail host Biomphalaria in an area highly endemic for schistosomiasis due to Schistosoma mansoni, evaluating the relationship between irrigation and types of natural water sources on one hand, and the influence of place and time of water exposure on the intensity of human infection on the other. A geographical information system (GIS was used to map the distribution of the intermediate snail hosts in Ilha das Flores, Sergipe, Brazil, combined with a clinical/epidemiological survey. We observed a direct correlation between the intensity of human infection with S. mansoni and irrigation projects. Malacological studies to identify snail species and infection rates showed that B. glabrata is the main species responsible for human schistosomiasis in the municipality, but that B. straminea also plays a role. Our results provide evidence for a competitive selection between the two snail species in rice fields with a predominance of B. glabrata in irrigation systems and B. straminea in natural water sources.

Influência do magnésio metálico e diferentes sais de magnésio em desovas de Biomphalaria glabrata (Say, 1818 Influence of metallic magnesium and various magnesium salts on egg-masses of Biomphalaria glabrata (Say, 1818

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Nelymar Martineli Mendes

1983-12-01

Full Text Available Soluções de magnésio metálico e diferentes sais de magnésio foram testadas em laboratório, a fim de comprovar a ação das mesmas sobre a oviposição de B. glabrata. Usaram-se, para cada solução, dez caramujos adultos originários da Pampulha, Belo Horizonte-MG (Brasil, criados em laboratório. No experimento I foram estudadas soluções em água desclorada de magnésio elementar (Mg, cloreto de magnésio (MgCl2.6H2O, carbonato de magnésio [(MgCO34.Mg(OH2.nH2O], nitrato de magnésio [Mg(NO32. 6H2O] e sulfato de magnésio (MgSO4.7H2O, e no experimento II, Mg, Mg + latossolo, MgCO3, MgCO3 + latossolo, sempre nas concentrações de 500 e 1.000 ppm. Durante duas semanas os planorbídeos permaneceram em água para adaptação; em seguida, por quatro semanas em exposição com as soluções testadas e, posteriormente, em água por mais duas semanas para recuperação. A cada sete dias as desovas eram contadas, eliminadas e as soluções renovadas. Foi observado que as soluções de Mg e MgCO3, isoladamente ou associada ao latossolo, produziram uma diminuição significativa do número de desovas dos caramujos, mas não parada completa de oviposição, quando comparados os períodos de adaptação com os de exposição. As soluções de Mg e MgCO3 não devem ser consideradas como produtos promissores para o controle da população de B. glabrata, em virtude da diminuição das desovas só terem sido observadas quando foram utilizadas concentrações muito altas.Solutions of magnesium metallic and other salts of magnesium were tested in the laboratory to study the action on B. glabrata oviposition. For each solution, 10 adult snails from Pampulha, Belo Horizonte-MG (Brazil, reared in the laboratory, were used. In experiment I solutions, in dechlorinated water, of magnesium (Mg, magnesium chloride (MgCl2. 6H2O, magnesium carbonate [(MgCO34.Mg(OH2.nH2O], magnesium nitrate [Mg(NO32.6H2O] and magnesium sulfate (MgSO4.7H2O were tested; and in

Elimination of Biomphalaria pfeifferi, Bulinus tropicus and Lymnaea natalensis by the ampullarid snail, Marisa cornuarietis, in a man-made dam in northern Tanzania.

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Nguma, J F; McCullough, F S; Masha, E

1982-03-01

Marisa cornuarietis is a well known ampullarid competitor/predator of Biomphalaria glabrata in Puerto Rico. For the first time in Africa a flourishing population of Marisa has been established in a small, permanent, man-made dam at Kisangara, near Moshi, Tanzania. Prior to the release of M. cornuarietis in June 1977, this dam supported thriving populations of the pulmonate snail hosts Biomphalaria pfeifferi and Lymnaea natalensis; Bulinus tropicus and the melaniid Melanoides tuberculata were also common. Some 24 months after the establishment of Marisa the three pulmonate species had been eliminated; only M. tuberculata remained at about the same population density as originally recorded. Marisa has not caused any obvious adverse environmental impact in the dam. There is at present no valid evidence that this ampullarid would be a threat to local rice production, which is the only crop at risk, but carefully designed field trials should be undertaken to confirm or refute this view. In view of the vast number of permanent, lentic habitats throughout the Afrotropical region, which act as important transmission sites of schistosomiasis and fascioliasis, the role of Marisa cornuarietis as a cost-effective biological control agent in integrated control operations deserves henceforth to be energetically explored.

A network of paralogous stress response transcription factors in the human pathogen Candida glabrata.

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Jawad eMerhej

2016-05-01

Full Text Available The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq, transcriptome analyses and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1 transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the cross-roads between redox homeostasis, oxygen consumption and iron metabolism.

Hybridism between Biomphalaria cousini and Biomphalaria amazonica and its susceptibility to Schistosoma mansoni

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Tatiana Maria Teodoro

2011-11-01

Full Text Available Molecular techniques can aid in the classification of Biomphalaria species because morphological differentiation between these species is difficult. Previous studies using phylogeny, morphological and molecular taxonomy showed that some populations studied were Biomphalaria cousini instead of Biomphalaria amazonica. Three different molecular profiles were observed that enabled the separation of B. amazonica from B. cousini. The third profile showed an association between the two and suggested the possibility of hybrids between them. Therefore, the aim of this work was to investigate the hybridism between B. cousini and B. amazonica and to verify if the hybrids are susceptible to Schistosoma mansoni. Crosses using the albinism factor as a genetic marker were performed, with pigmented B. cousini and albino B. amazonica snails identified by polymerase chain reaction-restriction fragment length polymorphism. This procedure was conducted using B. cousini and B. amazonica of the type locality accordingly to Paraense, 1966. In addition, susceptibility studies were performed using snails obtained from the crosses (hybrids and three S. mansoni strains (LE, SJ, AL. The crosses between B. amazonica and B. cousini confirmed the occurrence of hybrids. Moreover, hybrids can be considered potential hosts of S. mansoni because they are susceptible to LE, SJ and AL strains (4.4%, 5.6% and 2.2%, respectively. These results indicate that there is a risk of introducing schistosomiasis mansoni into new areas.

Defense response of susceptible and resistant Biomphalaria alexandrina snails against Schistosoma mansoni infection

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Iman F. Abou-El-Naga

2012-09-01

miracidial destruction soon after parasite penetration. The other type occurs in less resistant snails where a delayed resistance development occurs after the dissemination of the sporocysts in the snail tissues. It seems that B. alexandrina snails respond more or less similar to B. glabrata. The results also proved that the immune response of the internal defense system increased with increasing the number of the inherited resistant genes.En Egipto, Biomphalaria alexandrina es el huésped intermediario de Schistosoma mansoni. La supervivencia de los miracidios de Schistosoma en los caracoles varía entre las especies de Biomphalaria. El sistema de defensa interno es uno de los factores que influyen en el patrón de susceptibilidad de los caracoles. La interacción entre los caracoles Biomphalaria y S. mansoni requiere ser identificada para cada especie e incluso, entre los miembros de la misma especie con diferente grado de susceptibilidad. En el presente estudio, la primera generación de padres susceptibles y resistentes de B. alejandrina fue examinada histológicamente al día 30, después de la exposición. El trabajo fue realizado tanto para caracterizar la respuesta inmune, según las reacciones de los tejidos, de los caracoles susceptibles y resistentes de B. alejandrina contra S. mansoni. También, el estudio se diseñó para determinar el impacto en el aumento de la resistencia en los caracoles padres, en los mecanismos de interacción de sus crías contra la infección. Los resultados mostraron que la tasa de infección para las crías, de padres susceptibles, fue del 92%. No se originaron crías susceptibles de los padres resistentes. Cuando los padres incluían un número igual de caracoles susceptibles y resistentes, dieron como resultado crías con una tasa de infección del 20%. Los caracoles susceptibles que tuvieron padres susceptibles mostraron un mayor grado de susceptibilidad que los que tenían tanto padres sensibles como resistentes. Una caracter

Generational distribution of a Candida glabrata population: Resilient old cells prevail, while younger cells dominate in the vulnerable host.

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Bouklas, Tejas; Alonso-Crisóstomo, Luz; Székely, Tamás; Diago-Navarro, Elizabeth; Orner, Erika P; Smith, Kalie; Munshi, Mansa A; Del Poeta, Maurizio; Balázsi, Gábor; Fries, Bettina C

2017-05-01

Similar to other yeasts, the human pathogen Candida glabrata ages when it undergoes asymmetric, finite cell divisions, which determines its replicative lifespan. We sought to investigate if and how aging changes resilience of C. glabrata populations in the host environment. Our data demonstrate that old C. glabrata are more resistant to hydrogen peroxide and neutrophil killing, whereas young cells adhere better to epithelial cell layers. Consequently, virulence of old compared to younger C. glabrata cells is enhanced in the Galleria mellonella infection model. Electron microscopy images of old C. glabrata cells indicate a marked increase in cell wall thickness. Comparison of transcriptomes of old and young C. glabrata cells reveals differential regulation of ergosterol and Hog pathway associated genes as well as adhesion proteins, and suggests that aging is accompanied by remodeling of the fungal cell wall. Biochemical analysis supports this conclusion as older cells exhibit a qualitatively different lipid composition, leading to the observed increased emergence of fluconazole resistance when grown in the presence of fluconazole selection pressure. Older C. glabrata cells accumulate during murine and human infection, which is statistically unlikely without very strong selection. Therefore, we tested the hypothesis that neutrophils constitute the predominant selection pressure in vivo. When we altered experimentally the selection pressure by antibody-mediated removal of neutrophils, we observed a significantly younger pathogen population in mice. Mathematical modeling confirmed that differential selection of older cells is sufficient to cause the observed demographic shift in the fungal population. Hence our data support the concept that pathogenesis is affected by the generational age distribution of the infecting C. glabrata population in a host. We conclude that replicative aging constitutes an emerging trait, which is selected by the host and may even play an

Use of micronucleus test in the assessment of radiation effects in aquatic environments

International Nuclear Information System (INIS)

Araujo, Edvaldo F. de; Silva, Luanna R.S.; Lima, Pedro A. de S.; Amancio, Francisco F.; Melo, Ana Maria M. de A.; Silva, Edvane B. da; Silva, Ronaldo C. da

2011-01-01

The study of the effects of radioactive substances on the environment is accomplished by radioecology. This science has played an important role in combating all forms of pollution. The uncontrolled use of physical and chemical agents has been a concern for environmental regulatory agencies, due to the serious damage to ecosystems. Aquatic organisms are exposed to a variety of pollutants harmful to aquatic systems. The mollusks Biomphalaria glabrata has been featured as a bioindicator to possess characteristics such as short reproductive cycle ease of maintenance in the laboratory and low maintenance cost. The micronucleus assay has been shown to be a great test to identify mutagenic effects caused by physical and chemical agents. In this study the frequency of micronuclei in haemocytes of Biomphalaria glabrata exposed to high doses of 60 Co gamma radiation contributing to a further standardization of this test as an indicator of the presence of radioactive contamination in aquatic environments. The young adult snails of Biomphalaria glabrata were divided into groups and subjected to a dose of 0 (control), 40 and 60 Gy of gamma radiation. The results showed that snails irradiated with 40 Gy showed a smaller number of haemocytes, whereas those exposed to 60 Gy had a greater quantity of these cells compared to control group. It can be concluded that the morphological analysis and the frequency of micronuclei in haemocytes of Biomphalaria glabrata exposed to 60 Co gamma radiation may be used in studies of the action of high doses of radiation in aquatic environments (author)

Potencialidade de Biomphalaria tenagophila do lago Pampulha, Belo Horizonte, MG, como hospederia do Schistosoma mansoni Potentiality of Biomphalaria tenagophila from Pampulha lake, Belo Horizonte, Minas Gerais State, as a host of Schistosoma mansoni

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Cecília Pereira de Souza

1987-03-01

Full Text Available Caramujos Biomphalaria tenagophila descendentes de exemplares coletados no lago da Pampulha, Belo Horizonte, Minas Gerais, foram expostos a miracídios de quatro cepas de Schistosoma mansoni: LE e HK de origem local, Belo Horizonte, AL do Estado de Alagoas e SJ, de São José dos Campos, SP. As cepas LE, AL e SJ são mantidas em laboratório e HK foi obtida de fezes de paciente que reside próximo à Pampulha. As taxas de infecção experimental foram de 4% (LE, 6% (HK, 30% (SJ e 40% (AL. Esses indícios de infecção foram semelhantes aos obtidos por vários autores para populações de B. tenagophila de Minas Gerais. Caramujos infectados experimentalmente eliminaram número de cercárias comparável ao de B. glabrata do controle e de B. tenagophila capturada no lago, com infecção natural (cerca de 2.000 cercárias/molusco. Devido à alta densidade planorbídica atual em alguns pontos do lago, número de cercárias eliminadas por exemplares naturalmente infectados, afluxo de pessoas para pesca e lazer, contaminação das águas por dejetos humanos, os autores alertam para o risco de crescimento do foco de esquistossomose no local.Biomphalaria tenagophila snails, from a population originally obtained from "Pampulha" lake, Belo Horizonte, Minas Gerais State, Brazil, were exposed to miracidia from four strains of Schistosoma mansoni: "LE" and "HK" from Belo Horizonte, "AL" from alagoas and "SJ" from São José dos Campos, São Paulo. The "LE", "AL" and "SJ" strains are maintained in the laboratory and the "HK" strain was obtained from feces of a patient residing near to "Pampulha" lake. Infection rates were of 4% ("LE" strain, 6% ("HK" strain, 30% ("SJ" strain and 40% ("AL" strain. These infection rates were similar to those obtained by others authors for B. tenagophila from Minas Gerais. Experimentally infected snails when compared to B. glabrata of the control group and B. tenagophila naturally infected in "Pampulha" lake shed similar number

Susceptibilidad de Biomphalaria tenagophila de las cuencas de los ríos Paraná y Uruguay a Schistosoma mansoni Susceptibility of Biomphalaria tenagophila from the Paraná and Uruguay river basins to Schistosoma mansoni

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C. Edgardo Borda

1997-03-01

Full Text Available Con el fin de estudiar la posibilidad de extensión de la esquistosomiasis a las cuencas de los ríos Paraná y Uruguay se expusieron experimentalmente a infección por Schistosoma mansoni 1 711 caracoles criados en laboratorio a partir de ejemplares de Biomphalaria tenagophila recolectados en 15 poblaciones de dicha zona geográfica. Se utilizaron tres cepas de S. mansoni: la BH2, adaptada a B. glabrata, y las cepas SJ y SJ2, adaptadas a B. tenagophila. No se produjo infección de ninguno de los 543 caracoles expuestos a la cepa BH2 ni de los 668 expuestos a la SJ. En cambio, de los 500 expuestos a la cepa SJ2, fueron susceptibles a la infestación 4 de 163 caracoles (2% procedentes de Ayolas, una localidad de la cuenca del Paraná, y 8 de 45 (18% de los procedentes de Fuente Salto, en la cuenca del Uruguay. Estos hallazgos son similares a los de otras áreas geográficas en las que se han encontrado poblaciones de B. tenagophila que no se infectan y otras que sí son susceptibles a S. mansoni. Los resultados de este trabajo señalan la posibilidad de expansión de la esquistosomiasis a una amplia región de Sudamérica en la que se halla B. tenagophila.To study the possibility that schistosomiasis might be able to spread into the basins of the Paraná and Uruguay rivers, 1 711 snails were experimentally exposed to infection with Schistosoma mansoni. These snails were laboratory-bred progeny of Biomphalaria tenagophila collected from 15 populations in the geographic area under consideration. Three strains of S. mansoni were used: BH2, adapted to B. glabrata, and SJ and SJ2, adapted to B. tenagophila. None of the 543 snails exposed to the BH2 strain became infected, nor did any of the 668 exposed to SJ. However, of the 500 exposed the SJ2, 4 of 163 snails (2% from Ayolas, a locality in the Paraná basin, were susceptible, as were 8 of 45 (18% from Fuente Salto, in the Uruguay basin. These findings are similar to those of studies done in other

Deep mRNA sequencing of the Tritonia diomedea brain transcriptome provides access to gene homologues for neuronal excitability, synaptic transmission and peptidergic signalling.

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Adriano Senatore

Full Text Available The sea slug Tritonia diomedea (Mollusca, Gastropoda, Nudibranchia, has a simple and highly accessible nervous system, making it useful for studying neuronal and synaptic mechanisms underlying behavior. Although many important contributions have been made using Tritonia, until now, a lack of genetic information has impeded exploration at the molecular level.We performed Illumina sequencing of central nervous system mRNAs from Tritonia, generating 133.1 million 100 base pair, paired-end reads. De novo reconstruction of the RNA-Seq data yielded a total of 185,546 contigs, which partitioned into 123,154 non-redundant gene clusters (unigenes. BLAST comparison with RefSeq and Swiss-Prot protein databases, as well as mRNA data from other invertebrates (gastropod molluscs: Aplysia californica, Lymnaea stagnalis and Biomphalaria glabrata; cnidarian: Nematostella vectensis revealed that up to 76,292 unigenes in the Tritonia transcriptome have putative homologues in other databases, 18,246 of which are below a more stringent E-value cut-off of 1x10-6. In silico prediction of secreted proteins from the Tritonia transcriptome shotgun assembly (TSA produced a database of 579 unique sequences of secreted proteins, which also exhibited markedly higher expression levels compared to other genes in the TSA.Our efforts greatly expand the availability of gene sequences available for Tritonia diomedea. We were able to extract full length protein sequences for most queried genes, including those involved in electrical excitability, synaptic vesicle release and neurotransmission, thus confirming that the transcriptome will serve as a useful tool for probing the molecular correlates of behavior in this species. We also generated a neurosecretome database that will serve as a useful tool for probing peptidergic signalling systems in the Tritonia brain.

Nueva especie de Planorbidae (Gastropoda: Basommatophora en la Patagonia chilena: Biomphalaria cristiani sp. nov. First record of Planorbidae (Mollusca: Basommatophora in Chilean Patagonia: Biomphalaria cristiani sp. nov.

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Carmen Fuentealba

2012-11-01

Full Text Available En Chile la familia Planorbidae está representada por el género Biomphalaria Preston, 1910, compuesta por siete especies distribuidas desde Isluga hasta el río Puelo. De estas especies, solo B.peregrina, ampliamente distribuida en el neotrópico, y Biomphalaria aymara de Isluga, han sido reconocidas sobre la base de la morfología del sistema reproductor y la rádula, caracteres que fueron utilizados en el presente estudio para diferenciar a Biomphalaria cristiani como nueva especie del grupo y primer registro de la familia en la Patagonia chilena, ampliando su actual rango de distribución. Los caracteres que permiten la diagnosis de B. cristiani son el saco vaginal vestigial truncado, ausencia del desarrollo de los músculos suspensores del pene, vaina del pene corta en relación al prepucio, oviducto largo en relación al espermioducto y vaso deferente más delgado y largo que la vaina del pene, de tamano similar al prepucio. La localidad tipo de Biomphalaria cristiani sp. nov. es Laguna Cisnes (47°7'10.02"S, 72°27'40.65"W, región de Aysén.The family Planorbidae in Chile is represented by the genus Biomphalaria Preston, 1910, consisting of seven species distributed from Isluga to Puelo River. Of these species, only Biomphalaria peregrina widely distributed in the neotropical and Biomphalaria aymara from Isluga are recognized based on the morphology of the reproductive system and radula, characters that were used in the following study to differentiate Biomphalaria cristiani as a new species of this group and first record of the family in Chilean Patagonia, extending its current distribution range. The characters for the diagnosis of B. cristiani are: truncated vestigial vaginal pouch, lack of development of the penis retractor muscles, penis sheath shorter than the prepuce, oviduct longer than the spermiduct and vas deferens thinner and longer than the penis sheath, similar size to the prepuce. The type locality of B. cristiani nov. sp

Candida glabrata: an emerging oral opportunistic pathogen.

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Li, L; Redding, S; Dongari-Bagtzoglou, A

2007-03-01

Following the widespread use of immunosuppressive therapy and broad-spectrum antimycotic prophylaxis, C. glabrata has emerged as an important opportunistic pathogen in the oral mucosa. In the past, studies on the virulence factors and host-pathogen interactions of this organism were scarce, but continued to rise in recent years. Denture-wearing, immunosuppression, antibiotic therapy, and aging are risk factors for oral colonization or infection with C. glabrata. Compared with C. albicans, C. glabrata exhibits lower oral keratinocyte-adherence capacity, but higher denture-surface-adherence ability. The role of extracellular hydrolase production in the virulence of this organism does not appear to be as important as it is in C. albicans pathogenesis. Although traditionally thought of as a non-transforming yeast organism, both phenotypic switching and pseudohyphal formation have recently been identified in C. glabrata, but their role in pathogenesis is not known. With the exception of granulocyte monocyte colony-stimulating factor, C. glabrata triggers a lower proinflammatory cytokine response in oral epithelial cells than does C. albicans, in a strain-dependent manner. C. glabrata is less susceptible to killing by human beta-defensins than is C. albicans and exhibits various degrees of resistance to the antifungal activity of salivary histatins and mucins. In addition, C. glabrata possesses both innate and acquired resistance against antifungal drugs, due to its ability to modify ergosterol biosynthesis, mitochondrial function, or antifungal efflux. This resistance allows for its relative overgrowth over other susceptible species and may contribute to the recent emergence of C. glabrata infections in chronically immunocompromised populations. Further investigations on the virulence and host-pathogen interactions of C. glabrata are needed to better define the pathogenesis of oral C. glabrata infection in susceptible hosts.

Possible competitive displacement of planorbids by Melanoides tuberculata in Minas Gerais, Brazil

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Carlos Tito Guimarães

2001-09-01

Full Text Available Several species of snails, including Pomacea haustrum, Marisa cornuarietis and Helisoma duryi, have been identified as probable competitors and/or predators of planorbid intermediate hosts of Schistosoma. During the last few years, studies carried out in the Caribbean region have shown reductions and even disappearances of populations of Biomphalaria glabrata and B. straminea in breeding places where the snail Melanoides tuberculata was introduced. Observations made over a period of 10 years in two lakes close to Belo Horizonte, MG, showed that there were marked reductions in autochthonous populations of B. glabrata and B. straminea after the arrival of M. tuberculata, both Biomphalaria species disappearing completely after eight years.

Possible competitive displacement of planorbids by Melanoides tuberculata in Minas Gerais, Brazil.

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Guimarães, C T; Souza, C P; Soares Dd

2001-01-01

Several species of snails, including Pomacea haustrum, Marisa cornuarietis and Helisoma duryi, have been identified as probable competitors and/or predators of planorbid intermediate hosts of Schistosoma. During the last few years, studies carried out in the Caribbean region have shown reductions and even disappearances of populations of Biomphalaria glabrata and B. straminea in breeding places where the snail Melanoides tuberculata was introduced. Observations made over a period of 10 years in two lakes close to Belo Horizonte, MG, showed that there were marked reductions in autochthonous populations of B. glabrata and B. straminea after the arrival of M. tuberculata, both Biomphalaria species disappearing completely after eight years.

Transmission studies of intestinal schistosomiasis in Lake Albert, Uganda and experimental compatibility of local Biomphalaria spp

DEFF Research Database (Denmark)

Kazibwe, F.; Makanga, B.; Rubaire-Akiiki, C.

2010-01-01

schistosome-snail interactions and confirmation of transmission foci. Cercarial shedding patterns of field-caught Biomphalaria spp., as identified by morphology, were hourly observed over a ten day period and showed that Biomphalaria stanleyi produced significantly more cercariae than Biomphalaria sudanica...

Genetic variability in Brazilian populations of Biomphalaria straminea complex detected by simple sequence repeat anchored polymerase chain reaction amplification

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Caldeira Roberta L

2001-01-01

Full Text Available Biomphalaria glabrata, B. tenagophila and B. straminea are intermediate hosts of Schistosoma mansoni, in Brazil. The latter is of epidemiological importance in the northwest of Brazil and, due to morphological similarities, has been grouped with B. intermedia and B. kuhniana in a complex named B. straminea. In the current work, we have standardized the simple sequence repeat anchored polymerase chain reaction (SSR-PCR technique, using the primers (CA8RY and K7, to study the genetic variability of these species. The similarity level was calculated using the Dice coefficient and genetic distance using the Nei and Li coefficient. The trees were obtained by the UPGMA and neighbor-joining methods. We have observed that the most related individuals belong to the same species and locality and that individuals from different localities, but of the same species, present clear heterogeneity. The trees generated using both methods showed similar topologies. The SSR-PCR technique was shown to be very efficient in intrapopulational and intraspecific studies of the B. straminea complex snails.

Identification of Biomphalaria havanensis and Biomphalaria obstructa populations from Cuba using polymerase chain reaction and restriction fragment length polymorphism of the ribosomal RNA intergenic spacer

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Teofânia HDA Vidigal

2001-07-01

Full Text Available In Cuba, several Biomphalaria species have been reported such as B. orbignyi, B. schrammi, B. helophila, B. havanensis and B. peregrina; only the latter three are considered as potential hosts of Schistosoma mansoni. The specific identification of Biomphalaria species is based on anatomical and morphological characters of genital organs and shells. The correct identification of these snails is complicated by the high variation in these characters, similarity among species and in some cases by the small size of the snails. In this paper, we reported the classical morphological identification, the use of PCR and RFLP analysis of the internal transcribed spacer region of the ribosomal RNA genes for molecular identification of seven snail populations from different localities in Cuba. Using morphological and molecular analysis, we showed that among the studied Cuban Biomphalaria populations only B. havanensis and B. obstructa species were found.

Assimilation of NAD(+) precursors in Candida glabrata.

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Ma, Biao; Pan, Shih-Jung; Zupancic, Margaret L; Cormack, Brendan P

2007-10-01

The yeast pathogen Candida glabrata is a nicotinamide adenine dinucleotide (NAD(+)) auxotroph and its growth depends on the environmental supply of vitamin precursors of NAD(+). C. glabrata salvage pathways defined in this article allow NAD(+) to be synthesized from three compounds - nicotinic acid (NA), nicotinamide (NAM) and nicotinamide riboside (NR). NA is salvaged through a functional Preiss-Handler pathway. NAM is first converted to NA by nicotinamidase and then salvaged by the Preiss-Handler pathway. Salvage of NR in C. glabrata occurs via two routes. The first, in which NR is phosphorylated by the NR kinase Nrk1, is independent of the Preiss-Handler pathway. The second is a novel pathway in which NR is degraded by the nucleosidases Pnp1 and Urh1, with a minor role for Meu1, and ultimately converted to NAD(+) via the nicotinamidase Pnc1 and the Preiss-Handler pathway. Using C. glabrata mutants whose growth depends exclusively on the external NA or NR supply, we also show that C. glabrata utilizes NR and to a lesser extent NA as NAD(+) sources during disseminated infection.

Activity of Polyphenolic Compounds against Candida glabrata

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Ricardo Salazar-Aranda

2015-09-01

Full Text Available Opportunistic mycoses increase the morbidity and mortality of immuno-compromised patients. Five Candida species have been shown to be responsible for 97% of worldwide cases of invasive candidiasis. Resistance of C. glabrata and C. krusei to azoles has been reported, and new, improved antifungal agents are needed. The current study was designed to evaluatethe activity of various polyphenolic compounds against Candida species. Antifungal activity was evaluated following the M27-A3 protocol of the Clinical and Laboratory Standards Institute, and antioxidant activity was determined using the DPPH assay. Myricetin and baicalein inhibited the growth of all species tested. This effect was strongest against C. glabrata, for which the minimum inhibitory concentration (MIC value was lower than that of fluconazole. The MIC values against C. glabrata for myricitrin, luteolin, quercetin, 3-hydroxyflavone, and fisetin were similar to that of fluconazole. The antioxidant activity of all compounds was confirmed, and polyphenolic compounds with antioxidant activity had the greatest activity against C. glabrata. The structure and position of their hydroxyl groups appear to influence their activity against C. glabrata.

Epithelial GM-CSF induction by Candida glabrata.

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Li, L; Dongari-Bagtzoglou, A

2009-08-01

The main cytokine induced by the interaction of oral epithelial cells with C. glabrata is granulocyte monocyte colony-stimulating factor (GM-CSF); however, the mechanisms regulating this response are unknown. Based on previously published information on the interactions of C. albicans with oral epithelial cells, we hypothesized that interaction with viable C. glabrata triggers GM-CSF synthesis via NF-kappaB activation. We found that C. glabrata-induced GM-CSF synthesis was adhesion-dependent, enhanced by endocytosis, and required fungal viability. NF-kappaB activation was noted during interaction of epithelial cells with C. glabrata, and pre-treatment with an NF-kappaB inhibitor partly inhibited GM-CSF synthesis. Blocking TLR4 with anti-TLR4 antibody did not inhibit GM-CSF production. In contrast, an anti-CDw17 antibody triggered significant inhibition of NF-kappaB activation and GM-CSF synthesis. beta-glucans did not stimulate GM-CSF synthesis, suggesting that the CDw17/NF-kappaB/GM-CSF pathway may be beta-glucan-independent. This study provides new insights into the mechanism of GM-CSF induction by C. glabrata.

Susceptibility of Argentinean Biomphalaria tenagophila and Biomphalaria straminea to infection by Schistosoma mansoni and the possibility of geographic expansion of mansoni schistosomiasis

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Luciana Franceschi Simoes

2013-10-01

Full Text Available Introduction Human migration and the presence of natural vectors (mollusks of Schistosoma mansoni are the primary causes of the expansion of mansoni schistosomiasis into southern areas of South America. Water conditions are favorable for the expansion of this disease because of the extensive hydrographic network, which includes the basins of the Paraná and Uruguay rivers and favors mollusk reproduction. These rivers also aid agriculture and tourism in the area. Despite these favorable conditions, natural infection by S. mansoni has not yet been reported in Argentina, Uruguay, or Paraguay. Methods Two species of planorbid from Argentina, Biomphalaria straminea and B. tenagophila, were exposed to the miracidia of five Brazilian strains of S. mansoni. Results Biomphalaria tenagophila (Atalaya, Buenos Aires province was infected with the SJS strain (infection rate 3.3%, confirming the experimental susceptibility of this Argentinian species. Biomphalaria straminea (Rio Santa Lucía, Corrientes province was susceptible to two Brazilian strains: SJS (infection rate 6.7% and Sergipe (infection rate 6.7%. Conclusions These results demonstrate that species from Argentina have the potential to be natural hosts of S. mansoni and that the appearance of foci of mansoni schistosomiasis in Argentina is possible.

Genetic variability and identification of the intermediate snail hosts of Schistosoma mansoni

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Teofânia HDA Vidigal

1998-01-01

Full Text Available Studies based on shell or reproductive organ morphology and genetic considerations suggest extensive intraspecific variation in Biomphalaria snails. The high variability at the morphological and genetic levels, as well as the small size of some specimens and similarities between species complicate the correct identification of these snails. Here we review our work using methods based on polymerase chain reaction (PCR amplification for analysis of genetic variation and identification of Biomphalaria snails from Brazil, Argentina, Uruguay and Paraguay. Arbitrarily primed-PCR revealed that the genome of B. glabrata exihibits a remarkable degree of intraespecific polymorphism. Low stringency-PCR using primers for 18S rRNA permited the identification of B. glabrata, B. tenagophila and B. occidentalis. The study of individuals obtained from geographically distinct populations exhibits significant intraspecific DNA polymorphism, however specimens from the same species, exhibit some species specific LSPs. We also showed that PCR-restriction fragment of length polymorphism of the internal transcribed spacer region of Biomphalaria rDNA, using DdeI permits the differentiation of the three intermediate hosts of Schistosoma mansoni. The molecular biological techniques used in our studies are very useful for the generation of new knowledge concerning the systematics and population genetics of Biomphalaria snails.

Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE).

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Taft, A S; Vermeire, J J; Bernier, J; Birkeland, S R; Cipriano, M J; Papa, A R; McArthur, A G; Yoshino, T P

2009-04-01

Infection of the snail, Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke, Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of the S. mansoni miracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia and in vitro cultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of the B. glabrata embryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to the S. mansoni gene predictions (v4.0e) either by estimating theoretical 3' UTR lengths or using existing 3' EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

Genetic Variation between Biomphalaria alexandrina Snails Susceptible and Resistant to Schistosoma mansoni Infection

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Suzanne M. F. El-Nassery

2013-01-01

Full Text Available Much effort has been made to control schistosomiasis infection in Egypt. However, enduring effects from such strategies have not yet been achieved. In this study, we sought to determine the genetic variability related to the interaction between Biomphalaria alexandrina snails and Schistosoma mansoni. Using RAPD-PCR with eight (10 mers random primers, we were able to determine the polymorphic markers that differed between snails susceptible and resistant to Schistosoma mansoni infection using five primers out of the eight. Our results suggest that the RAPD-PCR technique is an efficient means by which to compare genomes and to detect genetic variations between schistosomiasis intermediate hosts. The RAPD technique with the above-noted primers can identify genomic markers that are specifically related to the Biomphalaria alexandrina/Schistosoma mansoni relationship in the absence of specific nucleotide sequence information. This approach could be used in epidemiologic surveys to investigate genetic diversity among Biomphalaria alexandrina snails. The ability to determine resistant markers in Biomphalaria alexandrina snails could potentially lead to further studies that use refractory snails as agents to control the spread of schistosomiasis.

2018-05-08T18:33:05Z https://www.ajol.info/index.php/all/oai oai:ojs ...

African Journals Online (AJOL)

Barringtonia racemosa, Leeythidaceae, Aedes aegypti, Dengue, Biomphalaria glabrata, mollusicides, schistosomiasis, piscicides The aqueous, methanol, chloroform, ethyl acetate, petroleum ether extracts of Barringtonia racemosa Blume pericarp and seed were evaluated for molluscicidal, larvicial and pisicidal activity ...

Candida glabrata Binding to Candida albicans Hyphae Enables Its Development in Oropharyngeal Candidiasis.

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Tati, Swetha; Davidow, Peter; McCall, Andrew; Hwang-Wong, Elizabeth; Rojas, Isolde G; Cormack, Brendan; Edgerton, Mira

2016-03-01

Pathogenic mechanisms of Candida glabrata in oral candidiasis, especially because of its inability to form hyphae, are understudied. Since both Candida albicans and C. glabrata are frequently co-isolated in oropharyngeal candidiasis (OPC), we examined their co-adhesion in vitro and observed adhesion of C. glabrata only to C. albicans hyphae microscopically. Mice were infected sublingually with C. albicans or C. glabrata individually, or with both species concurrently, to study their ability to cause OPC. Infection with C. glabrata alone resulted in negligible infection of tongues; however, colonization by C. glabrata was increased by co-infection or a pre-established infection with C. albicans. Furthermore, C. glabrata required C. albicans for colonization of tongues, since decreasing C. albicans burden with fluconazole also reduced C. glabrata. C. albicans hyphal wall adhesins Als1 and Als3 were important for in vitro adhesion of C. glabrata and to establish OPC. C. glabrata cell wall protein coding genes EPA8, EPA19, AWP2, AWP7, and CAGL0F00181 were implicated in mediating adhesion to C. albicans hyphae and remarkably, their expression was induced by incubation with germinated C. albicans. Thus, we found a near essential requirement for the presence of C. albicans for both initial colonization and establishment of OPC infection by C. glabrata.

Biological control of schistosome transmission in flowing water habitats.

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Jobin, W R; Laracuente, A

1979-09-01

Marisa cornuarietis was evaluated in Puerto Rico for control of schistosome transmission in flowing water. A population of Biomphalaria glabrata and their schistosome infections disappeared after introduction of 20,000 M. cornuarietis to an endemic stream, while in nearby untreated streams the B. glabrata population remained stable and the schistosome prevalence increased. This method cost U.S. $0.10 per capita for over a year of protection, 5%-10% of the cost of chemical control.

Biomphalaria prona (Gastropoda: Planorbidae: a morphological and biochemical study

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W. Lobato Paraense

1992-06-01

Full Text Available Two samples of Biomphalaria prona (Martens, 1873 from Lake Valencia (type locality and seven from other Venezuelan localities were studied morphologically (shell and reproductive system and biochemically (allozyme electrophoresis. In spite of marked differences in shell characters, all of them proved indistinguishable under the anatomic and biochemical criteria. So far B. prona has been considered an endemic species, restricted to Lake Valencia. It is now demonstrated that the extralacustrine populations refered to Biomphalaria havanensis (Pfeiffer, 1839 by several authors correspond in shell characters to an extreme variant of B. prona from the Lake and really belong to the last*mentioned species. They may be regarded as the result of a process of directional selection favoring a shell phenotype other than those making up the modal class in the Lake.

Biological and environmental factors associated with risk of schistosomiasis mansoni transmission in Porto de Galinhas, Pernambuco State, Brazil

OpenAIRE

Leal Neto, Onicio Batista; Gomes, Elainne Christine de Souza; Oliveira Junior, Fernando José Moreira de; Andrade, Rafael; Reis, Diego Leandro; Souza-Santos, Reinaldo; Bocanegra, Silvana; Barbosa, Constança Simões

2013-01-01

Schistosomiasis has expanded to the coast of Pernambuco State, Brazil, where there are frequent reports of Biomphalaria glabrata snails and human cases of the disease. This study analyzes factors related to schistosomiasis transmission risk in Porto de Galinhas. A one-year malacological survey was conducted to identify biological, abiotic, and environmental factors related to the host snail breeding sites. Data analysis used Excel 2010, GTM Pro, and ArcGis 10. A total of 11,012 B. glabrata sn...

The mating type-like loci of Candida glabrata.

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Yáñez-Carrillo, Patricia; Robledo-Márquez, Karina A; Ramírez-Zavaleta, Candy Y; De Las Peñas, Alejandro; Castaño, Irene

2014-01-01

Candida glabrata, a haploid and opportunistic fungal pathogen that has not known sexual cycle, has conserved the majority of the genes required for mating and cell type identity. The C. glabrata genome contains three mating-type-like loci called MTL1, MTL2 and MTL3. The three loci encode putative transcription factors, a1, α1 and α2 that regulate cell type identity and sexual reproduction in other fungi like the closely related Saccharomyces cerevisiae. MTL1 can contain either a or α information. MTL2, which contains a information and MTL3 with α information, are relatively close to two telomeres. MTL1 and MTL2 are transcriptionally active, while MTL3 is subject to an incomplete silencing nucleated at the telomere that depends on the silencing proteins Sir2, Sir3, Sir4, yKu70/80, Rif1, Rap1 and Sum1. C. glabrata does not seem to maintain cell type identity, as cell type-specific genes are expressed regardless of the type (or even absence) of mating information. These data highlight important differences in the control of mating and cell type identity between the non-pathogenic yeast S. cerevisiae and C. glabrata, which might explain the absence of a sexual cycle in C. glabrata. The fact that C. glabrata has conserved the vast majority of the genes involved in mating might suggest that some of these genes perhaps have been rewired to control other processes important for the survival inside the host as a commensal or as a human pathogen. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Dataset on usnic acid from Cladonia substellata Vainio (Lichen) schistosomiasis mansoni's vector control and environmental toxicity.

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Andrade de Araújo, Hallysson Douglas; Dos Santos Silva, Luanna Ribeiro; de Siqueira, Williams Nascimento; Martins da Fonseca, Caíque Silveira; da Silva, Nicácio Henrique; de Albuquerque Melo, Ana Maria Mendonça; Barroso Martins, Mônica Cristina; de Menezes Lima, Vera Lúcia

2018-04-01

This text presents complementary data corresponding to schistosomiasis mansoni's vector control and enviromental toxicity using usnic acid. These informations support our research article "Toxicity of Usnic Acid from Cladonia substellata (Lichen) to embryos and adults of Biomphalaria glabrata " by Araújo et al. [1], and focuses on the analysis of the detailed data regarding the different concentrations of Usnic Acid and their efficiency to B. glabrata mortality and non-viability, as also to environmental toxicity, evaluated by A. salina mortality.

Transcription factors Asg1p and Hal9p regulate pH homeostasis in Candida glabrata

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Jing eWu

2015-08-01

Full Text Available Candida glabrata is an important microorganism used in commercial fermentation to produce pyruvate, but very little is known about its mechanisms for surviving acid stress in culture. In this study, it was shown that transcription factors Asg1p and Hal9p play essential roles in C. glabrata in the tolerance of acid stress, as the deletion of CgASG1 or CgHAL9 resulted in the inability to survive in an acidic environment. Cgasg1 and Cghal9 mutant strains are unable to maintain pH homeostasis, as evidenced by a decrease in intracellular pH and an increase in reactive oxygen species production, which results in metabolic disorders. The results showed that intracellular acidification was partly due to the diminished activity of the plasma membrane proton pump, CgPma1p. In addition, transcriptome sequencing revealed that Cgasg1 and Cghal9 mutant strains displayed a variety of changes in gene expression under acidic conditions, including genes in the MAPK signaling pathway, plasma membrane or cell wall organization, trehalose accumulation, and the RIM101 signaling pathway. Lastly, quantitative reverse-transcribed PCR and cellular localization showed that CgAsg1p and CgHal9p played independent roles in response to acid stress.

The molluscicidal activity of coumarins from Ethulia conyzoides and of dicumarol

DEFF Research Database (Denmark)

Kady, M M; Brimer, L; Furu, P

1992-01-01

The molluscicidal principles of Ethulia conyzoides were identified as ethuliacoumarin A (1) and isoethuliacoumarin A (2). Ethuliacoumarin A possessed an LC90 between 19 and 23.5 ppm depending on the age of the snail against Biomphalaria glabrata, and between 12 and 15 ppm against Bulinus truncatu...

Probiotic yeast Saccharomyces boulardii (nom. nud.) modulates adhesive properties of Candida glabrata.

Science.gov (United States)

Tomičić, Zorica; Zupan, Jure; Matos, Tadeja; Raspor, Peter

2016-11-01

Following the widespread use of immunosuppressive therapy together with broad-spectrum antimycotic therapy, the frequency of mucosal and systemic infections caused by the pathogenic yeast Candida glabrata has increased in the past decades. Due to the resistance of C. glabrata to existing azole drugs, it is very important to look for new strategies helping the treatment of such fungal diseases. In this study, we investigated the effect of the probiotic yeast Saccharomyces boulardii (nom. nud.) on C. glabrata adhesion at different temperatures, pH values, and in the presence of fluconazole, itraconazole and amphotericin B. We also studied the adhesion of C. glabrata co-culture with Candida krusei, Saccharomyces cerevisiae, two bacterial probiotics Lactobacillus rhamnosus and Lactobacillus casei The method used to assess adhesion was crystal violet staining. Our results showed that despite the nonadhesiveness of S. boulardii cells, this probiotic significantly affected the adherence ability of C. glabrata This effect was highly dependent on C. glabrata strain and was either antagonistic or synergistic. Regarding the extrinsic factors, temperature did not indicate any significant influence on this S. boulardii modulatory effect, while at high pH and at increased concentrations of antimycotics, S. boulardii did not manage to repress the adhesion of C. glabrata strains. The experiments of C. glabrata co-cultures with other species showed that the adhesiveness of two separate cultures could not be used to predict the adhesiveness of their co-culture. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Variation spatiale et temporelle de la susceptibilité de Biomphalaria ...

African Journals Online (AJOL)

SARAH

31 janv. 2018 ... Schistosoma haematobium with observations on protein electrophoretic pattern of the snails. Veterinary. Parasitology, 161 : 207-212. Mostafa OM, El-Dafrawy SM, 2011. Susceptibility of. Biomphalaria spp. to infection with. Schistosoma mansoni in sympatric and allopatric combinations with observations on ...

Osteomyelitis Caused by Candida glabrata in the Distal Phalanx

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Shunichi Toki

2014-01-01

Full Text Available Osteomyelitis caused by Candida glabrata is rare and its optimal treatment is unknown. Here we report a case of osteomyelitis caused by C. glabrata in the distal phalanx in a 54-year-old woman. Despite partial resection of the nail and administering a 1-month course of antibiotics for paronychia, the local swelling remained and an osteolytic lesion was found. C. glabrata osteomyelitis of the distal phalanx was later diagnosed after curettage. Thereafter, the patient was treated with antifungal agents for 3 months. The infection eventually resolved, and radiological healing of the osteolytic lesion was achieved. Antifungal susceptibility testing should be performed in the case of osteomyelitis caused by nonalbicans Candida species, due to their resistance to fluconazole.

Candida glabrata um patogénio emergente?

OpenAIRE

Matilde, Filipa Alexandra Veiga

2014-01-01

Dissertação para obtenção do grau de Mestre no Instituto Superior de Ciências da Saúde Egas Moniz Nas últimas décadas as infecções fúngicas têm aumentado exponencialmente. Apesar de Candida albicans (C. albicans) continuar a ser a espécie isolada com maior frequência, as espécies não albicans tem vindo a proliferar rapidamente. Candida glabrata (C. glabrata) é uma das espécies emergentes como patogénio oportunista humano, sendo responsável maioritariamente por candidoses invasivas em pacie...

MALDI-TOF typing highlights geographical and fluconazole resistance clusters in Candida glabrata.

Science.gov (United States)

Dhieb, C; Normand, A C; Al-Yasiri, M; Chaker, E; El Euch, D; Vranckx, K; Hendrickx, M; Sadfi, N; Piarroux, R; Ranque, S

2015-06-01

Utilizing matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra for Candida glabrata typing would be a cost-effective and easy-to-use alternative to classical DNA-based typing methods. This study aimed to use MALDI-TOF for the typing of C. glabrata clinical isolates from various geographical origins and test its capacity to differentiate between fluconazole-sensitive and -resistant strains.Both microsatellite length polymorphism (MLP) and MALDI-TOF mass spectra of 58 C. glabrata isolates originating from Marseilles (France) and Tunis (Tunisia) as well as collection strains from diverse geographic origins were analyzed. The same analysis was conducted on a subset of C. glabrata isolates that were either susceptible (MIC ≤ 8 mg/l) or resistant (MIC ≥ 64 mg/l) to fluconazole.According to the seminal results, both MALDI-TOF and MLP classifications could highlight C. glabrata population structures associated with either geographical dispersal barriers (p typing to investigate C. glabrata infection outbreaks and predict the antifungal susceptibility profile of clinical laboratory isolates. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biomphalaria straminea no Peru e sua suscetibilidade a cepas brasileiras de Schistosoma mansoni

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C.A. Cuba Cuba

1977-12-01

Full Text Available Em Maio de 1973, um dos autores (C.A.C. coletou na localidade de Imacita, Província de Bagua, Departamento de Amazonas, vários espécimes de Biomphalaria straminea (Dunker, 1848, uma espécie que, até então, não havia sido assinalada no Peru. Descendentes destes indivíduos foram submetidos a provas de suscetibilidade às cepas BH e SJ de Schistosoma mansoni que, em condições naturais, evoluem em B. glabrata de Belo Horizonte e B. tenagophila de São José dos Campos, respectivamente. Oitenta espécimens foram expostos à cepa BH dos quais em 13 ou 16,2% a infecção evoluiu caracteristicamente até a formação de esporocistos secundários sem haver, contudo, eliminação de cercárias, mesmo no indivíduo que apresentou uma sobrevivência de 88 dias após a exposição. Não se verificou cura espontânea neste lote. Entre as 40 B. straminea expostas à cepa SJ 9 ou 22,5% infectaram-se, sendo que apenas duas eliminaram poucas cercárias aos 57 e 77 dias após a exposição, por dois dias consecutivos, tendo uma morrido e uma se curado espontaneamente. A cura espontânea do parasitismo foi notado em mais dois indivíduos, nos quais a infecção foi observada através da concha. Cortes histológicos seriados de 9 caramujos, expostos individualmente a 50 miracídios da cepa BH e fixados entre 6 e 120 horas após a exposição, mostraram esporocistos em desenvolvimento e esporocistos invadidos por amebócitos, sem formação de granulomas por parte do hospedeiro, fato assinalado em caramujos suscetíveis. A população estudada comportou-se experimentalmente de modo semelhante a outras populações de B. straminea testadas em laboratório, isto é, com baixa suscetibilidade, embora tal comportamento não afaste a possibilidade dela vir a manter o ciclo do parasita em sua área de distribuição.In May 1973 one of the Authors (C.A.C. collected specimens of Biomphalaria straminea (Dunker 1848 at imacita, Bagua Province, Amazonas, Pem. This

Breeding of Biomphalaria tenagophila in mass scale

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Florence Mara Rosa

2013-02-01

Full Text Available An efficient method for breeding Biomphalaria tenagophila (Taim lineage/RS was developed over a 5-year-period (2005-2010. Special facilities were provided which consisted of four cement tanks (9.4 x 0.6 x 0.22 m, with their bottom covered with a layer of sterilized red earth and calcium carbonate. Standard measures were adopted, as follows: each tank should contain an average of 3000 specimens, and would be provided with a daily ration of 35,000 mg complemented with lettuce. A green-house effect heating system was developed which constituted of movable dark canvas covers, which allowed the temperature to be controlled between 20 - 24 ºC. This system was essential, especially during the coldest months of the year. Approximately 27,000 specimens with a diameter of 12 mm or more were produced during a 14-month-period. The mortality rates of the newly-hatched and adult snails were 77% and 37%, respectively. The follow-up of the development system related to 310 specimens of B. tenagophila demonstrated that 70-day-old snails reached an average of 17.0 ± 0.9 mm diameter. The mortality rates and the development performance of B. tenagophila snails can be considered as highly satisfactory, when compared with other results in literature related to works carried out with different species of the genus Biomphalaria, under controlled laboratory conditions.

Compatibilidad entre nueve cepas de Biomphalaria glabrata de áreas endémicas y no endémicas y una cepa de Schistosoma mansoni venezolanas

OpenAIRE

Pino,Luz A.; Matinella,Liboria; Morales C.,Gustavo

1999-01-01

Se infectaron experimentalmente 9 lotes de 32 caracoles B. glabrata (de 5 a 7mm de diámetro) con miracidios de la cepa C5 de Schistosoma mansoni a razón de 5 miracidios por caracol, pertenecientes a las siguientes cepas: En el área endémica de transmisión de Esquistosomiasis mansoni a) Sector Puerta Negra, Lago Valencia, b) Cagua c) Ingenio Bolívar (Estado Aragua) d) Mariara e) Caserío El 25 f) Güigüe (Estado Carabobo). Fuera del área endémica de transmisión g) Anzoátegui (Estado Lara), h) Ch...

Candida glabrata Esophagitis: Are We Seeing the Emergence of a New Azole-Resistant Pathogen?

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Aze Wilson

2014-01-01

Full Text Available Background. Candida glabrata (C. glabrata has become a recognized pathogen in fungal esophagitis. A proportion of these isolates are azole-resistant which may have treatment implications. Variability in the prevalence of this organism exists in the limited data available. Objective. To determine the incidence of C. glabrata esophagitis in a North American hospital setting and to highlight factors that may predispose patients to this condition. Methods. Patient charts were collected from January 1, 2009 to July 30, 2011. Any charts of patients identified as having esophagitis with a positive fungal culture were reviewed for the species of Candida and the presence of factors that would predispose them to esophageal candidiasis. Results. The prevalence of Candida esophagitis based on culture was 2.2% (37 subjects. C. glabrata was the 2nd most prevalent pathogen identified (24.3% or 9 subjects. Of the C. glabrata cohort, all patients had at least one factor predisposing them to candidiasis. Conclusion. C. glabrata esophagitis makes up a large portion of the candidal esophagitis seen in hospital. C. glabrata infections were associated with at least one risk factor for candidal infection. Given its resistance to azole-based therapy, this may have treatment implications for how candidal esophagitis is approached by the clinician.

Enhanced Efflux Pump Activity in Old Candida glabrata Cells.

Science.gov (United States)

Bhattacharya, Somanon; Fries, Bettina C

2018-03-01

We investigated the effect of replicative aging on antifungal resistance in Candida glabrata Our studies demonstrate significantly increased transcription of ABC transporters and efflux pump activity in old versus young C. glabrata cells of a fluconazole-sensitive and -resistant strain. In addition, higher tolerance to killing by micafungin and amphotericin B was noted and is associated with higher transcription of glucan synthase gene FKS1 and lower ergosterol content in older cells. Copyright © 2018 American Society for Microbiology.

Oxidative stress response to menadione and cumene hydroperoxide in the opportunistic fungal pathogen Candida glabrata

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Mayra Cuéllar-Cruz

2009-07-01

Full Text Available Candida glabrata is an opportunistic fungal pathogen that can cause severe invasive infections and can evade phagocytic cell clearance. We are interested in understanding the virulence of this fungal pathogen, in particular its oxidative stress response. Here we investigated C. glabrata, Saccharomyces cerevisiae and Candida albicans responses to two different oxidants: menadione and cumene hydroperoxide (CHP. In log-phase, in the presence of menadione, C. glabrata requires Cta1p (catalase, while in a stationary phase (SP, Cta1p is dispensable. In addition, C. glabrata is less resistant to menadione than C. albicans in SP. The S. cerevisiae laboratory reference strain is less resistant to menadione than C. glabrata and C. albicans; however S. cerevisiaeclinical isolates (CIs are more resistant than the lab reference strain. Furthermore, S. cerevisiae CIs showed an increased catalase activity. Interestingly, in SP C. glabrata and S. cerevisiae are more resistant to CHP than C. albicans and Cta1p plays no apparent role in detoxifying this oxidant.

Dissection of Ire1 functions reveals stress response mechanisms uniquely evolved in Candida glabrata.

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Taiga Miyazaki

2013-01-01

Full Text Available Proper protein folding in the endoplasmic reticulum (ER is vital in all eukaryotes. When misfolded proteins accumulate in the ER lumen, the transmembrane kinase/endoribonuclease Ire1 initiates splicing of HAC1 mRNA to generate the bZIP transcription factor Hac1, which subsequently activates its target genes to increase the protein-folding capacity of the ER. This cellular machinery, called the unfolded protein response (UPR, is believed to be an evolutionarily conserved mechanism in eukaryotes. In this study, we comprehensively characterized mutant phenotypes of IRE1 and other related genes in the human fungal pathogen Candida glabrata. Unexpectedly, Ire1 was required for the ER stress response independently of Hac1 in this fungus. C. glabrata Ire1 did not cleave mRNAs encoding Hac1 and other bZIP transcription factors identified in the C. glabrata genome. Microarray analysis revealed that the transcriptional response to ER stress is not mediated by Ire1, but instead is dependent largely on calcineurin signaling and partially on the Slt2 MAPK pathway. The loss of Ire1 alone did not confer increased antifungal susceptibility in C. glabrata contrary to UPR-defective mutants in other fungi. Taken together, our results suggest that the canonical Ire1-Hac1 UPR is not conserved in C. glabrata. It is known in metazoans that active Ire1 nonspecifically cleaves and degrades a subset of ER-localized mRNAs to reduce the ER load. Intriguingly, this cellular response could occur in an Ire1 nuclease-dependent fashion in C. glabrata. We also uncovered the attenuated virulence of the C. glabrata Δire1 mutant in a mouse model of disseminated candidiasis. This study has unveiled the unique evolution of ER stress response mechanisms in C. glabrata.

Susceptibilidad de Biomphalaria tenagophila de las cuencas de los ríos Paraná y Uruguay a Schistosoma mansoni

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C. Edgardo Borda

1997-03-01

Full Text Available Con el fin de estudiar la posibilidad de extensión de la esquistosomiasis a las cuencas de los ríos Paraná y Uruguay se expusieron experimentalmente a infección por Schistosoma mansoni 1 711 caracoles criados en laboratorio a partir de ejemplares de Biomphalaria tenagophila recolectados en 15 poblaciones de dicha zona geográfica. Se utilizaron tres cepas de S. mansoni: la BH2, adaptada a B. glabrata, y las cepas SJ y SJ2, adaptadas a B. tenagophila. No se produjo infección de ninguno de los 543 caracoles expuestos a la cepa BH2 ni de los 668 expuestos a la SJ. En cambio, de los 500 expuestos a la cepa SJ2, fueron susceptibles a la infestación 4 de 163 caracoles (2% procedentes de Ayolas, una localidad de la cuenca del Paraná, y 8 de 45 (18% de los procedentes de Fuente Salto, en la cuenca del Uruguay. Estos hallazgos son similares a los de otras áreas geográficas en las que se han encontrado poblaciones de B. tenagophila que no se infectan y otras que sí son susceptibles a S. mansoni. Los resultados de este trabajo señalan la posibilidad de expansión de la esquistosomiasis a una amplia región de Sudamérica en la que se halla B. tenagophila.

[Evaluation of a rapid trehalase test for the identification of Candida glabrata].

Science.gov (United States)

Kirdar, Sevin; Gültekin, Berna; Evcil, Gonca; Ozkütük, Aydan; Sener, Asli Gamze; Aydin, Neriman

2009-04-01

Candida species which cause local infections, may also lead to fatal systemic infections. The increasing incidence of non-albicans Candida, especially fluconazole susceptible or resistant dose-dependent C. glabrata, increased the importance of rapid and accurate species level identification for Candida. Rapid and correct identification of C. glabrata is essential for the initiation of the appropriate antifungal therapy. This study was conducted to evaluate the performance of the rapid trehalase test in the diagnosis of C. glabrata isolates. A total of 173 Candida strains isolated from various clinical specimens and identified according to germ tube test, growth on cornmeal Tween 80 agar and the colony morphologies on Mast-CHROMagar Candida medium (Mast Diagnostics, UK), were included to the study. The identification of non-albicans Candida species were also confirmed by API 20CAUX (BioMerieux, France) system. Accordingly 86 (50%) of the isolates were identified as C. glabrata, 48 (28%) C. albicans, 17 (10%) C. krusei, 13 (8%) C. tropicalis, 5 (3%) C. parapsilosis, 3 (2%) C. kefyr and 1 (1%) Cutilis. In order to detect the presence of trehalase enzyme in Condida strains, all isolates were grown on Sabouraud dextrose agar containing 4% glucose and then one yeast colony was emulsified in 50 microl of citrate buffer containing 4% (wt/vol) trehalose for 3 h at 37 degrees C. Presence of glucose which emerged after the action of trehalase on trehalose, was detected by a commercial "urinary glucose detection dipstick" (Spinreacta, Spain). All C. glabrata strains yielded positive result by trehalase test. None C. glabrata isolates were found negative by trehalase test except for one strain of C. tropicalis. In this study, the trehalase test allowed identification of C. globrata with 100% sensitivity and 98.9% specificity. It was concluded that trehalase test is a rapid, cost-effective and simple test that can be used for the accurate identification of C. glabrata.

Candida (Torulopsis glabrata) liver abscesses eight years after orthotopic liver transplantation.

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Annunziata, G M; Blackstone, M; Hart, J; Piper, J; Baker, A L

1997-04-01

The authors report the case of a 48-year-old man in whom candida (Torulopsis glabrata) liver abscesses developed 8 years after liver transplantation. After a week of fever, computed tomography and Doppler ultrasonography showed several fluid-filled loculations in the left lobe of the liver and hepatic arterial stenosis. Aspirates from the abscesses contained T. glabrata organisms. This complication probably developed because hepatic arterial stenosis resulted in bile infarcts (bilomas), which were contaminated via the biliary tract with candida from the biliary-enteric anastomosis. Catheter drainage and administration of amphotericin B for 10 weeks permitted successful retransplantation. T. glabrata liver abscesses, a life threatening complication that can occur long after liver transplantation, can be successfully managed by aggressive medical treatment followed by retransplantation.

Candida glabrata olecranon bursitis treated with bursectomy and intravenous caspofungin.

Science.gov (United States)

Skedros, John G; Keenan, Kendra E; Trachtenberg, Joel D

2013-01-01

Orthopedic surgeons are becoming more involved in the care of patients with septic arthritis and bursitis caused by yeast species. This case report involves a middle-aged immunocompromised female who developed a Candida glabrata septic olecranon bursitis that developed after she received a corticosteroid injection in the olecranon bursa for presumed aseptic bursitis. Candida (Torulopsis) glabrata is the second most frequently isolated Candida species from the bloodstream in the United States. Increased use of fluconazole and other azole antifungal agents as a prophylactic treatment for recurrent Candida albicans infections in immunocompromised individuals is one reason why there appears to be increased resistance of C. glabrata and other nonalbicans Candida (NAC) species to fluconazole. In this patient, this infection was treated with surgery (bursectomy) and intravenous caspofungin, an echinocandin. This rare infectious etiology coupled with this intravenous antifungal treatment makes this case novel among cases of olecranon bursitis caused by yeasts.

Specific Identification of Biomphalaria tenagophila and Biomphalaria occidentalis Populations by the Low Stringency Polymerase Chain Reaction

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Edina Rodrigues Pires

1997-01-01

Full Text Available Although Biomphalaria occidentalis and B. tenagophila are indistinguishable on the basis of shell morphology and the majority of their genital organs, only the latter is susceptible to infection with Schistosoma mansoni. Thus, the identification of these species is fundamental to epidemiological studies of schistosomiasis. Here we describe a simple and rapid method for differentiating B. tenagophila from B. occidentalis based on low stringency polymerase chain reaction and using a pair of primers specific for the amplification of the 18S rRNA gene. Analysis of the low stringency product profiles of populations of these snails from different geographical regions confirmed this approach as being applicable to the identification of B. tenagophila and B. occidentalis in cases where classical morphology is inconclusive

Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study.

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Emeline Deleury

Full Text Available Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance

Candida glabrata-pneumonia in a non-immuno-suppressed patient: Imaging by digital radiology and CT

International Nuclear Information System (INIS)

Bankier, A.; Fleischmann, D.; Wiesmayr, M.; Laczika, K.; Huebsch, P.

1994-01-01

Pneumonias caused by Candida glabrata are extremely rare and occur almost exclusively in immunocompromised patients. We report an atypical case of Candida glabrata pneumonia in a non-immunocompromised patient and describe the imaging findings on digital radiography and computed tomography. (orig.) [de

Biological control and invading freshwater snails. A case study.

Science.gov (United States)

Pointier, J P; Augustin, D

1999-12-01

Introductions of four species of freshwater snails occurred between 1972 and 1996 onto Guadeloupe Island. Two of them, Melanoides tuberculata and Marisa cornuarietis, were subsequently used as biological control agents against Biomphalaria glabrata, the snail intermediate host of intestinal schistosomiasis. In 1996, a general survey was carried out in 134 sites which had already been investigated in 1972. The total number of mollusc species had increased from 19 to 21. Site numbers housing B. glabrata and two other species had strongly declined. This decline may be mainly attributed to a competitive displacement by M. tuberculata and M. cornuarietis as illustrated by several biological control programmes. There were no changes in the remainder of the malacological fauna.

Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms

DEFF Research Database (Denmark)

Ahmad, Khadija Mohamed; Ishchuk, Olena P.; Hellborg, Linda

2013-01-01

chromosomes, which were smaller than 0.5 Mb. Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes). We suggest that at least two mechanisms could...... exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable. Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes...

Characterization of Biomphalaria orbignyi, Biomphalaria peregrina and Biomphalaria oligoza by polymerase chain reaction and restriction enzyme digestion of the internal transcribed spacer region of the RNA ribosomal gene

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Spatz Linus

2000-01-01

Full Text Available The correct identification of Biomphalaria oligoza, B. orbignyi and B. peregrina species is difficult due to the morphological similarities among them. B. peregrina is widely distributed in South America and is considered a potential intermediate host of Schistosoma mansoni. We have reported the use of the polymerase chain reaction and restriction fragment length polymorphism analysis of the internal transcribed spacer region of the ribosomal DNA for the molecular identification of these snails. The snails were obtained from different localities of Argentina, Brazil and Uruguay. The restriction patterns obtained with MvaI enzyme presented the best profile to identify the three species. The profiles obtained with all enzymes were used to estimate genetic similarities among B. oligoza, B. peregrina and B. orbignyi. This is also the first report of B. orbignyi in Uruguay.

Isolamento genético de populações de caramujos do gênero Biomphalaria

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Aluízio Bezerra Coutinho

1976-08-01

Full Text Available Experiências de intrecruzamento de caramujos do gênero Biomphalaria de várias procedências de Pernambuco, Brasil, utilizando o albinismo como mercador genético mostraram que ocorre na região duas populações isoladas que não se intercruzam. Uma das populações è constituída por caramujos que podem atingir diâmetros de concha até em torno de 30 mm, enquanto que a outra atinge somente em torno de 10 mm mesmo nas melhores condições ambientais.Breending experiments with snails of the genus Biomphalaria from several beeding sites in Pernambuco, Brazil, using albinism as the genetics tag have shown that two isolated non-interbreeding populations occur in the region. One of the populations is made up of snails which consistently reached diameter sizes around 30 mm, while the other of snails reaching only around 10 mm shell diameter, even when in the best environmental conditions.

An unexpected response of torulopsis glabrata fusion products to x-irradiation

International Nuclear Information System (INIS)

Galeotti, C.L.; Sriprakash, K.S.; Batum, C.M.; Clark-Walker, G.D.

1981-01-01

Intra-species fusion products of Saccharomyces cerevisiae, Saccharomyces unisporus and Torulopsis glabrata have been isolated following polyethylene glycol-induced fusion of protoplasts and selection for prototrophic colonies. Staining with lomofungin showed that all fusion products were uninucleate. Measurement of DNA content mostly gave values between haploid and diploid levels indicating that the majority of fusion products were aneuploid. Nevertheless fusion products of S. cerevisiae and S. unisporus were, as expected, more resistant to X-irradiation than their haploid parents. By contrast, the X-ray doze-response curve of all T. glabrata fusion products was indistinguishable from their progenitors despite the fact that mitotic segregants could be recovered amongst the survivors to X-rays. A possible explanation for the behaviour towards X-rays of T. glabrata fusion products is that this species lacks a DNA repair pathway involving recombination between homologous chromosomes. We conclude from this study that the shape of the X-ray dose-response curve should not be taken to indicate the ploidy of new yeast isolates without supporting data. (orig.)

Candida glabrata Biofilms: How Far Have We Come?

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Célia F. Rodrigues

2017-03-01

Full Text Available Infections caused by Candida species have been increasing in the last decades and can result in local or systemic infections, with high morbidity and mortality. After Candida albicans, Candida glabrata is one of the most prevalent pathogenic fungi in humans. In addition to the high antifungal drugs resistance and inability to form hyphae or secret hydrolases, C. glabrata retain many virulence factors that contribute to its extreme aggressiveness and result in a low therapeutic response and serious recurrent candidiasis, particularly biofilm formation ability. For their extraordinary organization, especially regarding the complex structure of the matrix, biofilms are very resistant to antifungal treatments. Thus, new approaches to the treatment of C. glabrata’s biofilms are emerging. In this article, the knowledge available on C. glabrata’s resistance will be highlighted, with a special focus on biofilms, as well as new therapeutic alternatives to control them.

Candida glabrata Biofilms: How Far Have We Come?

Science.gov (United States)

Rodrigues, Célia F.; Rodrigues, Maria Elisa; Silva, Sónia; Henriques, Mariana

2017-01-01

Infections caused by Candida species have been increasing in the last decades and can result in local or systemic infections, with high morbidity and mortality. After Candida albicans, Candida glabrata is one of the most prevalent pathogenic fungi in humans. In addition to the high antifungal drugs resistance and inability to form hyphae or secret hydrolases, C. glabrata retain many virulence factors that contribute to its extreme aggressiveness and result in a low therapeutic response and serious recurrent candidiasis, particularly biofilm formation ability. For their extraordinary organization, especially regarding the complex structure of the matrix, biofilms are very resistant to antifungal treatments. Thus, new approaches to the treatment of C. glabrata’s biofilms are emerging. In this article, the knowledge available on C. glabrata’s resistance will be highlighted, with a special focus on biofilms, as well as new therapeutic alternatives to control them. PMID:29371530

Susceptibility of Biomphalaria amazonica and Biomphalaria occidentalis from Manso Dam, Mato Grosso, Brazil to infection with three strains of Schistosoma mansoni

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Monica Ammon Fernandez

2006-10-01

Full Text Available As well as malaria and yellow fever, schistosomiasis is one of the main endemic diseases associated to environments which suffered some impact related to the development of great economic projects, as for example the construction of hydroelectric power stations. Aiming to investigate the occurrence and distribution of freshwater snails of medical and veterinary importance in the area which suffered impact from the Manso hydroelectric power station a survey was performed during the period of 2002 to 2003 and revealed the occurrence of populations of Biomphalaria amazonica and Biomphalaria occidentalis. Studies on parasite-mollusc compatibility were undertaken using five B. amazonica colonies (Barão de Melgaço, Poconé, Santo Antônio do Leverger, and Chapada dos Guimarães, in the Manso and Casca rivers, and four B. occidentalis colonies (Cuiabá, Santo Antônio do Leverger, and Chapada dos Guimarães, in the Água Fria district and Casca river were exposed to miracidia of Schistosoma mansoni. Of 257 snails of B. amazonica used, 17 became infected (infection index of 6.61% and all specimens of B. occidentalis proved unsusceptible. According to the strains used, of the 158 snails exposed to BH miracidia, 6 became infected (3.79%; of the 44 exposed to SJ miracidia, 6 became infected (13.63%; and of the 55 snails of B. amazonica exposed to EC miracidia, 5 became infected (9.09%. These results point out the low possibility of introduction of schistosomiasis in those areas, but we believe it can not be discarded as due the presence of B. amazonica.

Alien Planorbid (Mollusca, Gastropoda Pulmonata) from South West Africa erroneously recorded as Biomphalaria Pfeifferi

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Bruggen, van A.C.

1974-01-01

In 1970 I published a record of the freshwater snail Biomphalaria pfeifferi (Krauss, 1848) (fam. Planorbidae) for South West Africa: "Sandamap Farm, Spitzkoppe" (Van Bruggen, 1970: 45, figs. 1-13). Dr. D. S. Brown of the Medical Research Council (London) kindly drew my attention to the fact that

Development of a Candida glabrata dominant nutritional transformation marker utilizing the Aspergillus nidulans acetamidase gene (amdS).

Science.gov (United States)

Fu, Jianmin; Blaylock, Morganne; Wickes, Cameron F; Welte, William; Mehrtash, Adrian; Wiederhold, Nathan; Wickes, Brian L

2016-05-01

The gene encoding Aspergillus nidulans acetamidase (amdS) was placed under control of Candida albicans ACT1 promoter and terminator sequences and then cloned into a plasmid containing C. glabrata ARS10,CEN8 or ARS10+CEN8 sequences. All plasmids transformed C. glabrata wild-type cells to acetamide+, with the ARS-only containing plasmid transforming cells at the highest frequencies (>1.0 × 10(4) transformants μg(-1)). Plasmids were rapidly lost under non-selective conditions with the frequency dependent on chromosomal element, thus recycling the acetamide- phenotype. The amdS plasmid was used to transform a set of clinical isolates resistant to a variety of antifungal drugs. All strains were successfully transformed to the acetamide+ phenotype at high frequency, confirming that this plasmid construct could be used as a simple dominant marker on virtually any strain. Gap repair experiments demonstrated that just as in Saccharomyces cerevisiae, gap repair functions efficiently inC. glabrata, suggesting that C. glabrata has numerous similarities toS. cerevisiae with regard to ease of molecular manipulation. The amdS system is inexpensive and efficient, and combined with existing C. glabrata plasmid elements, confers a high transformation frequency for C. glabrata with a phenotype that can be easily recycled. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Murine Model of Candida glabrata Vaginitis Shows No Evidence of an Inflammatory Immunopathogenic Response.

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Evelyn E Nash

Full Text Available Candida glabrata is the second most common organism isolated from women with vulvovaginal candidiasis (VVC, particularly in women with uncontrolled diabetes mellitus. However, mechanisms involved in the pathogenesis of C. glabrata-associated VVC are unknown and have not been studied at any depth in animal models. The objective of this study was to evaluate host responses to infection following efforts to optimize a murine model of C. glabrata VVC. For this, various designs were evaluated for consistent experimental vaginal colonization (i.e., type 1 and type 2 diabetic mice, exogenous estrogen, varying inocula, and co-infection with C. albicans. Upon model optimization, vaginal fungal burden and polymorphonuclear neutrophil (PMN recruitment were assessed longitudinally over 21 days post-inoculation, together with vaginal concentrations of IL-1β, S100A8 alarmin, lactate dehydrogenase (LDH, and in vivo biofilm formation. Consistent and sustained vaginal colonization with C. glabrata was achieved in estrogenized streptozotocin-induced type 1 diabetic mice. Vaginal PMN infiltration was consistently low, with IL-1β, S100A8, and LDH concentrations similar to uninoculated mice. Biofilm formation was not detected in vivo, and co-infection with C. albicans did not induce synergistic immunopathogenic effects. This data suggests that experimental vaginal colonization of C. glabrata is not associated with an inflammatory immunopathogenic response or biofilm formation.

A Murine Model of Candida glabrata Vaginitis Shows No Evidence of an Inflammatory Immunopathogenic Response.

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Nash, Evelyn E; Peters, Brian M; Lilly, Elizabeth A; Noverr, Mairi C; Fidel, Paul L

2016-01-01

Candida glabrata is the second most common organism isolated from women with vulvovaginal candidiasis (VVC), particularly in women with uncontrolled diabetes mellitus. However, mechanisms involved in the pathogenesis of C. glabrata-associated VVC are unknown and have not been studied at any depth in animal models. The objective of this study was to evaluate host responses to infection following efforts to optimize a murine model of C. glabrata VVC. For this, various designs were evaluated for consistent experimental vaginal colonization (i.e., type 1 and type 2 diabetic mice, exogenous estrogen, varying inocula, and co-infection with C. albicans). Upon model optimization, vaginal fungal burden and polymorphonuclear neutrophil (PMN) recruitment were assessed longitudinally over 21 days post-inoculation, together with vaginal concentrations of IL-1β, S100A8 alarmin, lactate dehydrogenase (LDH), and in vivo biofilm formation. Consistent and sustained vaginal colonization with C. glabrata was achieved in estrogenized streptozotocin-induced type 1 diabetic mice. Vaginal PMN infiltration was consistently low, with IL-1β, S100A8, and LDH concentrations similar to uninoculated mice. Biofilm formation was not detected in vivo, and co-infection with C. albicans did not induce synergistic immunopathogenic effects. This data suggests that experimental vaginal colonization of C. glabrata is not associated with an inflammatory immunopathogenic response or biofilm formation.

Time-kill assay and Etest evaluation for synergy with polymyxin B and fluconazole against Candida glabrata.

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Pankey, George; Ashcraft, Deborah; Kahn, Heather; Ismail, Abdulrahim

2014-10-01

Fluconazole-resistant Candida glabrata is an emerging pathogen that causes fungemia. Polymyxin B, a last-resort antibiotic used to treat multidrug-resistant Gram-negative bacterial infections, has been found to possess in vitro fungicidal activity and showed synergy with fluconazole against a single strain of C. glabrata. Since both agents may be used simultaneously in intensive care unit (ICU) patients, this study was performed to test for possible synergy of this combination against 35 C. glabrata blood isolates, using 2 methods: a time-kill assay and an experimental MIC-MIC Etest method. Thirty-five genetically unique C. glabrata bloodstream isolates were collected from 2009 to 2011, identified using an API 20C system, and genotyped by repetitive sequence-based PCR (rep-PCR). MICs were determined by Etest and broth microdilution methods. Synergy testing was performed using a modified bacterial Etest synergy method and time-kill assay, with final results read at 24 h. The Etest method showed synergy against 19/35 (54%) isolates; the time-kill assay showed synergy against 21/35 (60%) isolates. Isolates not showing drug synergy had an indifferent status. Concordance between methods was 60%. In vitro synergy of polymyxin B and fluconazole against the majority of C. glabrata isolates was demonstrated by both methods. The bacterial Etest synergy method adapted well when used with C. glabrata. Etest was easier to perform than time-kill assay and may be found to be an acceptable alternative to time-kill assay with antifungals. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Lymnaea columella: two new Brazilian localities in the states of Amazonas and Bahia

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W. Lobato Paraense

1986-03-01

Full Text Available The occurrence of Lymnaea columella is recorded in Tefé, Amazonas state, where it was found together with Drepanotrema anatinum, Physa marmorata and pomacea sp. L. columella was also collected in Salvador, Bahia state, at the dique do Tororó, an urban lake formely mentioned (as "lac Baril" by Moricand (1853 as a breeding-place of Biomphalaria glabrata, Drepanotrema cimex, D. depressissimum, Pomacea lineata, P. decussata and Ancylus moricandi. The four first-mentioned species, as well as physa cubensis and Hemisinus brasiliensis, were also collected now. This is the first record of a lymnaeid in the Northeastern region of Brazil.É registrada a ocorrência de Lymnaea columella em Tefé, Estado do Amazonas, onde foi encontrada juntamente com Physa marmorata e Pomacea sp. L. columella foi também coletada em Salvador, Estado da Bahia, no Dique do Tororó, lago urbano antes mencionado por Moricand (1853 como criadouro de Biomphalaria glabrata, Drepanotrema cimex, D. depressissimum, Pomacea lineata, P. decussata e Ancylus moricandi. As quatro primeiras espécies mencionadas, assim como Physa cubensis e Hemisinus brasiliensis, também foram agora coletadas. Este é o primeiro registro de um limneídeo na região Nordeste do Brasil

Probiotic Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 exhibit strong antifungal effects against vulvovaginal candidiasis-causing Candida glabrata isolates.

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Chew, S Y; Cheah, Y K; Seow, H F; Sandai, D; Than, L T L

2015-05-01

This study investigates the antagonistic effects of the probiotic strains Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 against vulvovaginal candidiasis (VVC)-causing Candida glabrata. Growth inhibitory activities of Lact. rhamnosus GR-1 and Lact. reuteri RC-14 strains against C. glabrata were demonstrated using a spot overlay assay and a plate-based microtitre assay. In addition, these probiotic lactobacilli strains also exhibited potent candidacidal activity against C. glabrata, as demonstrated by a LIVE/DEAD yeast viability assay performed using confocal laser scanning microscopy. The metabolic activities of all C. glabrata strains were completely shut down in response to the challenges by the probiotic lactobacilli strains. In addition, both probiotic lactobacilli strains exhibited strong autoaggregation and coaggregation phenotypes in the presence of C. glabrata, which indicate that these lactobacilli strains may exert their probiotic effects through the formation of aggregates and, thus the consequent prevention of colonization by C. glabrata. Probiotic Lact. rhamnosus GR-1 and Lact. reuteri RC-14 strains exhibited potent antagonistic activities against all of the tested C. glabrata strains. These lactobacilli exhibited antifungal effects, including those attributed to their aggregation abilities, and their presence caused the cessation of growth and eventual cell death of C. glabrata. This is the first study to report on the antagonistic effects of these probiotic lactobacilli strains against the non-Candida albicans Candida (NCAC) species C. glabrata. © 2015 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

Terpenes isolated of Coussarea platyphylla Muell. Arg. (Rubiaceae)

International Nuclear Information System (INIS)

Araujo, Francieli Casassa Vieira de; Marques, Fabio Goncalves; Silva, Cleuza Conceicao da; Santin, Silvana Maria de Oliveira; Nakamura, Celso Vataru; Zamuner, Maria Lucilia Motinha; Souza, Maria Conceicao de

2009-01-01

The phytochemical investigation of Coussarea platyphylla led to the isolation of triterpenes betulonic and betulinic acid, monoterpenes monotropein and monotropein salt, the diterpene trans-phytol and steroids. The structures of the isolated compounds were assigned on the basis of spectroscopic data, including two-dimensional NMR methods. The antiproliferative properties against human cancer cell lines and molluscicidal activity against Biomphalaria glabrata of the crude methanolic extract and of its fractions were investigated. (author)

Terpenos isolados de Coussarea platyphylla Müll. Arg. (Rubiaceae Terpenes isolated of Coussarea platyphylla Müll. Arg. (Rubiaceae

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Francieli Casassa Vieira de Araujo

2009-01-01

Full Text Available The phytochemical investigation of Coussarea platyphylla led to the isolation of triterpenes betulonic and betulinic acid, monoterpenes monotropein and monotropein salt, the diterpene trans-phytol and esteroids. The structures of the isolated compounds were assigned on the basis of spectroscopic data, including two-dimensional NMR methods. The antiproliferative properties against human cancer cell lines and molluscicidal activity against Biomphalaria glabrata of the crude methanolic extract and of its fractions were investigated.

Terpenes isolated of Coussarea platyphylla Muell. Arg. (Rubiaceae); Terpenos isolados de Coussarea platyphylla Muell. Arg. (Rubiaceae)

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Araujo, Francieli Casassa Vieira de; Marques, Fabio Goncalves; Silva, Cleuza Conceicao da; Santin, Silvana Maria de Oliveira [Universidade Estadual de Maringa, PR (Brazil). Dept. de Quimica], e-mail: smoliveira@uem.br; Nakamura, Celso Vataru [Universidade Estadual de Maringa, PR (Brazil). Dept. de Microbiologia; Zamuner, Maria Lucilia Motinha [Universidade Estadual de Maringa, PR (Brazil). Dept. de Farmacia e Farmacologia; Souza, Maria Conceicao de [Universidade Estadual de Maringa, PR (Brazil). Dept. de Biologia

2009-07-01

The phytochemical investigation of Coussarea platyphylla led to the isolation of triterpenes betulonic and betulinic acid, monoterpenes monotropein and monotropein salt, the diterpene trans-phytol and steroids. The structures of the isolated compounds were assigned on the basis of spectroscopic data, including two-dimensional NMR methods. The antiproliferative properties against human cancer cell lines and molluscicidal activity against Biomphalaria glabrata of the crude methanolic extract and of its fractions were investigated. (author)

Change in schistosome sex ratio under the influence of a biotic environmental-related factor.

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Moné, H

1997-04-01

Schistosoma mansoni is a dioecious trematode responsible for intestinal schistosomiasis in man. The sex ratio was determined for S. mansoni adults derived from cercariae obtained from infected Biomphalaria glabrata maintained in the presence of the nonvector molluse. Marisa cornuarietis. The presence of M. cornuarietis is responsible for enhanced growth of B. glabrata and for a change in the sex ratio of the schistosome, which becomes more male-biased as compared to control snails maintained in aquaria lacking M. cornuarietis. This is the first time the presence of another species in the environment has been shown to influence schistosome sex ratios. Two nonexclusive hypotheses are proposed to explain this variation in the sex ratio: sexual competition between male and female sporocysts; and sex reversal.

Identification of Candida glabrata genes involved in pH modulation and modification of the phagosomal environment in macrophages.

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Lydia Kasper

Full Text Available Candida glabrata currently ranks as the second most frequent cause of invasive candidiasis. Our previous work has shown that C. glabrata is adapted to intracellular survival in macrophages and replicates within non-acidified late endosomal-stage phagosomes. In contrast, heat killed yeasts are found in acidified matured phagosomes. In the present study, we aimed at elucidating the processes leading to inhibition of phagosome acidification and maturation. We show that phagosomes containing viable C. glabrata cells do not fuse with pre-labeled lysosomes and possess low phagosomal hydrolase activity. Inhibition of acidification occurs independent of macrophage type (human/murine, differentiation (M1-/M2-type or activation status (vitamin D3 stimulation. We observed no differential activation of macrophage MAPK or NFκB signaling cascades downstream of pattern recognition receptors after internalization of viable compared to heat killed yeasts, but Syk activation decayed faster in macrophages containing viable yeasts. Thus, delivery of viable yeasts to non-matured phagosomes is likely not triggered by initial recognition events via MAPK or NFκB signaling, but Syk activation may be involved. Although V-ATPase is abundant in C. glabrata phagosomes, the influence of this proton pump on intracellular survival is low since blocking V-ATPase activity with bafilomycin A1 has no influence on fungal viability. Active pH modulation is one possible fungal strategy to change phagosome pH. In fact, C. glabrata is able to alkalinize its extracellular environment, when growing on amino acids as the sole carbon source in vitro. By screening a C. glabrata mutant library we identified genes important for environmental alkalinization that were further tested for their impact on phagosome pH. We found that the lack of fungal mannosyltransferases resulted in severely reduced alkalinization in vitro and in the delivery of C. glabrata to acidified phagosomes. Therefore

Relative Abundances of Candida albicans and Candida glabrata in In Vitro Coculture Biofilms Impact Biofilm Structure and Formation.

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Olson, Michelle L; Jayaraman, Arul; Kao, Katy C

2018-04-15

Candida is a member of the normal human microbiota and often resides on mucosal surfaces such as the oral cavity or the gastrointestinal tract. In addition to their commensality, Candida species can opportunistically become pathogenic if the host microbiota is disrupted or if the host immune system becomes compromised. An important factor for Candida pathogenesis is its ability to form biofilm communities. The two most medically important species- Candida albicans and Candida glabrata -are often coisolated from infection sites, suggesting the importance of Candida coculture biofilms. In this work, we report that biofilm formation of the coculture population depends on the relative ratio of starting cell concentrations of C. albicans and C. glabrata When using a starting ratio of C. albicans to C. glabrata of 1:3, ∼6.5- and ∼2.5-fold increases in biofilm biomass were observed relative to those of a C. albicans monoculture and a C. albicans / C. glabrata ratio of 1:1, respectively. Confocal microscopy analysis revealed the heterogeneity and complex structures composed of long C. albicans hyphae and C. glabrata cell clusters in the coculture biofilms, and reverse transcription-quantitative PCR (qRT-PCR) studies showed increases in the relative expression of the HWP1 and ALS3 adhesion genes in the C. albicans / C. glabrata 1:3 biofilm compared to that in the C. albicans monoculture biofilm. Additionally, only the 1:3 C. albicans / C. glabrata biofilm demonstrated an increased resistance to the antifungal drug caspofungin. Overall, the results suggest that interspecific interactions between these two fungal pathogens increase biofilm formation and virulence-related gene expression in a coculture composition-dependent manner. IMPORTANCE Candida albicans and Candida glabrata are often coisolated during infection, and the occurrence of coisolation increases with increasing inflammation, suggesting possible synergistic interactions between the two Candida species in

Heteroresistance to Fluconazole Is a Continuously Distributed Phenotype among Candida glabrata Clinical Strains Associated with In Vivo Persistence

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Ronen Ben-Ami

2016-08-01

Full Text Available Candida glabrata causes persistent infections in patients treated with fluconazole and often acquires resistance following exposure to the drug. Here we found that clinical strains of C. glabrata exhibit cell-to-cell variation in drug response (heteroresistance. We used population analysis profiling (PAP to assess fluconazole heteroresistance (FLCHR and to ask if it is a binary trait or a continuous phenotype. Thirty (57.6% of 52 fluconazole-sensitive clinical C. glabrata isolates met accepted dichotomous criteria for FLCHR. However, quantitative grading of FLCHR by using the area under the PAP curve (AUC revealed a continuous distribution across a wide range of values, suggesting that all isolates exhibit some degree of heteroresistance. The AUC correlated with rhodamine 6G efflux and was associated with upregulation of the CDR1 and PDH1 genes, encoding ATP-binding cassette (ABC transmembrane transporters, implying that HetR populations exhibit higher levels of drug efflux. Highly FLCHRC. glabrata was recovered more frequently than nonheteroresistant C. glabrata from hematogenously infected immunocompetent mice following treatment with high-dose fluconazole (45.8% versus 15%, P = 0.029. Phylogenetic analysis revealed some phenotypic clustering but also variations in FLCHR within clonal groups, suggesting both genetic and epigenetic determinants of heteroresistance. Collectively, these results establish heteroresistance to fluconazole as a graded phenotype associated with ABC transporter upregulation and fluconazole efflux. Heteroresistance may explain the propensity of C. glabrata for persistent infection and the emergence of breakthrough resistance to fluconazole.

Interaction of gamma radiation on the functionality of the molluscicidal extract of Anacardium occidentale Linn

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Santos, Gustavo Henrique Farias dos [Grupo de Estudos em Radioprotecao e Radioecologia (GERAR) . Departamento de Energia Nuclear. Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil); Silva, Edvane Borges da [Centro Academico de Vitoria. Universidade Federal de Pernambuco (UFPE), Vitoria de Santo Antao, PE (Brazil); Amorim, Elba Lucia C.; Peixoto Sobrinho, Tadeu J.S., E-mail: elba@ufpe.br [Departamento de Ciencias Farmaceuticas. Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil); Melo, Ana Maria Mendonca de Albuquerque; Lima, Claudia Sampaio de Andrade [Departamento de Biofisica e Radiobiologia. Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil)

2011-07-01

Biological control of Biomphalaria glabrata that is the intermediate host of Schistosoma mansoni, through molluscicides has been an alternative against schistosomiasis. Many studies have been developed to obtain molluscicide products, from plants. Anacardium occidentale L. (cashew), a plant rich in phenolic compounds shows molluscicidal activity in earlier assays. However there is an interest of enhancing the action of bioactive substances in order to use it in small concentrations, reducing costs in their utilization. This study were conducted using ethanolic extracts of bark and leaves of A. occidentale, before and after exposure to gamma radiation from {sup 60}Co, checking their secondary metabolites, their biological activity against Biomphalaria glabrata and environmental toxicity. The extracts of A. occidentale were obtained by cold maceration in 70% ethanol, filtered, dried and divided into two experimental groups: control (0 kGy) and irradiated at a dose of 10 kGy. The quantification of metabolites was performed in six replicates for the determination of total phenols by Folin-Ciocalteau method and tannins, the precipitation of casein. Tests for biological control of embryos and adults of B. glabrata snails and assessment of environmental toxicity (using Artemia salina larvae) were performed in triplicate, following a period of 24 hours of exposure to extracts at a concentration of 100 mg/L and its respective controls. Data were expressed as percentages of means and standard deviations. The results showed that the gamma radiation from {sup 60}Co resulted in leaf extracts, increased levels of total phenols and tannins, which enhanced the lethality for embryos and adults of B. glabrata. There was a reduction of the toxicity of leaf extracts after irradiation in the Artemia salina. Since in extracts of bark, gamma radiation did not alter the levels of total phenols and tannins, however, it was noted potentiation of lethality of adult snails of B. glabrata. The

Interaction of gamma radiation on the functionality of the molluscicidal extract of Anacardium occidentale Linn

International Nuclear Information System (INIS)

Santos, Gustavo Henrique Farias dos; Silva, Edvane Borges da; Amorim, Elba Lucia C.; Peixoto Sobrinho, Tadeu J.S.; Melo, Ana Maria Mendonca de Albuquerque; Lima, Claudia Sampaio de Andrade

2011-01-01

Biological control of Biomphalaria glabrata that is the intermediate host of Schistosoma mansoni, through molluscicides has been an alternative against schistosomiasis. Many studies have been developed to obtain molluscicide products, from plants. Anacardium occidentale L. (cashew), a plant rich in phenolic compounds shows molluscicidal activity in earlier assays. However there is an interest of enhancing the action of bioactive substances in order to use it in small concentrations, reducing costs in their utilization. This study were conducted using ethanolic extracts of bark and leaves of A. occidentale, before and after exposure to gamma radiation from 60 Co, checking their secondary metabolites, their biological activity against Biomphalaria glabrata and environmental toxicity. The extracts of A. occidentale were obtained by cold maceration in 70% ethanol, filtered, dried and divided into two experimental groups: control (0 kGy) and irradiated at a dose of 10 kGy. The quantification of metabolites was performed in six replicates for the determination of total phenols by Folin-Ciocalteau method and tannins, the precipitation of casein. Tests for biological control of embryos and adults of B. glabrata snails and assessment of environmental toxicity (using Artemia salina larvae) were performed in triplicate, following a period of 24 hours of exposure to extracts at a concentration of 100 mg/L and its respective controls. Data were expressed as percentages of means and standard deviations. The results showed that the gamma radiation from 60 Co resulted in leaf extracts, increased levels of total phenols and tannins, which enhanced the lethality for embryos and adults of B. glabrata. There was a reduction of the toxicity of leaf extracts after irradiation in the Artemia salina. Since in extracts of bark, gamma radiation did not alter the levels of total phenols and tannins, however, it was noted potentiation of lethality of adult snails of B. glabrata. The analysis

Analysis of the first and second internal transcribed spacer sequences of the ribosomal DNA in Biomphalaria tenagophila complex (Mollusca: Planorbidae

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Teofânia HDA Vidigal

2004-03-01

Full Text Available The first and second internal transcribed spacer regions (ITS1 and ITS2 of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis were sequenced and compared. The alignment lengths of these regions were about 655 bp and 481 bp, respectively. Phylogenetic relationships among the Biomphalaria species were inferred by Maximum Parsimony and Neighbor-joining methods. The phylogenetic trees produced, in most of the cases, were in accordance with morphological systematics and other molecular data previously obtained by polymerase chain reaction and restriction fragment length polymorphism analysis. The present results provide support for the proposal that B. tenagophila represents a complex comprising B. tenagophila, B. occidentalis and B. t. guaibensis.

Analgesic effect of leaf extract from Ageratina glabrata in the hot plate test

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Guadalupe García P

2011-10-01

Full Text Available Ageratina glabrata (Kunth R.M. King & H. Rob., Asteraceae (syn. Eupatorium glabratum Kunth is widely distributed throughout Mexico and popularly known as "chamizo blanco" and "hierba del golpe" for its traditional use as external analgesic remedy. Though glabrata species has been chemically studied, there are no experimentally asserted reports about possible analgesic effects which can be inferred from its genus Ageratina. To fill the gap, we evaluated A. glabrata extracts in an animal model of nociception exploiting thermal stimuli. NMR and mass analyses identified a new thymol derivative, 10-benzoiloxy-6,8,9-trihydroxy-thymol isobutyrate (1, which was computationally converted into a ring-closed structure to explain interaction with the COX-2 enzyme in a ligand-receptor docking study. The resulting docked pose is in line with reported crystal complexes of COX-2 with chromene ligands. Based on the present results of dichloromethane extracts from its dried leaves, it is safe to utter that the plant possesses analgesic effects in animal tests which are mediated through inhibition of COX-2 enzyme.

Neglected tropical diseases: prevalence and risk factors for schistosomiasis and soil-transmitted helminthiasis in a region of Minas Gerais State, Brazil.

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Couto, Luzivalda D; Tibiriça, Sandra H C; Pinheiro, Izabella O; Mitterofhe, Adalberto; Lima, Adilson C; Castro, Milton F; Gonçalves, Murilo; Silva, Marcio R; Guimarães, Ricardo J P S; Rosa, Florence M; Coimbra, Elaine S

2014-06-01

Among the neglected tropical diseases (NTDs), schistosomiasis and the three main soil-transmitted helminthiases (STHs), i.e., ascariasis, trichuriasis and hookworm infection, represent the most common infections in developing countries. In Brazil, there is a lack of epidemiological data in many parts of the country, which favors the unawareness of the real situation concerning these diseases. Due to this, we investigated the occurrence of schistosomiasis and STHs in a region of Minas Gerais State, Brazil. One stool sample was collected from 503 individuals, whose ages ranged from 0.1 to 91.2 years, and screened using both the Kato-Katz and the Formol-Ether methods. In parallel, a malacological survey was carried out in the main water bodies of the district, and Biomphalaria susceptibility assays and kernel-based techniques were also performed. No individual was found infected with Ascaris lumbricoides or hookworm. Schistosoma mansoni was the most common parasite found (1.6%). The prevalence was higher in males and the chance of acquiring the disease increased by 43.35 times with contact with a body of water. None of the Biomphalaria tenagophila and B. glabrata specimens were found naturally infected, but B. glabrata was highly susceptible to infection with Schistosoma mansoni. Using kernel-based techniques, clusters of Biomphalaria were found near the households where the infected individuals lived. Schistosomiasis was the most prevalent parasitic infection found. Our findings show that the occurrence of this disease has been underestimated by the local health care service, and highlight the importance of epidemiological surveillance in areas of low prevalence for schistosomiasis. © The Author 2014. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Unexpected effects of azole transporter inhibitors on antifungal susceptibility in Candida glabrata and other pathogenic Candida species.

Science.gov (United States)

Nagayoshi, Yohsuke; Miyazaki, Taiga; Shimamura, Shintaro; Nakayama, Hironobu; Minematsu, Asuka; Yamauchi, Shunsuke; Takazono, Takahiro; Nakamura, Shigeki; Yanagihara, Katsunori; Kohno, Shigeru; Mukae, Hiroshi; Izumikawa, Koichi

2017-01-01

The pathogenic fungus Candida glabrata is often resistant to azole antifungal agents. Drug efflux through azole transporters, such as Cdr1 and Cdr2, is a key mechanism of azole resistance and these genes are under the control of the transcription factor Pdr1. Recently, the monoamine oxidase A (MAO-A) inhibitor clorgyline was shown to inhibit the azole efflux pumps, leading to increased azole susceptibility in C. glabrata. In the present study, we have evaluated the effects of clorgyline on susceptibility of C. glabrata to not only azoles, but also to micafungin and amphotericin B, using wild-type and several mutant strains. The addition of clorgyline to the culture media increased fluconazole susceptibility of a C. glabrata wild-type strain, whereas micafungin and amphotericin B susceptibilities were markedly decreased. These phenomena were also observed in other medically important Candida species, including Candida albicans, Candida parapsilosis, Candida tropicalis, and Candida krusei. Expression levels of CDR1, CDR2 and PDR1 mRNAs and an amount of Cdr1 protein in the C. glabrata wild-type strain were highly increased in response to the treatment with clorgyline. However, loss of Cdr1, Cdr2, Pdr1, and a putative clorgyline target (Fms1), which is an ortholog of human MAO-A, or overexpression of CDR1 did not affect the decreased susceptibility to micafungin and amphotericin B in the presence of clorgyline. The presence of other azole efflux pump inhibitors including milbemycin A4 oxime and carbonyl cyanide 3-chlorophenylhydrazone also decreased micafungin susceptibility in C. glabrata wild-type, Δcdr1, Δcdr2, and Δpdr1 strains. These findings suggest that azole efflux pump inhibitors increase azole susceptibility but concurrently induce decreased susceptibility to other classes of antifungals independent of azole transporter functions.

Estudos sobre o comportamento dos Planorbídeos: I - uma técnica de observação e registro comportamental por cinematografia Studies on the behavior of planorbids: I - a technique for behavioral observation and recording by use of cinematography

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Otávio S. Pieri

1980-01-01

Full Text Available Uma técnica envolvendo cinematografia com lapso de tempo foi elaborada para o estudo da atividade comportamental dos planorbídeos em condições de laboratório. As observações realizam-se em uma câmara dotada de ciclo de iluminação dia-noite, e os registros são feitos com uma filmadora super-8, operada quadro a quadro, sob luz de flash estroboscópico. Essa técnica tem permitido mensurações rigorosas de diferentes aspectos do comportamento de Biomphalaria glabrata (say, 1818, e pode ser utilizada na análise do nível de resposta dos planorbídeos aos moluscicidas, em testes experimentais, e dos comportamentos de proteção frente a condições adversas em geral.A technique involving time-lapse cinematography was developed for studying the behavioral repertoire of planorbids in laboratory conditions. Observations were carried out within a chamber with controlled light and temperature; recording was done by single frame shooting at 10 second intervals, with synchronized strobed flash. This technique has allowed accurate measurements of different aspects of the activity of Biomphalaria glabrata (Say, 1818, and can be useful in analysing the level of response of planorbids to molluscicides, in experimental tests, as well as their protective behavior under general adverse conditions.

Metabolic engineering of Candida glabrata for diacetyl production.

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Xiang Gao

Full Text Available In this study, Candida glabrata, an efficient pyruvate-producing strain, was metabolically engineered for the production of the food ingredient diacetyl. A diacetyl biosynthetic pathway was reconstructed based on genetic modifications and medium optimization. The former included (i channeling carbon flux into the diacetyl biosynthetic pathway by amplification of acetolactate synthase, (ii elimination of the branched pathway of α-acetolactate by deleting the ILV5 gene, and (iii restriction of diacetyl degradation by deleting the BDH gene. The resultant strain showed an almost 1∶1 co-production of α-acetolactate and diacetyl (0.95 g L(-1. Furthermore, addition of Fe3+ to the medium enhanced the conversion of α-acetolactate to diacetyl and resulted in a two-fold increase in diacetyl production (2.1 g L(-1. In addition, increased carbon flux was further channeled into diacetyl biosynthetic pathway and a titer of 4.7 g L(-1 of diacetyl was achieved by altering the vitamin level in the flask culture. Thus, this study illustrates that C. glabrata could be tailored as an attractive platform for enhanced biosynthesis of beneficial products from pyruvate by metabolic engineering strategies.

The Effect of Molybdenum Fertilization on Arachis Glabrata Biomass ...

African Journals Online (AJOL)

The effect of molybdenum fertilization on biomass and the number of nodules of Arachis glabrata was assessed at the Teaching and Research Farm of the University of Dschang in 2011 at different periods of mowing. A factorial design comparing four doses of molybdenum as ammonium molybdate (0, 0.75, 1.5 and 2.25 ...

Fluconazole affects the alkali-metal-cation homeostasis and susceptibility to cationic toxic compounds of Candida glabrata.

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Elicharova, Hana; Sychrova, Hana

2014-08-01

Candida glabrata is a salt-tolerant and fluconazole (FLC)-resistant yeast species. Here, we analyse the contribution of plasma-membrane alkali-metal-cation exporters, a cation/proton antiporter and a cation ATPase to cation homeostasis and the maintenance of membrane potential (ΔΨ). Using a series of single and double mutants lacking CNH1 and/or ENA1 genes we show that the inability to export potassium and toxic alkali-metal cations leads to a slight hyperpolarization of the plasma membrane of C. glabrata cells; this hyperpolarization drives more cations into the cells and affects cation homeostasis. Surprisingly, a much higher hyperpolarization of C. glabrata plasma membrane was produced by incubating cells with subinhibitory concentrations of FLC. FLC treatment resulted in a substantially increased sensitivity of cells to various cationic drugs and toxic cations that are driven into the cell by negative-inside plasma-membrane potential. The effect of the combination of FLC plus cationic drug treatment was enhanced by the malfunction of alkali-metal-cation transporters that contribute to the regulation of membrane potential and cation homeostasis. In summary, we show that the combination of subinhibitory concentrations of FLC and cationic drugs strongly affects the growth of C. glabrata cells. © 2014 The Authors.

Failed Reverse Total Shoulder Arthroplasty Caused by Recurrent Candida glabrata Infection with Prior Serratia marcescens Coinfection

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John G. Skedros

2014-01-01

Full Text Available This report describes a 58-year-old insulin-dependent diabetic male patient who initially sustained a proximal humerus fracture from a fall. The fracture fixation failed and then was converted to a humeral hemiarthroplasty, which became infected with Candida glabrata and Serratia marcescens. After these infections were believed to be cured with antibacterial and antifungal treatments and two-stage irrigation and debridement, he underwent conversion to a reverse total shoulder arthroplasty. Unfortunately, the C. glabrata infection recurred and, nearly 1.5 years after implantation of the reverse total shoulder, he had a resection arthroplasty (removal of all implants and cement. His surgical and pharmacologic treatment concluded with (1 placement of a tobramycin-impregnated cement spacer also loaded with amphotericin B, with no plan for revision arthroplasty (i.e., the spacer was chronically retained, and (2 chronic use of daily oral fluconazole. We located only three reported cases of Candida species causing infection in shoulder arthroplasties (two C. albicans, one C. parapsilosis. To our knowledge, a total shoulder arthroplasty infected with C. glabrata has not been reported, nor has a case of a C. glabrata and S. marcescens periprosthetic coinfection in any joint. In addition, it is well known that S. marcescens infections are uncommon in periprosthetic joint infections.

Um inimigo natural dos caramujos do gênero Biomphalaria

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Aluízio Bezerra Coutinho

1976-12-01

Full Text Available A formiga carnívora Paratrechina longicornis exerce predação ativa sobre os caramujos do gênero Biomphalaria. Assim que os caramujos são deixados no seco pela retirada ou dessecamento das águas na estação seca, são atacados e rapidamente devorados pelas formigas. Somente os caramujos enterrados na lama argilosa ou aqueles que tiverem a abertura das conchas obturadas por tampões de argila endurecida pela secura conseguem escapar à predação e retornarem à atividade quando a volta da estação chuvosa traz água para os vivedouros dessecados. Obviamente outras espécies de formigas carnívoras podem assumir idêntica função ecológica.

Occurrence and characterization of Candida nivariensis from a culture collection of Candida glabrata clinical isolates in Malaysia.

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Tay, Sun Tee; Lotfalikhani, Azadeh; Sabet, Negar Shafiei; Ponnampalavanar, Sasheela; Sulaiman, Sofiah; Na, Shiang Ling; Ng, Kee Peng

2014-10-01

Candida nivariensis and C. bracarensis have been recently identified as emerging yeast pathogens which are phenotypically indistinguishable from C. glabrata. However, there is little data on the prevalence and antifungal susceptibilities of these species. This study investigated the occurrence of C. nivariensis and C. bracarensis in a culture collection of 185 C. glabrata isolates at a Malaysian teaching hospital. C. nivariensis was discriminated from C. glabrata using a PCR assay as described by Enache-Angoulvant et al. (J Clin Microbiol 49:3375-9, 2011). The identity of the isolates was confirmed by sequence analysis of the D1D2 domain and internal transcribed spacer region of the yeasts. The isolates were cultured on Chromogenic CHROMagar Candida (®) agar (Difco, USA), and their biochemical and enzymic profiles were determined. Antifungal susceptibilities of the isolates against amphotericin B, fluconazole, voriconazole and caspofungin were determined using E tests. Clotrimazole MICs were determined using a microbroth dilution method. There was a low prevalence (1.1 %) of C. nivariensis in our culture collection of C. glabrata. C. nivariensis was isolated from a blood culture and vaginal swab of two patients. C. nivariensis grew as white colonies on Chromogenic agar and demonstrated few positive reactions using biochemical tests. Enzymatic profiles of the C. nivariensis isolates were similar to that of C. glabrata. The isolates were susceptible to amphotericin B, fluconazole, voriconazole and caspofungin. Clotrimazole resistance is suspected in one isolate. This study reports for the first time the emergence of C. nivariensis in our clinical setting.

Overexpression of Aldo-Keto-Reductase in Azole-resistant Clinical Isolates of Candida Glabrata Determined by cDNA-AFLP

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Mansour Heidari

2013-01-01

Full Text Available Background: Candida glabrata causes significant medical problems in immunocompromised patients. Many strains of this yeast are intrinsically resistant to azole antifungal agents, and treatment is problematic, leading to high morbidity and mortality rates in immunosuppressed individuals. The primary goal of this study was to investigate the genes involved in the drug resistance of clinical isolates of C. glabrata.Methods: The clinical isolates of C. glabrata were collected in an epidemiological survey of candidal infection inimmunocompromised patients and consisted of four fluconazole and itraconazole resistant isolates, two fluconazoleand itraconazole sensitive isolates, and C. glabrata CBS 138 as reference strain. Antifungal susceptibility patterns ofthe organisms were determined beforehand by the Clinical and Laboratory Standards Institute (CLSI. The potentialgene(s implicated in antifungal resistance were investigated using complementary DNA- Amplified Fragment Length Polymorphism (cDNA-AFLP. Semi-quantitative RT-PCR was carried out to evaluate the expression of gene(s in resistant isolates as compared to sensitive and reference strains.Results and conclusions: The aldo-keto-reductase superfamily (AKR gene was upregulated in the resistant clinicalisolates as assessed by cDNA-AFLP. Semi-quantitative RT-PCR revealed AKR mRNA expression approximately twice that seen in the sensitive isolates. Overexpression of the AKR gene was associated with increased fluconazole and itraconazole resistance in C. glabrata. The data suggest that upregulation of the AKR gene might give a new insight into the mechanism of azole resistance.

Ecological review of hydroelectric reservoirs in Puerto Rico

Energy Technology Data Exchange (ETDEWEB)

Jobin, W.R.; Ferguson, F.F.; Brown, R.

1976-10-01

A review of published literature and available data on the ecology of hydroelectric reservoirs and other lakes in Puerto Rico yielded various studies on unrelated elements in the aquatic ecology, but very few comprehensive investigations. The majority of the island-wide studies pertained to surveys on snails related to the parasitic disease bilharzia. A survey of 28 major lakes in 1976 showed that Biomphalaria glabrata had gradually been displaced from most of the lakes by Marisa cornuarietis and Tarebia granifera, two foreign snails which do not transmit bilharzia. Of the 17 lakes containing B. glabrata in 1956, only 8 remained infested in 1966 and only 5 in 1976, twenty years after the introduction of Marisa cornuarietis. Although the trend indicates that the lakes may be safe from transmission a monitoring system is necessary before the lakes could be used for recreation.

Molluscicidal saponins from a Zimbabwean strain of Phytolacca dodecandra

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Thiilborg, S. T.; Christensen, S. B.; Cornett, Claus

1994-01-01

Three new monodesmosidic saponins, all glycosides of 2 beta-hydroxyoleanolic acid, were isolated from an aqueous extract of a Zimbabwean strain of Phytolacca dodecandra. Their structures were, mainly by spectroscopic methods (LSIMS, H-1 NMR, COSY, NOESY, TOCSY, J-resolved (1)HNMR, (13)CNMR, HETCOR......-hydroxyoleanolic acid. Two of the saponins were submitted to a preliminary screening for molluscicidal activity against the schistosomiasis transmitting snail Biomphalaria glabrata and showed, respectively, strong and weak activity. In addition, four saponins previously reported from other strains of Phytolacca...

Synergistic effects of tacrolimus and azole antifungal compounds in fluconazole-susceptible and fluconazole-resistant Candida glabrata isolates

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Laura Bedin Denardi

2015-03-01

Full Text Available In vitro interaction between tacrolimus (FK506 and four azoles (fluconazole, ketoconazole, itraconazole and voriconazole against thirty clinical isolates of both fluconazole susceptible and -resistant Candida glabrata were evaluated by the checkerboard microdilution method. Synergistic, indifferent or antagonism interactions were found for combinations of the antifungal agents and FK506. A larger synergistic effect was observed for the combinations of FK506 with itraconazole and voriconazole (43%, followed by that of the combination with ketoconazole (37%, against fluconazole-susceptible isolates. For fluconazole-resistant C. glabrata, a higher synergistic effect was obtained from FK506 combined with ketoconazole (77%, itraconazole (73%, voriconazole (63% and fluconazole (60%. The synergisms that we observed in vitro, notably against fluconazole-resistant C. glabrata isolates, are promising and warrant further analysis of their applications in experimental in vivo studies.

Candida krusei and Candida glabrata reduce the filamentation of Candida albicans by downregulating expression of HWP1 gene.

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de Barros, Patrícia Pimentel; Freire, Fernanda; Rossoni, Rodnei Dennis; Junqueira, Juliana Campos; Jorge, Antonio Olavo Cardoso

2017-07-01

Pathogenicity of Candida albicans is associated with its capacity switch from yeast-like to hyphal growth. The hyphal form is capable to penetrate the epithelial surfaces and to damage the host tissues. Therefore, many investigations have focused on mechanisms that control the morphological transitions of C. albicans. Recently, certain studies have showed that non-albicans Candida species can reduce the capacity of C. albicans to form biofilms and to develop candidiasis in animal models. Then, the objective of this study was to evaluate the effects of Candida krusei and Candida glabrata on the morphogenesis of C. albicans. Firstly, the capacity of reference and clinical strains of C. albicans in forming hyphae was tested in vitro. After that, the expression of HWP1 (hyphal wall protein 1) gene was determined by quantitative real-time PCR (polymerase chain reaction) assay. For both reference and clinical strains, a significant inhibition of the hyphae formation was observed when C. albicans was incubated in the presence of C. krusei or C. glabrata compared to the control group composed only by C. albicans. In addition, the culture mixed of C. albicans-C. krusei or C. albicans-C. glabrata reduced significantly the expression of HWP1 gene of C. albicans in relation to single cultures of this specie. In both filamentation and gene expression assays, C. krusei showed the higher inhibitory activity on the morphogenesis of C. albicans compared to C. glabrata. C. krusei and C. glabrata are capable to reduce the filamentation of C. albicans and consequently decrease the expression of the HWP1 gene.

Biological and environmental factors associated with risk of schistosomiasis mansoni transmission in Porto de Galinhas, Pernambuco State, Brazil Factores biológicos y ambientales asociados al riesgo de transmisión de la esquistosomiasis mansoni en la localidad de Porto de Galinhas, Pernambuco, Brasil Fatores biológicos e ambientais associados ao risco de transmissão da esquistossomose mansoni na localidade de Porto de Galinhas, Pernambuco, Brasil

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Onicio Batista Leal Neto

2013-02-01

Full Text Available Schistosomiasis has expanded to the coast of Pernambuco State, Brazil, where there are frequent reports of Biomphalaria glabrata snails and human cases of the disease. This study analyzes factors related to schistosomiasis transmission risk in Porto de Galinhas. A one-year malacological survey was conducted to identify biological, abiotic, and environmental factors related to the host snail breeding sites. Data analysis used Excel 2010, GTM Pro, and ArcGis 10. A total of 11,012 B. glabrata snails were captured in 36 breeding sites, and 11 schistosomiasis transmission foci were identified. A negative correlation was found between breeding site temperature and snail density and infection rate, and a positive correlation with pH and salinity. The rainy season showed a positive correlation with snail density and infection rate. The study emphasizes the factors involved in the maintenance of schistosomiasis breeding sites, in light of persistence of this disease in Porto de Galinhas for more than 10 years.La esquistosomiasis se expande hacia el litoral de Pernambuco, Brasil, donde han sido frecuentes los registros de caracoles Biomphalaria glabrata y casos humanos de la enfermedad. Este estudio presenta factores relacionados con el riesgo de transmisión de la esquistosomiasis en la localidad Porto de Galinhas. Durante un año se llevó a cabo una investigación malacológica para identificar factores biológicos, abióticos y ambientales, relacionados con los criaderos de los moluscos huéspedes. Para el análisis de los datos se utilizaron los softwares Excel 2010, GTM Pro y ArcGis 10. Se recogieron 11.012 caracoles B. glabrata en los 36 criaderos identificados, siendo diagnosticados 11 focos de transmisión de la esquistosomiasis. Se verificó la correlación negativa entre la temperatura de los criaderos, densidad y tasa de infección de los caracoles, y la correlación positiva entre el pH y salinidad. El período de lluvia presentó una

Synergistic anticandidal activity of menthol in combination with itraconazole and nystatin against clinical Candida glabrata and Candida krusei isolates.

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Sharifzadeh, Aghil; Khosravi, Ali Reza; Shokri, Hojjatollah; Tari, Paria Samadi

2017-06-01

Candida glabrata (C. glabrata) and C. krusei are now emerging as serious hospital acquired infections in immunocompromised patients. Menthol, a terpenic compound, has been reported to have antifungal activity. The aim of this study was to investigate the effect of menthol in combination with itraconazole or nystatin against C. glabrata and C. krusei isolates. The effects of menthol along with itraconazole and nystatin, were evaluated by the Clinical Laboratory Standards Institute (CLSI) M44-A and CLSI M27-A3 methods. The fractional inhibitory concentration index (FICI) was determined for menthol plus itraconazole and nystatin combinations using the checkerboard method. The mean of minimum inhibitory concentration (MIC) values of menthol, nystatin and itraconazole were 53.2, 2.30 and 1.50 μg/ml for C. glabrata isolates and 121, 1.08 and 0.38 μg/ml for C. krusei isolates, respectively. Menthol in combination with itraconazole or nystatin exhibited the synergistic effects against all species of Candida tested. FICI values for menthol plus itraconazole and nystatin combinations ranged from 0.250 to 0.561 and 0.139 to 0.623 for C. glabrata isolates, and 0.182 to 0.750 and 0.188 to 0.760 for C. krusei, respectively. These results support the potential use of menthol as an anticandidal agent, and it can be used complementarily with other conventional antifungal agents. Copyright © 2017. Published by Elsevier Ltd.

Ensaios preliminares em laboratório para verificar a ação moluscicida de algumas espécies da flora brasileira Preliminary laboratory tests of the molluscicide activity of some species of Brazilian flora

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Nelymar Martineli Mendes

1984-10-01

Full Text Available Estudou-se em laboratório a atividade moluscicida de 68 extratos de 23 plantas brasileiras. As soluções em água desclorada dos extratos hexânicos e etanólico, nas concentrações de 1, 10 e 100 ppm, foram testadas sobre caramujos adultos e desovas de Biomphalaria glabrata, criados em laboratório. As plantas que demonstraram ação moluscicida na concentração de 100 ppm foram: Arthemisia verlotorum Lamotte, Caesalpinia peltophoroides Benth, Cassia rugosa G.Don., Eclipta alba Hassk, Euphorbia pulcherrima Willd, Euphorbia splendens Bojer, Joannesia princeps Vell, Leonorus sibiricus L.,Macrosiphonia guaranitica Muell,Nerium oleander L., Palicourea nicotianaefolia Cham, e Schlech., Panicum maximum M., Rumex crispus L., Ruta graveolens L., e Stryphnodendron barbatiman M.The molluscicide activity of sixty-eight extracts from twenty-three Brazilian plants was studied in the laboratory. The solutions, in dechlorinated water, of hexanic and ethylic extracts at 1, 10 and 100 ppm concentrations, were tested on adult snails and egg masses of Biomphalaria glabrata, reared in the laboratory. The plants with molluscicide activity on adult snails and/or egg masses at 100 ppm concentration were: Arthemisia verlotorum Lamotte, Caesalpinia peltophoroides Benth, Cassia rugosa G. Don, Eclipta alba Hassk, Euphorbia pulcherrima Willd, Euphorbia splendens Bojer, Joannesia princeps Vell, Leonorus sibiricus L., Macrosiphonia guaranitica Muell, Nerium oleander L., Palicourea nicotianaefolia Cham. and Schlech., Panicum maximum M., Rumex crispus L., Ruta graveolens L. and Stryphnodendron barbatiman M.

The suitability of several aquatic snails as intermediate hosts for Angiostrongylus cantonensis.

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Yousif, F; Lämmler, G

1975-10-16

Sixteen species of aquatic snails of four families were tested by quantitative technique under standardized conditions for their suitability as intermediate hosts for Angiostrongylus cantonensis. These species were the planorbid snails Biomphalaria glabrata, Biomphalaria alexandrina, Planorbis planorbis, Planorbis intermixtus, Bulinus truncatus, Bulinus contortus, Bulinus africanus, Bulinus tropicus and Helisoma sp.; the lymnaeid snails Lymnaea natalensis, Lymnaea tomentosa, Lymnaea stagnalis, and Stagnicola elodes; the physid snail Physa acuta (an Egyptian and a German strain) and the ampullariid snails Marisa cornuarietis and Lanistes carinatus. All these snail species proved to be susceptible to infection with A. cantonensis, and first stage larvae reached the infective third stage in all of them. However, the rate and intensity of infection varied with different species. B. glabrata was the most susceptible snail species with a 100% infection rate and an average percentage recovery of third stage larvae of 26.1. This was followed by S. elodes and B. africanus, with a 100% infection rate and an average percentage recovery of third stage larvae of 15.6 and 14.6 respectively. The rest of snail species proved to be less susceptible. For comparative evaluation of the suitability of the various snail species as intermediate hosts of A. cantonensis a "Capacity Index" was determined. This index should provide a useful method for the evaluation of the suitability of various snails as intermediate hosts of nematode parasites under standardized conditions in the laboratory.

Susceptibility of Biomphalaria spp. to infection with Schistosoma mansoni in sympatric and allopatric combinations with observations on the genetic variability between snails.

Science.gov (United States)

Mostafa, Osama M S; El-Dafrawy, Shadia M

2011-08-25

This investigation was carried out to study the susceptibility of Saudi Biomphalaria arabica to Egyptian Schistosoma mansoni in comparison with the susceptibility of Egyptian Biomphalaria alexandrina to the same parasite. This was in order to know the possibility that the parasite might be able to spread into Saudi Arabia and to determine the genetic variability between Egyptian B. alexandrina and Saudi Biomphalaria arabica snails. Lab bred Egyptian B. alexandrina and Saudi B. arabica snails were exposed individually to 10 freshly hatched Egyptian S. mansoni miracidia/snail. The mortality rate, infection rate, prepatent period, duration of cercarial shedding and cercariae production per snail were recorded in both the sympatric couple (Egyptian B. alexandrina and Egyptian S. mansoni) and in the allopatric combination (Saudi B. arabica and Egyptian S. mansoni). The results revealed that, the survival rate of snails exposed to Egyptian S. mansoni miracidia at 34th day post-exposure (at first cercarial shedding) was higher in B. arabica than in B. alexandrina. After shedding, the mortality rate was higher in the B. arabica, compared to B. alexandrina. The infection rate was higher in B. arabica than B. alexandrina; the mean of prepatent period was shorter in the B. arabica than in the B. alexandrina. However, the duration of cercarial shedding was longer in the Egyptian snails and the cercarial production per snail was higher in B. alexandrina snails than in B. arabica. To study the genetic variability between B. alexandrina and B. arabica, RAPD-PCR on the genomic DNA of snails was done. RAPD-PCR revealed significant variation between the two snail species. In conclusion, the results suggest that B. arabica can play a role in the transmission of Egyptian S. mansoni in Saudi Arabia and therefore this parasite might be able to spread into the Kingdom. In addition, the RAPD-PCR results demonstrated genetic variability between the two species which may be related to the

Silver colloidal nanoparticles: antifungal effect against adhered cells and biofilms of Candida albicans and Candida glabrata.

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Monteiro, D R; Gorup, L F; Silva, S; Negri, M; de Camargo, E R; Oliveira, R; Barbosa, D B; Henriques, M

2011-08-01

The aim of this study was to evaluate the effect of silver nanoparticles (SN) against Candida albicans and Candida glabrata adhered cells and biofilms. SN (average diameter 5 nm) were synthesized by silver nitrate reduction with sodium citrate and stabilized with ammonia. Minimal inhibitory concentration (MIC) tests were performed for C. albicans (n = 2) and C. glabrata (n = 2) grown in suspension following the Clinical Laboratory Standards Institute microbroth dilution method. SN were applied to adhered cells (2 h) or biofilms (48 h) and after 24 h of contact their effect was assessed by enumeration of colony forming units (CFUs) and quantification of total biomass (by crystal violet staining). The MIC results showed that SN were fungicidal against all strains tested at very low concentrations (0.4-3.3 μg ml(-1)). Furthermore, SN were more effective in reducing biofilm biomass when applied to adhered cells (2 h) than to pre-formed biofilms (48 h), with the exception of C. glabrata ATCC, which in both cases showed a reduction ∼90%. Regarding cell viability, SN were highly effective on adhered C. glabrata and respective biofilms. On C. albicans the effect was not so evident but there was also a reduction in the number of viable biofilm cells. In summary, SN may have the potential to be an effective alternative to conventional antifungal agents for future therapies in Candida-associated denture stomatitis.

Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata

DEFF Research Database (Denmark)

Poláková, S.; Blume, C.; Zárate, J. A.

2009-01-01

, Candida glabrata, for their genome structure and stability. This organism has recently become the second most prevalent yeast pathogen in humans. Although the gene sequences were well conserved among different strains, their chromosome structures differed drastically. The most frequent events reshaping...

Ocorrência de linhagens humana e silvestre de Schistosoma mansoni, na pré-amazônia: I - estudo em moluscos Occurrence of wild and human strains of Schistosoma mansoni in lower Amazonia: I - study in moluscs

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Othon de Carvalho Bastos

1982-10-01

Full Text Available Foram isoladas na região da Baixada Maranhense (Brasil, linhagens humana (H e silvestre(S de Schistosoma mansoni a partir de miracídios eclodidos de ovos encontrados em fezes de doentes humanos autóctones da Região e de fígados de roedores silvestres naturalmente infectados. Biomphalaria glabrata, descentes de caramujos coletados no campo, foram expostos, isoladamente, aos miracídios H e S, mantidos isolados em moluscário e observados durante 100 dias. Moluscos normais foram mantidos nas mesmas condições de ambiente em que foram submetidos os infectados e tomados como controle da experiência. Foram anotados os indices de infecção dos moluscos, as datas da eliminação de cercárias, quantidade de larvas eliminadas e mortalidade dos moluscos. Os dados sugeriram melhor adaptação do esquistossomo da linhagem H à B. glabrata. A linhagem S, por sua vez, foi três vezes mais virulenta do que a linhagem H. Estes dados foram comparados com os encontrados na literatura especializada e verificado diversidades nos comportamentos parasitológicos das linhagens em estudo, quando comparados com os encontrados nas linhagens H e S oriundas do Vale do Rio Paraíba do Sul, no Estado de São Paulo (Brasil.The wild (W and human (H strains of Schistosoma mansoni were isolated in the Lowland Region of the Maranhão State (Brazil. The snail progenies from Biomphalaria glabrata collected from that region were exposed to the W miracidia, obtained from livers of wild rodents, and H miracidia from eggs in human stools. A control gruop of normal snails was kept in the same conditions as the infected one. The date of the elimination of cercariae, the quantity of eliminated larvae, the infection index of the moluscs and the mortality rate of the snails were recorded. These data suggested better adaptation of the H strain to B. glabrata. The W strain presented three times more virulence to snails than the H strain. These results were compared with published

Mini-chromosomes among danish Candida glabrata isolates originated through two different mechanisms

DEFF Research Database (Denmark)

Ahmad, K. M.; Ishchuk, O.; Hellborg, L.

2012-01-01

We analyzed 201 strains of the pathogenic yeast Candida glabrata from patients, mainly suffering from systemic infection, at Danish hospitals during 1985 – 1999. Our analysis showed that these strains were closely related but exhibited large karyotype polymorphism. Nine strains contained mini-chr...

Competitive Interactions between C. albicans, C. glabrata and C. krusei during Biofilm Formation and Development of Experimental Candidiasis

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Rossoni, Rodnei Dennis; Barbosa, Júnia Oliveira; Vilela, Simone Furgeri Godinho; dos Santos, Jéssica Diane; de Barros, Patrícia Pimentel; Prata, Márcia Cristina de Azevedo; Anbinder, Ana Lia; Fuchs, Beth Burgwyn; Jorge, Antonio Olavo Cardoso; Mylonakis, Eleftherios; Junqueira, Juliana Campos

2015-01-01

In this study, we evaluated the interactions between Candida albicans, Candida krusei and Candida glabrata in mixed infections. Initially, these interactions were studied in biofilms formed in vitro. CFU/mL values of C. albicans were lower in mixed biofilms when compared to the single biofilms, verifying 77% and 89% of C. albicans reduction when this species was associated with C. glabrata and C. krusei, respectively. After that, we expanded this study for in vivo host models of experimental candidiasis. G. mellonella larvae were inoculated with monotypic and heterotypic Candida suspensions for analysis of survival rate and quantification of fungal cells in the haemolymph. In the groups with single infections, 100% of the larvae died within 18 h after infection with C. albicans. However, interaction groups achieved 100% mortality after 72 h of infection by C. albicans-C. glabrata and 96 h of infection by C. albicans-C. krusei. C. albicans CFU/mL values from larvae hemolymph were lower in the interacting groups compared with the monoespecies group after 12 h of infection. In addition, immunosuppressed mice were also inoculated with monotypic and heterotypic microbial suspensions to induce oral candidiasis. C. albicans CFU/mL values recovered from oral cavity of mice were higher in the group with single infection by C. albicans than the groups with mixed infections by C. albicans-C. glabrata and C. albicans-C. krusei. Moreover, the group with single infection by C. albicans had a higher degree of hyphae and epithelial changes in the tongue dorsum than the groups with mixed infections. We concluded that single infections by C. albicans were more harmful for animal models than mixed infections with non-albicans species, suggesting that C. albicans establish competitive interactions with C. krusei and C. glabrata during biofilm formation and development of experimental candidiasis. PMID:26146832

Competitive Interactions between C. albicans, C. glabrata and C. krusei during Biofilm Formation and Development of Experimental Candidiasis.

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Rossoni, Rodnei Dennis; Barbosa, Júnia Oliveira; Vilela, Simone Furgeri Godinho; dos Santos, Jéssica Diane; de Barros, Patrícia Pimentel; Prata, Márcia Cristina de Azevedo; Anbinder, Ana Lia; Fuchs, Beth Burgwyn; Jorge, Antonio Olavo Cardoso; Mylonakis, Eleftherios; Junqueira, Juliana Campos

2015-01-01

In this study, we evaluated the interactions between Candida albicans, Candida krusei and Candida glabrata in mixed infections. Initially, these interactions were studied in biofilms formed in vitro. CFU/mL values of C. albicans were lower in mixed biofilms when compared to the single biofilms, verifying 77% and 89% of C. albicans reduction when this species was associated with C. glabrata and C. krusei, respectively. After that, we expanded this study for in vivo host models of experimental candidiasis. G. mellonella larvae were inoculated with monotypic and heterotypic Candida suspensions for analysis of survival rate and quantification of fungal cells in the haemolymph. In the groups with single infections, 100% of the larvae died within 18 h after infection with C. albicans. However, interaction groups achieved 100% mortality after 72 h of infection by C. albicans-C. glabrata and 96 h of infection by C. albicans-C. krusei. C. albicans CFU/mL values from larvae hemolymph were lower in the interacting groups compared with the monoespecies group after 12 h of infection. In addition, immunosuppressed mice were also inoculated with monotypic and heterotypic microbial suspensions to induce oral candidiasis. C. albicans CFU/mL values recovered from oral cavity of mice were higher in the group with single infection by C. albicans than the groups with mixed infections by C. albicans-C. glabrata and C. albicans-C. krusei. Moreover, the group with single infection by C. albicans had a higher degree of hyphae and epithelial changes in the tongue dorsum than the groups with mixed infections. We concluded that single infections by C. albicans were more harmful for animal models than mixed infections with non-albicans species, suggesting that C. albicans establish competitive interactions with C. krusei and C. glabrata during biofilm formation and development of experimental candidiasis.

Isolamento genético de populações de caramujos do gênero Biomphalaria

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Aluízio Bezerra Coutinho

1976-08-01

Full Text Available Experiências de intrecruzamento de caramujos do gênero Biomphalaria de várias procedências de Pernambuco, Brasil, utilizando o albinismo como mercador genético mostraram que ocorre na região duas populações isoladas que não se intercruzam. Uma das populações è constituída por caramujos que podem atingir diâmetros de concha até em torno de 30 mm, enquanto que a outra atinge somente em torno de 10 mm mesmo nas melhores condições ambientais.

Chronic vulvovaginal candidiasis: characteristics of women with Candida albicans, C glabrata and no candida.

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Geiger, A M; Foxman, B; Sobel, J D

1995-01-01

INTRODUCTION--Although as many as 5% of all women complain of chronic vulvovaginitis, little is known about these women. They may often be misdiagnosed and the role of vaginal yeast culture in diagnosing vulvovaginal candidiasis (VVC) among them has not been clearly defined. METHODS--To address these deficiencies, we tabulated initial diagnoses among new patients and conducted a medical record-based, unmatched case-control study among women reporting a history of chronic vulvovaginitis (four or more episodes in the past year) at a vulvovaginitis specialty clinic. Clinical presentation and medical history were compared for women who had a positive vaginal yeast culture for either Candida albicans or C glabrata, or who had a negative culture. RESULTS--One-third of the women had no apparent vulvovaginal disease at their initial visit. All women reported similar symptoms, except for an increased prevalence of painful sexual intercourse in women with C albicans (chi 2 p = 0.014 versus women with C glabrata and p vulvovaginitis. Among women with VVC, subtle differences in clinical presentation do not reliably distinguish women with C albicans from those with C glabrata. Our study also indicates that vaginal yeast cultures, while not necessary for every patient, are valuable in confirming negative diagnoses, detecting microscopy false-negatives, and identifying non-C albicans isolates. Images PMID:7490047

Transcriptome

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... Also: Talking Glossary of Genetic Terms Definitions for genetic terms used on this page En Español: Transcriptoma Transcriptome What is a transcriptome? What can a transcriptome tell us? How can transcriptome data be used to explore gene function? What is ...

Studies of radiation gamma effects of 60 Co on fecundity, fertility and survival of Biomphalaria straminea (Dunker, 1848)

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Albuquerque Melo, Ana M.M. de; Motta, Mauricy A. da

1997-01-01

The effects of gamma 60 Co radiation on fecundity, fertility and survival of Biomphalaria straminea was carried out with these mollusks kept in totality reproductive isolation and grouped, for their possible utilization in the study of radiation effect in biological system. Biomphalaria straminea species are disseminated in Brazil, specially in Northeast region. The snails were exposed to the following doses of gamma radiation: 2.5; 5.0; 7.5; 10; 15; 20; 25; 30; 35; 40; 45; 55; 60; 80; 160; 320; and 640 gy source was a Gamma Cell Co model RL (rate dose = 0,31 Gy/min). The fecundity was observed through the count of the spawing abd eggs number/snail/day; the fecundity and fertility when the radiation dose increased; it was evidenced that the grouped mollusks presented a better performance in respectivity when compared with the isolated ones. After the statistical analysis was observed that fercundity and fertility were closely related. The survival, presented higher levels of resistence in isolated mollusks than in grouped ones. The DL50/30 obtained for the isolated mollusks submitted the radiation was about 90 Gy and for the grouped ones 70 Gy. (author). 29 refs., 3 figs., 2 tabs

Molecular Characterization of Brevibacillus laterosporus and Its Potential Use in Biological Control

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de Oliveira, Edmar Justo; Rabinovitch, Leon; Monnerat, Rose Gomes; Passos, Liana Konovaloff Jannotti; Zahner, Viviane

2004-01-01

Thirty-three strains of Brevibacillus laterosporus, including three novel strains isolated from Brazilian soil samples, were examined for genetic variability by the use of different PCR-based methods. Molecular markers that could characterize bacterial strains with regards to their pathogenic potential were investigated. In addition, toxicity was assessed by the use of insects belonging to the orders Lepidoptera and Coleoptera and the mollusk Biomphalaria glabrata. Among the targets tested, Biomphalaria glabrata demonstrated the highest degree of sensitivity to B. laterosporus, with some strains inducing 90 to 100% mortality in snails aged 3 and 12 days posteclosion. Larvae of the coleopteron Anthonomus grandis were also susceptible, presenting mortality levels of between 33 and 63%. Toxicity was also noted towards the lepidopteron Anticarsia gemmatalis. In contrast, no mortality was recorded among test populations of Tenebrio molitor or Spodoptera frugiperda. The application of intergenic transcribed spacer PCR and BOX-PCR generated 15 and 17 different genotypes, respectively. None of the molecular techniques allowed the identification of a convenient marker that was associated with any entomopathogenic phenotype. However, a 1,078-bp amplicon was detected for all strains of B. laterosporus when a primer for amplification of the BOXA1R region was used. Similarly, a 900-bp amplicon was generated from all isolates by use of the primer OPA-11 for randomly amplified polymorphic DNA analysis. These amplicons were not detected for other phenotypically related Brevibacillus species, indicating that they represent markers that are specific for B. laterosporus, which may prove useful for the isolation and identification of new strains of this species. PMID:15528531

Rural tourism as risk factor for the transmission of schistosomiasis in Minas Gerais, Brazil.

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Enk, Martin J; Caldeira, Roberta L; Carvalho, Omar S; Schall, Virginia T

2004-01-01

Recently, the booming rural tourism in endemic areas of the state of Minas Gerais was identified as a contributing factor in the dissemination of the infection with Schistosoma mansoni. This article presents data from six holiday resorts in a rural district approximately 100 km distant from Belo Horizonte, MG, Brazil, where a possibly new and until now unperceived way of transmission was observed. The infection takes place in swimming pools and little ponds, which are offered to tourists and the local population for fishing and leisure activities. The health authorities of the district reported cases of schistosomiasis among the local population after visiting these sites. As individuals of the non-immune middle class parts of the society of big urban centers also frequent these resorts, infection of these persons cannot be excluded. A malacological survey revealed the presence of molluscs of the species Biomphalaria glabrata and Biomphalaria straminea at the resorts. The snails (B. glabrata) of one resort tested positive for S. mansoni. In order to resolve this complex problem a multidisciplinary approach including health education, sanitation measures, assistance to the local health services, and evolvement of the local political authorities, the local community, the tourism association, and the owners of the leisure resorts is necessary. This evidence emphasizes the urgent need for a participative strategic plan to develop the local tourism in an organized and well-administered way. Only so this important source of income for the region can be ensured on the long term without disseminating the disease and putting the health of the visitors at risk.

Interactions between Candida albicans and Candida glabrata in biofilms: Influence of the strain type, culture medium and glucose supplementation.

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Hosida, Thayse Yumi; Cavazana, Thamires Priscila; Henriques, Mariana; Pessan, Juliano Pelim; Delbem, Alberto Carlos Botazzo; Monteiro, Douglas Roberto

2018-04-01

The relationship among Candida species may be influenced by several factors. Thus, this study evaluated the interactions between Candida albicans and Candida glabrata in biofilms, varying the strain type, culture medium and glucose supplementation. Biofilms were formed for 48 hours in Sabouraud dextrose broth (SDB) or RPMI 1640, supplemented with 0%, 1% or 5% glucose. Each strain of C. albicans was combined with two strains of C. glabrata, generating four biofilm associations, which were quantified by colony-forming units (CFUs), total biomass and metabolic activity. Data were analysed by ANOVA and Tukey's HSD test (α = 0.05). For CFUs, all associations were classified as indifferent for biofilms formed in RPMI 1640, while for SDB the interactions were antagonistic for C. albicans and indifferent for C. glabrata. The association of reference strains resulted in a dual-species biofilm with biomass significantly higher than that observed for each single biofilm developed in SDB. The metabolic activity of dual-species biofilms did not significantly differ from that found for single ones, except for co-culture of the reference strains. Glucose supplementation and culture media had a significant influence on all parameters. In conclusion, the strain type, culture medium and glucose supplementation influenced the interactions between C. albicans and C. glabrata. © 2017 Blackwell Verlag GmbH.

Candida glabrata tryptophan-based pigment production via the Ehrlich pathway.

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Brunke, Sascha; Seider, Katja; Almeida, Ricardo Sergio; Heyken, Antje; Fleck, Christian Benjamin; Brock, Matthias; Barz, Dagmar; Rupp, Steffen; Hube, Bernhard

2010-04-01

Pigments contribute to the pathogenicity of many fungi, mainly by protecting fungal cells from host defence activities. Here, we have dissected the biosynthetic pathway of a tryptophan-derived pigment of the human pathogen Candida glabrata, identified key genes involved in pigment production and have begun to elucidate the possible biological function of the pigment. Using transcriptional analyses and a transposon insertion library, we have identified genes associated with pigment production. Targeted deletion mutants revealed that the pigment is a by-product of the Ehrlich pathway of tryptophan degradation: a mutant lacking a tryptophan-upregulated aromatic aminotransferase (Aro8) displayed significantly reduced pigmentation and a recombinantly expressed version of this protein was sufficient for pigment production in vitro. Pigment production is tightly regulated as the synthesis is affected by the presence of alternative nitrogen sources, carbon sources, cyclic AMP and oxygen. Growth of C. glabrata on pigment inducing medium leads to an increased resistance to hydrogen peroxide, an effect which was not observed with a mutant defective in pigmentation. Furthermore, pigmented yeast cells had a higher survival rate when exposed to human neutrophils and caused increased damage in a monolayer model of human epithelia, indicating a possible role of pigmentation during interactions with host cells.

Discriminative power of fatty acid methyl ester (FAME) analysis using the microbial identification system (MIS) for Candida (Torulopsis) glabrata and Saccharomyces cerevisiae.

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Peltroche-Llacsahuanga, H; Schmidt, S; Lütticken, R; Haase, G

2000-12-01

Candida (Torulopsis) glabrata is frequently isolated in cases of fungal infection and commonly shows acquired or innate fluconazole resistance. Saccharomyces cerevisiae, an emerging opportunistic yeast pathogen, causes serious systemic infections in immunocompromised, and vaginitis and superficial infections in immunocompetent patients. For both species reliable identification in the routine laboratory is mandatory, but species identification of strains, e.g. trehalose-negative C. glabrata, may be difficult. Therefore, gas-liquid chromatography (GLC) of whole cell fatty acid methyl ester (FAME) profiles, that is independent of assimilation profiles of strains and suitable for reliable and rapid identification of clinically important yeasts, was applied. However, frequent misidentification of C. glabrata as S. cerevisiae has been reported when using the Yeast Clinical Database of MIS. Accuracy of MIS identification may be strongly influenced by the amounts of cell mass analyzed. Therefore, the present study compared the MIS results of these two yeasts achieved with different cell masses. Primarily we optimized, especially with respect to cost-effectiveness, the recommended streaking technique yielding a maximal recovery of 90-130 mg of cell mass from one plate, enabling testing of poor growing strains of C. glabrata. For all C. glabrata strains tested (n = 10) the highest identification scores (SI [Similarity Index] range 0.525-0.963, median 0.832) were achieved with 30 to 45 mg of cell mass. Only 5 of 10 S. cerevisiae strains revealed good library comparisons (SI > or = 0.5) when using 30 mg of cell mass, whereas with 45 mg all strains but two revealed this SI-level. For S. cerevisiae a higher amount of cell mass processed (up to 90 mg) was correlated with better identification scores (SI range using 90 mg: 0.464-0.870, median, 0.737). Several passages prior to FAME analysis of C. glabrata strains on recommended media revealed narrowing of SI ranges, but

Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae determined by a polymerase chain reaction-restriction fragment length polymorphism

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Caldeira Roberta Lima

1998-01-01

Full Text Available The freshwater snails Biomphalaria straminea, B. intermedia, B. kuhniana and B. peregrina, are morphologically similar; based on this similarity the first three species were therefore grouped in the complex B. straminea. The morphological identification of these species is based on characters such as vaginal wrinkling, relation between prepuce: penial sheath:deferens vas and number of muscle layers in the penis wall. In this study the polymerase chain reaction restriction fragment length polymorphism technique was used for molecular identification of these molluscs. This technique is based on the amplification of the internal transcribed spacer regions ITS1 e ITS2 of the ribosomal RNA gene and subsequent digestion of these fragments by restriction enzymes. Six enzymes were tested: Dde I, Mnl I, Hae III, Rsa I, Hpa II e Alu I. The restriction patterns obtained with DdeI presented the best profile for separation of the four species of Biomphalaria. The profiles obtained with all the enzymes were used to estimate the genetic distances among the species through analysis of common banding patterns.

Differentiation of Candida albicans, Candida glabrata, and Candida krusei by FT-IR and chemometrics by CHROMagar™ Candida.

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Wohlmeister, Denise; Vianna, Débora Renz Barreto; Helfer, Virginia Etges; Calil, Luciane Noal; Buffon, Andréia; Fuentefria, Alexandre Meneghello; Corbellini, Valeriano Antonio; Pilger, Diogo André

2017-10-01

Pathogenic Candida species are detected in clinical infections. CHROMagar™ is a phenotypical method used to identify Candida species, although it has limitations, which indicates the need for more sensitive and specific techniques. Infrared Spectroscopy (FT-IR) is an analytical vibrational technique used to identify patterns of metabolic fingerprint of biological matrixes, particularly whole microbial cell systems as Candida sp. in association of classificatory chemometrics algorithms. On the other hand, Soft Independent Modeling by Class Analogy (SIMCA) is one of the typical algorithms still little employed in microbiological classification. This study demonstrates the applicability of the FT-IR-technique by specular reflectance associated with SIMCA to discriminate Candida species isolated from vaginal discharges and grown on CHROMagar™. The differences in spectra of C. albicans, C. glabrata and C. krusei were suitable for use in the discrimination of these species, which was observed by PCA. Then, a SIMCA model was constructed with standard samples of three species and using the spectral region of 1792-1561cm -1 . All samples (n=48) were properly classified based on the chromogenic method using CHROMagar™ Candida. In total, 93.4% (n=45) of the samples were correctly and unambiguously classified (Class I). Two samples of C. albicans were classified correctly, though these could have been C. glabrata (Class II). Also, one C. glabrata sample could have been classified as C. krusei (Class II). Concerning these three samples, one triplicate of each was included in Class II and two in Class I. Therefore, FT-IR associated with SIMCA can be used to identify samples of C. albicans, C. glabrata, and C. krusei grown in CHROMagar™ Candida aiming to improve clinical applications of this technique. Copyright © 2017 Elsevier B.V. All rights reserved.

Candida species isolated from different body sites and their antifungal susceptibility pattern: Cross-analysis of Candida albicans and Candida glabrata biofilms.

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Cataldi, Valentina; Di Campli, Emanuela; Fazii, Paolo; Traini, Tonino; Cellini, Luigina; Di Giulio, Mara

2017-08-01

Candida species are regular commensal in humans, but-especially in immunocompromised patients-they represent opportunistic pathogens giving rise to systemic infection. The aim of the present work was to isolate and characterize for their antifungal profile Candida species from different body sites and to analyze the biofilms produced by C. albicans and C. glabrata isolates. Eighty-one strains of Candida species from 77 patients were identified. Epidemiological study showed that the most isolated species were C. albicans (44), C. glabrata (13) and C. parapsilosis (13) mainly from Hematology, Infectious Diseases, Medicine, Neonatology and Oncology Divisions, the majority of the biological samples were swabs (44) and blood cultures (16). The analysis of the biofilm formation was performed at 24 and 48-hours comparing resistant and susceptible strains of C. albicans to resistant and susceptible strains of C. glabrata. Candida albicans has a greater ability to form biofilm compared to C. glabrata, both in the susceptible and resistant strains reaching maturity after 24 hours with a complex structure composed of blastospores, pseudohyphae, and hyphae embedded in a matrix. On the contrary, C. glabrata biofilm was composed exclusively of blastospores that in the resistant strain, after 24 hours, were organized in a compact multilayer different to the discontinuous structure observed in the susceptible analyzed strains. In conclusion, the increasing of the incidence of Candida species infection together with their emerging drug resistance also related to the biofilm forming capability underline the need to monitor their distribution and susceptibility patterns for improving the surveillance and for a correct management of the infection. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Inheritance of Schistosoma mansoni infection incompatibility in Biomphalaria alexandrina snails

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Iman F Abou El Naga

2010-03-01

Full Text Available In this study, we looked at the inheritance of susceptibility and resistance to Schistosoma mansoni infection in the first generation of crossbred Biomphalaria alexandrina snails. Our ultimate goal is to use such information to develop a biological method of controlling schistosomiasis. We infected laboratory-bred snails with S. mansoni miracidia and examined cercarial shedding to determine susceptibility and resistance. Five parental groups were used: Group I contained 30 susceptible snails, Group II contained 30 resistant snails, Group III contained 15 susceptible and 15 resistant snails, Group IV contained 27 susceptible and three resistant snails and Group V contained three susceptible and 27 resistant snails. The percentage of resistant snails in the resulting progeny varied according to the ratio of susceptible and resistant parents per group; they are 7%, 100%, 68%, 45% and 97% from Groups I, II, III, IV and V, respectively. On increasing the percentage of resistant parent snails, the percentage of resistant progeny increased, while cercarial production in their susceptible progeny decreased.

Antiestrogenic constituents of the Thai medicinal plants Capparis flavicans and Vitex glabrata.

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Luecha, Prathan; Umehara, Kaoru; Miyase, Toshio; Noguchi, Hiroshi

2009-11-01

Antiestrogenic compounds were investigated from Thai indigenous plants for galactogogues since estrogen is reported to suppress lactation in breastfeeding women. The aerial parts of the Thai medicinal plant Capparis flavicans, which has traditionally been used to promote lactation, gave the new compound capparoside A (1), along with 28 known compounds. The leaves of Vitex glabrata belong to the same genus as the chaste tree (Vitex agnus-castus), which is used traditionally to support lactation, and afforded the new compounds khainaoside A (14), khainaoside B (15), and khainaoside C (16), together with six known compounds. The isolates were tested for their biological activity using the estrogen-responsive human breast cancer cell lines MCF-7 and T47D. Syringaresinol (3) and principin (6), from C. flavicans, and khainaoside A (14) showed the most potent inhibitory effects on estrogen-enhanced cell proliferation among all compounds isolated. These results suggest that the lactation-promoting properties of C. flavicans might be related to the inhibitory effect on excess estrogen of women who experience insufficient breastfeeding and highlight the possibility of using V. glabrata leaves for their antiestrogenic properties.

Relação entre a patogenicidade do Schistoma mansoni em camundongos e a susceptibilidade do molusco vetor: II. Número de ovos nas fezes e número e tamanho dos granulomas nas vísceras Relationship between the pathogenicity of Schistoma mansoni in mice and the susceptibility of the vector mollusc: II. Number of eggs in the feces and number and size of granulomas in the visceras

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Eliana Maria Zanotti-Magalhães

1993-12-01

Full Text Available Estudou-se a influência da susceptibilidade de moluscos vetores do S. mansoni no desenvolvimento da patogenicidade do trematódeo no hospedeiro definitivo. Foram utilizadas progênies de moluscos Biomphalaria tenagophila e Biomphalaria glabrata selecionadas para o caráter susceptibilidade ao S. mansoni das linhagens SJ e BH, respectivamente. Cercárias oriundas das gerações P, F1 F2, F3 e F4 foram usadas para a infecção de camundongos Swiss, que foram sacrificados oito semanas após a exposição às larvas. Por esta ocasião verificou-se o número de ovos nas fezes e o número de granulomas no fígado, baço e intestino. Avaliou-se também o tamanho das reações granulomatosas nestas vísceras. Concluiu-se que a maior susceptibilidade de B. tenagophila induziu a uma maior eliminação de ovos do parasita nas fezes. Verificou-se maior número de granulomas por área de tecido hepático em roedores infectados com cercárias oriundas de moluscos mais susceptíveis. Nos mesmos roedores, constatou-se relação inversa entre a área dos granulomas esplênicos, hepáticos e intestinais e a taxa de infecção dos moluscos que forneceram as cercárias para a infecção dos camundongos.The influence of the susceptibility of the vector snails of S. mansoni on the development of the pathogenicity of the worm to the host was studied. Off-spring of snails Biomphalaria glabrata and Biomphalaria tenagophila were used, selected with regard to the susceptibility to S. mansoni of the strains BH and SJ trait, respectively. Parenteral, F1,F2, F3 and F4 generation cercariae were used for the infection of Swiss mice, which were killed eight weeks after infection. The number of eggs in the feces and the number of granulomas in the liver, spleen and intestines were counted. The size of the granulomatous reactions was evaluated. The results led to the conclusion that greater susceptibility of B. tenagophila was associated with a larger egg production in the feces

Estudos preliminares com bromoacetamida, um novo moluscicida

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Naftale Katz

1985-09-01

Full Text Available A bromoacetamida tem sido testada como moluscicida na República Popular da China, para tratamento de criadouros de Oncomelania, hospedeiro do Schistosoma japonicum, com bons resultados. O produto é solúvel em água, o que simplifica seu uso. Foram feitos ensaios biológicos preliminares deste produto em caramujos adultos (Biomphalaria glabrata, B. tenagophila e B. straminea, recém-eclodidos e desovas. Paralelamente foram feitos ensaios com o pentaclorofenol para avaliar a suscetibilidade dos caramujos. O produto foi testado também sobre peixes, Lebistes reticulatus. Os moluscos testados mediam 8-10 mm de diâmetro; os recém-eclodidos tinham 1-3 dias de idade e as desovas 0-1 dia de idade. A temperatura da água durante os experimentos variou de 24,3 a 27,0°C. O produto foi ativo para caramujos adultos, recém-eclodidos e desovas, em concentrações em tomo de 1 a 4 ppm. Para os peixes o produto foi menos tóxico do que para os caramujos (CLço 7,5 ppm. Estes resultados indicam que a bromoacetamida apresenta propriedades moluscicidas promissoras para o controle da Biomphalaria spp.Bromocetamide has been tested as molluscicide, with good results, in the People's Republic of China, on Oncomelania, host of Schistosoma japonicum. We have conducted preliminary assays with bromoacetamide on adult snails (B. glabrata, B. tenagophila and B. straminea, newly hatched smails and egg-masses. This product has been also tested on fishes (Lebistes reticulatus. Comparative assays have been made with pentaclorophenol to evaluate the suceptibility of the snails. Snails tested had a diameter of 8-10 mm; the newly hatched were 1-3 days old and the eggs-masses. 0-1 day old. The temperature of the water varied from 24.3 to 27.5° C. Bromoacetamide was active on adult and newly hatched snails and egg-masses, in concentrations from 1-4ppm. The product was less toxic for jish (LC90 = 7,5 ppm. These results indicate that bromoacetamide has promising molluscicide

Bird attributes, plant characteristics, and seed dispersal of Pera glabrata (Schott, 1858), (Euphorbiaceae) in a disturbed cerrado area.

Science.gov (United States)

Francisco, M R; Lunardi, V O; Galetti, M

2007-11-01

Several plant characteristics, such as fruit production, nutrient reward, secondary compounds, and fruit color display, affect fruit choice by birds. On the other hand, several bird attributes affect their efficiency as dispersers. Here we investigate the ornithochoric seed dispersal of Pera glabrata Schott (Euphorbiaceae) in a cerrado fragment in southeastern Brazil. A set of bird attributes, such as frequency of visits, number of diaspores eaten, time spent foraging, methods of taking and handling the diaspores and agonistic interactions were analyzed in order to infer about the potential of each species to act as a seed disperser. Birds were the unique seed dispersers of these oil-rich diaspores. We observed 414 bird visits during 60 hours of focal observations in five trees from December 1999 to January 2000. Twenty bird species from seven families ate the diaspores of P. glabrata, but only 14 species were considered potential seed dispersers because they swallowed the diaspores, increasing the probabilities for the seeds to be defecated and/or regurgitated away from the parent trees. The main potential seed dispersers were: Turdus leucomelas (Muscicapidae), Dacnis cayana (Emberizidae), Colaptes melanochloros (Picidae) and Elaenia spp. (Tyrannidae). We did not find any significant seasonal change in the number of visits on the fruiting trees throughout the day. We also did not find any relation between the number of visits per tree and fruit production. The most effective seed dispersers of P. glabrata were generalist birds, which have a high visiting rate, high fruit consumption rate, and spend short periods on the plants. The large number of species recorded as potential seed dispersers of P. glabrata, being most of them very abundant even in Brazilian disturbed areas, may guarantee seed dispersal of this plant in small fragments and regenerating areas.

Biological screening of Brazilian medicinal plants

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Tânia Maria de Almeida Alves

2000-06-01

Full Text Available In this study, we screened sixty medicinal plant species from the Brazilian savanna ("cerrado" that could contain useful compounds for the control of tropical diseases. The plant selection was based on existing ethnobotanic information and interviews with local healers. Plant extracts were screened for: (a molluscicidal activity against Biomphalaria glabrata, (b toxicity to brine shrimp (Artemia salina L., (c antifungal activity in the bioautographic assay with Cladosporium sphaerospermum and (d antibacterial activity in the agar diffusion assay against Staphylococcus aureus, Escherichia coli, Bacillus cereus and Pseudomonas aeruginosa. Forty-two species afforded extracts that showed some degree of activity in one or more of these bioassays.

Endogenous growth factor stimulation of hemocyte proliferation induces resistance to Schistosoma mansoni challenge in the snail host.

Science.gov (United States)

Pila, Emmanuel A; Gordy, Michelle A; Phillips, Valerie K; Kabore, Alethe L; Rudko, Sydney P; Hanington, Patrick C

2016-05-10

Digenean trematodes are a large, complex group of parasitic flatworms that infect an incredible diversity of organisms, including humans. Larval development of most digeneans takes place within a snail (Gastropoda). Compatibility between snails and digeneans is often very specific, such that suitable snail hosts define the geographical ranges of diseases caused by these worms. The immune cells (hemocytes) of a snail are sentinels that act as a crucial barrier to infection by larval digeneans. Hemocytes coordinate a robust and specific immunological response, participating directly in parasite killing by encapsulating and clearing the infection. Hemocyte proliferation and differentiation are influenced by unknown digenean-specific exogenous factors. However, we know nothing about the endogenous control of hemocyte development in any gastropod model. Here, we identify and functionally characterize a progranulin [Biomphalaria glabrata granulin (BgGRN)] from the snail B. glabrata, a natural host for the human blood fluke Schistosoma mansoni Granulins are growth factors that drive proliferation of immune cells in organisms, spanning the animal kingdom. We demonstrate that BgGRN induces proliferation of B. glabrata hemocytes, and specifically drives the production of an adherent hemocyte subset that participates centrally in the anti-digenean defense response. Additionally, we demonstrate that susceptible B. glabrata snails can be made resistant to infection with S. mansoni by first inducing hemocyte proliferation with BgGRN. This marks the functional characterization of an endogenous growth factor of a gastropod mollusc, and provides direct evidence of gain of resistance in a snail-digenean infection model using a defined factor to induce snail resistance to infection.

Further studies on the molecular systematics of Biomphalaria snails from Brazil

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Teofânia HDA Vidigal

2000-01-01

Full Text Available The polymerase chain reaction and restriction fragment length polymorphism (RFLP of the internal transcribed spacer (ITS region of the rRNA gene, using the enzyme DdeI were used for the molecular identification of ten species and one subspecies of Brazilian Biomphalaria. Emphasis is given to the analysis of B. oligoza, B. schrammi and B. amazonica. The RFLP profiles obtained using this enzyme were highly distinctive for the majority of the species and exhibited low levels of intraspecific polymorphism among specimens from different regions of Brazil. However, B. peregrina and B. oligoza presented very similar profiles that complicated their identification at the molecular level and suggested a very close genetic similarity between the two species. Others enzymes including HaeIII, HpaII, AluI and MnlI were tested for their ability to differentiate these species. For B. amazonica three variant profiles produced with DdeI were observed. The study demonstrated that the ITS contains useful genetic markers for the identification of these snails

Rapid Discrimination between Candida glabrata, Candida nivariensis, and Candida bracarensis by Use of a Singleplex PCR ▿

OpenAIRE

Enache-Angoulvant, A.; Guitard, J.; Grenouillet, F.; Martin, T.; Durrens, P.; Fairhead, C.; Hennequin, C.

2011-01-01

We report here a PCR-based assay using a single primer pair targeting the RPL31 gene that allows discrimination between Candida glabrata, Candida bracarensis, and Candida nivariensis according to the size of the generated amplicon.

Time to positivity and detection of growth in anaerobic blood culture vials predict the presence of Candida glabrata in candidemia: a two-center European cohort study.

Science.gov (United States)

Cobos-Trigueros, Nazaret; Kaasch, Achim J; Soriano, Alex; Torres, Jorge-Luis; Vergara, Andrea; Morata, Laura; Zboromyrska, Yuliya; De La Calle, Cristina; Alejo, Izaskun; Hernández, Cristina; Cardozo, Celia; Marco, Franscesc; Del Río, Ana; Almela, Manel; Mensa, Josep; Martínez, José Antonio

2014-08-01

This study shows the accuracy of exclusive or earlier growth in anaerobic vials to predict Candida glabrata in a large series of candidemic patients from two European hospitals using the Bactec 9240 system. Alternatively, C. glabrata can be predicted by a time to positivity cutoff value, which should be determined for each setting. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Estudos preliminares com bromoacetamida, um novo moluscicida

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Naftale Katz

1985-09-01

Full Text Available A bromoacetamida tem sido testada como moluscicida na República Popular da China, para tratamento de criadouros de Oncomelania, hospedeiro do Schistosoma japonicum, com bons resultados. O produto é solúvel em água, o que simplifica seu uso. Foram feitos ensaios biológicos preliminares deste produto em caramujos adultos (Biomphalaria glabrata, B. tenagophila e B. straminea, recém-eclodidos e desovas. Paralelamente foram feitos ensaios com o pentaclorofenol para avaliar a suscetibilidade dos caramujos. O produto foi testado também sobre peixes, Lebistes reticulatus. Os moluscos testados mediam 8-10 mm de diâmetro; os recém-eclodidos tinham 1-3 dias de idade e as desovas 0-1 dia de idade. A temperatura da água durante os experimentos variou de 24,3 a 27,0°C. O produto foi ativo para caramujos adultos, recém-eclodidos e desovas, em concentrações em tomo de 1 a 4 ppm. Para os peixes o produto foi menos tóxico do que para os caramujos (CLço 7,5 ppm. Estes resultados indicam que a bromoacetamida apresenta propriedades moluscicidas promissoras para o controle da Biomphalaria spp.

Compatibilidad entre nueve cepas de Biomphalaria glabrata de áreas endémicas y no endémicas y una cepa de Schistosoma mansoni venezolanas

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Pino Luz A.

1999-01-01

Full Text Available Se infectaron experimentalmente 9 lotes de 32 caracoles B. glabrata (de 5 a 7mm de diámetro con miracidios de la cepa C5 de Schistosoma mansoni a razón de 5 miracidios por caracol, pertenecientes a las siguientes cepas: En el área endémica de transmisión de Esquistosomiasis mansoni a Sector Puerta Negra, Lago Valencia, b Cagua c Ingenio Bolívar (Estado Aragua d Mariara e Caserío El 25 f Güigüe (Estado Carabobo. Fuera del área endémica de transmisión g Anzoátegui (Estado Lara, h Chabasquén (Estado Portuguesa, i Sector La Elvira, Caripe (Estado Monagas. El período prepatente intramolusco, osciló entre 23 y 25 días, para las 9 cepas evaluadas. La duración total de la infección fue muy variable desde 20 días para la cepa Chabasquén, hasta 93 días para la de Güigüe.La producción total promedio de cercarias al tercer día de iniciada la emisión varió desde X = 74,4 para la cepa de Mariara, hasta X = 591,7 para la cepa de Chabasquén. Se evidenció la existencia de diferencias estadísticamente significativas (H = 97,4, P < 0,05 en la producción total de cercarias al tercer día de iniciada la emisión, detectándose diferencias estadísticamente significativas para casi todas las 36 combinaciones, excepto para las cuatro siguientes: Mariara/Ingenio Bolívar, Cagua/Caserío El 25, Lago de Valencia/Güigüe y Güigüe/Caripe.En lo que respecta al porcentaje de caracoles que presentaron cura espontánea, los valores mas elevados se obtuvieron en las cepas del Lago de Valencia (88,8%, Cagua (85,2%, Chabasquén (82,6%, Caripe (82,6% y Anzoátegui (80%. Mientras que el porcentaje mas bajo se obtuvo para la cepa de Güigüe (21,4%.

Potassium Uptake Mediated by Trk1 Is Crucial for Candida glabrata Growth and Fitness

Czech Academy of Sciences Publication Activity Database

Llopis-Torregrosa, Vincent; Hušeková, Barbora; Sychrová, Hana

2016-01-01

Roč. 11, č. 4 (2016), e0153374 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GAP302/12/1151; GA ČR(CZ) GA16-03398S EU Projects: European Commission(XE) 606786 - ImResFun Institutional support: RVO:67985823 Keywords : Candida glabrata * potassium uptake * Trk1 protein Subject RIV: EE - Microbiology, Virology Impact factor: 2.806, year: 2016

The Effectiveness of Voriconazole in Therapy of Candida glabrata's Biofilms Oral Infections and Its Influence on the Matrix Composition and Gene Expression.

Science.gov (United States)

Rodrigues, Célia F; Gonçalves, Bruna; Rodrigues, Maria Elisa; Silva, Sónia; Azeredo, Joana; Henriques, Mariana

2017-08-01

Candida glabrata is one of most prevalent yeast in fungal infections, especially in immunocompromised patients. Its azole resistance results in a low therapeutic response, particularly when associated with biofilms. The main goal of this work was to study the effectiveness of voriconazole (Vcz) against C. glabrata biofilms oral pathologies, as esophageal or oropharyngeal candidiasis. Antifungal susceptibilities were determined in pre-formed 24-h-biofilms and ERG genes expression was determined by qRT-PCR. Protein quantification was performed using BCA ® Kit, carbohydrate was estimated according to the Dubois assay and β-1,3 glucans concentration were determined using Glucatell ® kit. Finally, ergosterol, Vcz, and fluconazole (Flu) concentrations within the biofilm matrices were determined by RP-HPLC. Results showed that C. glabrata biofilms were more susceptible to Vcz than to Flu and that ERG genes expression evidenced an overexpression of the three ERG genes in the presence of both azoles. The matrix content presented a remarked decrease in proteins and an increase in carbohydrates, namely β-1,3 glucans. Ergosterol was successfully detected and quantified in the biofilm matrices, with no differences in all the considered conditions. Vcz demonstrated better diffusion through the biofilms and better cell penetration capacities, than Flu, indicating that the structure of the drug molecule fully influences its dissemination through the biofilm matrices. This work showed that Vcz is notably more effective than Flu for the treatment of resistant C. glabrata oral biofilms, which demonstrates a clinical relevance in its future use for the treatment of oropharyngeal/esophageal candidiasis caused by this species.

Reversal of fluconazole resistance induced by a synergistic effect with Acca sellowiana in Candida glabrata strains.

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R M Machado, Gabriella da; Pippi, Bruna; Dalla Lana, Daiane Flores; Amaral, Ana Paula S; Teixeira, Mário Lettieri; Souza, Kellen C B de; Fuentefria, Alexandre M

2016-11-01

The increased incidence of non-albicans Candida (NAC) resistant to fluconazole (FLZ) makes it necessary to use new therapeutic alternatives. Acca sellowiana (O.berg) Burret (Myrtaceae) is a guava with several proven biological activities. The interaction with fluconazole can be a feasible alternative to overcome this resistance. This study evaluates the in vitro antifungal activity of fractions obtained from the lyophilized aqueous extract of the leaves of A. sellowiana against resistant strains of NAC. The antifungal activity of the fractions was evaluated at 500 μg/mL by microdilution method. Checkerboard assay was performed to determine the effect of the combination of the F2 fraction and antifungal at concentrations: MIC/4, MIC/2, MIC, MIC × 2 and MIC × 4. Candida glabrata showed the lowest MIC values (500-3.90 μg/mL) and the F2 active fraction was the most effective. The association of F2 with FLZ showed a strong synergistic effect (FICI ≤ 0.5) against 100% of C. glabrata resistant isolates. Moreover, the F2 active fraction has demonstrated that probably acts in the cell wall of these yeasts. There was no observed acute dermal toxicity of lyophilized aqueous extract of leaves of A. sellowiana on pig ear skin cells. The interaction between substances present in the F2 active fraction is possibly responsible for the antifungal activity presented by this fraction. This study is unprecedented and suggests that the combination of F2 active fraction and FLZ might be used as an alternative treatment for mucocutaneus infections caused by C. glabrata resistant.

Enhanced oxidative killing of azole-resistant Candida glabrata strains with ERG11 deletion.

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Kan, V L; Geber, A; Bennett, J E

1996-01-01

The susceptibility of genetically defined Candida glabrata strains to killing by H2O2 and neutrophils was assessed. Fluconazole-susceptible L5L and L5D strains demonstrated survival rates higher than those of two fluconazole-resistant strains lacking the ERG11 gene coding for 14 alpha-demethylase. Fluconazole resistance can occur by mechanisms which increase fungal susceptibility to oxidative killing by H2O2 and neutrophils. PMID:8807069

One small step for a yeast--microevolution within macrophages renders Candida glabrata hypervirulent due to a single point mutation.

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Sascha Brunke

2014-10-01

Full Text Available Candida glabrata is one of the most common causes of candidemia, a life-threatening, systemic fungal infection, and is surpassed in frequency only by Candida albicans. Major factors contributing to the success of this opportunistic pathogen include its ability to readily acquire resistance to antifungals and to colonize and adapt to many different niches in the human body. Here we addressed the flexibility and adaptability of C. glabrata during interaction with macrophages with a serial passage approach. Continuous co-incubation of C. glabrata with a murine macrophage cell line for over six months resulted in a striking alteration in fungal morphology: The growth form changed from typical spherical yeasts to pseudohyphae-like structures - a phenotype which was stable over several generations without any selective pressure. Transmission electron microscopy and FACS analyses showed that the filamentous-like morphology was accompanied by changes in cell wall architecture. This altered growth form permitted faster escape from macrophages and increased damage of macrophages. In addition, the evolved strain (Evo showed transiently increased virulence in a systemic mouse infection model, which correlated with increased organ-specific fungal burden and inflammatory response (TNFα and IL-6 in the brain. Similarly, the Evo mutant significantly increased TNFα production in the brain on day 2, which is mirrored in macrophages confronted with the Evo mutant, but not with the parental wild type. Whole genome sequencing of the Evo strain, genetic analyses, targeted gene disruption and a reverse microevolution experiment revealed a single nucleotide exchange in the chitin synthase-encoding CHS2 gene as the sole basis for this phenotypic alteration. A targeted CHS2 mutant with the same SNP showed similar phenotypes as the Evo strain under all experimental conditions tested. These results indicate that microevolutionary processes in host-simulative conditions

SNF3 as high affinity glucose sensor and its function in supporting the viability of Candida glabrata under glucose-limited environment

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Tzu Shan eNg

2015-12-01

Full Text Available Candida glabrata is an emerging human fungal pathogen that has efficacious nutrient sensing and responsiveness ability. It can be seen through its ability to thrive in diverse range of nutrient limited-human anatomical sites. Therefore, nutrient sensing particularly glucose sensing is thought to be crucial in contributing to the development and fitness of the pathogen. This study aimed to elucidate the role of SNF3 (Sucrose Non Fermenting 3 as a glucose sensor and its possible role in contributing to the fitness and survivability of C. glabrata in glucose-limited environment. The SNF3 knockout strain was constructed and subjected to different glucose concentrations to evaluate its growth, biofilm formation, amphotericin B susceptibility, ex vivo survivability and effects on the transcriptional profiling of the sugar receptor repressor (SRR pathway-related genes. The SNF3Δ strain showed a retarded growth in low glucose environments (0.01% and 0.1% in both fermentation and respiration-preferred conditions but grew well in high glucose concentration environments (1% and 2%. It was also found to be more susceptible to amphotericin B in low glucose environment (0.1% and macrophage engulfment but showed no difference in the biofilm formation capability. The deletion of SNF3 also resulted in the down-regulation of about half of hexose transporters genes (4 out of 9. Overall, the deletion of SNF3 causes significant reduction in the ability of C. glabrata to sense limited surrounding glucose and consequently disrupts its competency to transport and perform the uptake of this critical nutrient. This study highlighted the role of SNF3 as a high affinity glucose sensor and its role in aiding the survivability of C. glabrata particularly in glucose limited environment.

Next-generation transcriptome assembly

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey A.; Wang, Zhong

2011-09-01

Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

New polymeric formulation for control of biomphalaria Alexandria based on pharmaceutical waste gelatin

International Nuclear Information System (INIS)

Kenawy, E.; El-Maghraby, A.

2005-01-01

In the recent years, important new areas of application for plastics have emerged in medicine such as devices for the controlled release of drugs. The increases in the use of plastic materials in all sectors of industry have led to a continuous increase in the generation of plastic wastes. Recycling allow the waste to be reintroduced into the consumption cycle. Pharmaceutical companies which manufacture soft gels with different shapes, sizes and colors based mainly on gelatin formulations produce huge amount of gelatin waste. Schistosomiasis is one of the most important public health problems in our country. We now report the utilization of gelatin scrap by incorporating them in biodegradable films containing the molluscicide niclosamide for control of Biomphalaria Alexandrina snails. The preparation of the gelatin films will be described. The release of niclosamide from the prepared blends was investigated. The prepared formulations proved to be useful compared with free niclosamide

Fluconazole Resistance Associated with Drug Efflux and Increased Transcription of a Drug Transporter Gene, PDH1, in Candida glabrata

Science.gov (United States)

Miyazaki, Haruko; Miyazaki, Yoshitsugu; Geber, Antonia; Parkinson, Tanya; Hitchcock, Christopher; Falconer, Derek J.; Ward, Douglas J.; Marsden, Katherine; Bennett, John E.

1998-01-01

Sequential Candida glabrata isolates were obtained from the mouth of a patient infected with human immunodeficiency virus type 1 who was receiving high doses of fluconazole for oropharyngeal thrush. Fluconazole-susceptible colonies were replaced by resistant colonies that exhibited both increased fluconazole efflux and increased transcripts of a gene which codes for a protein with 72.5% identity to Pdr5p, an ABC multidrug transporter in Saccharomyces cerevisiae. The deduced protein had a molecular mass of 175 kDa and was composed of two homologous halves, each with six putative transmembrane domains and highly conserved sequences of ATP-binding domains. When the earliest and most azole-susceptible isolate of C. glabrata from this patient was exposed to fluconazole, increased transcripts of the PDR5 homolog appeared, linking azole exposure to regulation of this gene. PMID:9661006

FKS2 Mutations Associated with Decreased Echinocandin Susceptibility of Candida glabrata following Anidulafungin Therapy

OpenAIRE

Costa-de-Oliveira, Sofia; Miranda, Isabel Marcos; Silva, Raquel M.; Pinto e Silva, Ana; Rocha, Rita; Amorim, Antonio; Rodrigues, Acacio Goncalves; Pina-Vaz, Cidalia

2011-01-01

This is the first case report of Candida glabrata-disseminated candidiasis describing the acquisition of echinocandin resistance following anidulafungin treatment. The initial isolates recovered were susceptible to echinocandins. However, during 27 days of anidulafungin treatment, two resistant strains were isolated (from the blood and peritoneal fluid). The resistant peritoneal fluid isolate exhibited a Ser663Pro mutation in position 1987 of FKS2 HS1 (hot spot 1), whereas the resistant blood...

[Comparison of microdilution and disk diffusion methods for the detection of fluconazole and voriconazole susceptibility against clinical Candida glabrata isolates and determination of changing susceptibility with new CLSI breakpoints].

Science.gov (United States)

Hazırolan, Gülşen; Sarıbaş, Zeynep; Arıkan Akdağlı, Sevtap

2016-07-01

Candida albicans is the most frequently isolated species as the causative agent of Candida infections. However, in recent years, the isolation rate of non-albicans Candida species have increased. In many centers, Candida glabrata is one of the commonly isolated non-albicans species of C.glabrata infections which are difficult-to-treat due to decreased susceptibility to fluconazole and cross-resistance to other azoles. The aims of this study were to determine the in vitro susceptibility profiles of clinical C.glabrata isolates against fluconazole and voriconazole by microdilution and disk diffusion methods and to evaluate the results with both the previous (CLSI) and current species-specific CLSI (Clinical and Laboratory Standards Institute) clinical breakpoints. A total of 70 C.glabrata strains isolated from clinical samples were included in the study. The identification of the isolates was performed by morphologic examination on cornmeal Tween 80 agar and assimilation profiles obtained by using ID32C (BioMérieux, France). Broth microdilution and disk diffusion methods were performed according to CLSI M27-A3 and CLSI M44-A2 documents, respectively. The results were evaluated according to CLSI M27-A3 and M44-A2 documents and new vs. species-specific CLSI breakpoints. By using both previous and new CLSI breakpoints, broth microdilution test results showed that voriconazole has greater in vitro activity than fluconazole against C.glabrata isolates. For the two drugs tested, very major error was not observed with disk diffusion method when microdilution method was considered as the reference method. Since "susceptible" category no more exists for fluconazole vs. C.glabrata, the isolates that were interpreted as susceptible by previous breakpoints were evaluated as susceptible-dose dependent by current CLSI breakpoints. Since species-specific breakpoints remain yet undetermined for voriconazole, comparative analysis was not possible for this agent. The results obtained

Fluconazole affects the alkali-metal-cation homeostasis and susceptibility to cationic toxic compounds of Candida glabrata

Czech Academy of Sciences Publication Activity Database

Elicharová, Hana; Sychrová, Hana

2014-01-01

Roč. 160, č. 8 (2014), s. 1705-1713 ISSN 1350-0872 R&D Projects: GA ČR GAP302/12/1151; GA MŠk(CZ) ED1.1.00/02.0109 Institutional research plan: CEZ:AV0Z50110509 Institutional support: RVO:67985823 Keywords : Candida glabrata * fluconazole * membrane potential Subject RIV: EE - Microbiology, Virology Impact factor: 2.557, year: 2014

Experimental Evaluation of the Pathogenicity of Different Strains of Schistosoma mansoni

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Antônio Aurélio Euzébio

2012-01-01

Full Text Available The pathogenesis of three different Schistosoma mansoni strains from the Brazilian states of Minas Gerais (BH strain and São Paulo (SJ and SD strains was evaluated in experimentally infected mice. Observations of the most severe clinical cases among local patients treated (SD strain in the city of Campinas (São Paulo, Brazil formed the basis of this study. Mice were used as definitive hosts and were infected with cercariae from Biomphalaria tenagophila (SJ and SD strains and Biomphalaria glabrata (BH strains. The parameters analyzed were as follows: number of S. mansoni eggs in mice feces; number of granulomas per tissue area in liver, spleen, lungs, pancreas, and ascending colon; measurements of hepatic and intestinal granulomas; number of adult worms; and measurements of trematode eggs. The comparison among the three strains indicated that the SD strain, isolated in Campinas, presented a higher worm recovery relative to the number of penetrating cercariae. In addition, when compared to the SJ and BH strains, the SD strain demonstrated similar pathogenicity to the BH strain, with a greater quantity of granulomas in the viscera, as well as larger granulomas and eggs. Furthermore, a greater quantity of trematode eggs was also shed in the feces.

A geoprocessing approach for studying and controlling schistosomiasis in the state of Minas Gerais, Brazil

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Ricardo José de Paula Souza Guimarães

2010-07-01

Full Text Available Geographical information systems (GIS are tools that have been recently tested for improving our understanding of the spatial distribution of disease. The objective of this paper was to further develop the GIS technology to model and control schistosomiasis using environmental, social, biological and remote-sensing variables. A final regression model (R² = 0.39 was established, after a variable selection phase, with a set of spatial variables including the presence or absence of Biomphalaria glabrata, winter enhanced vegetation index, summer minimum temperature and percentage of houses with water coming from a spring or well. A regional model was also developed by splitting the state of Minas Gerais (MG into four regions and establishing a linear regression model for each of the four regions: 1 (R² = 0.97, 2 (R² = 0.60, 3 (R² = 0.63 and 4 (R² = 0.76. Based on these models, a schistosomiasis risk map was built for MG. In this paper, geostatistics was also used to make inferences about the presence of Biomphalaria spp. The result was a map of species and risk areas. The obtained risk map permits the association of uncertainties, which can be used to qualify the inferences and it can be thought of as an auxiliary tool for public health strategies.

Uptake and loss of Cesium - 134 by the snail Biomphalaria glabrata (Say, 1818)

International Nuclear Information System (INIS)

Kikuchi, O.K.; Mastro, N.L. del.

1988-07-01

The uptake and loss of Cs-134 produced in IEA-R1 reactor of IPEN was observed in fresh water adult snails. Two activites were employed: 3.700 and 18.500 Bq/1. A monochannel analyses was used for radiactivity couting and the number of egg-laying and embryo were registered. Maximum uptake occured approximately at 8 th day and the biological half-life was about 6 days. Although the egg-laying and embryo number were diminished with Cs-134 presence, it is not possible to affirm that result due to the small number of animals used. (author) [pt

Genotyping of the MTL loci and susceptibility to two antifungal agents of Candida glabrata clinical isolates

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María Teresa Lavaniegos-Sobrino

2009-08-01

Full Text Available The opportunistic fungal pathogen Candida glabrata is the second most common isolate from bloodstream infections worldwide and is naturally less susceptible to the antifungal drug fluconazole than other Candida species. C. glabrata is a haploid yeast that contains three mating-type like loci (MTL, although no sexual cycle has been described. Strains containing both types of mating information at the MTL1 locus are found in clinical isolates, but it is thought that strains containing type a information are more common. Here we investigated if a particular combination of mating type information at each MTLlocus is more prevalent in clinical isolates from hospitalized patients in Mexico and if there is a correlation between mating information and resistance to fluconazole and 5-fluorocytosine. We found that while both types of information at MTL1 are equally represented in a collection of 64 clinical isolates, the vast majority of isolates contain a-type information at MTL2 and α-type at MTL3. We also found no correlation of the particular combination of mating type information at the three MTL loci and resistance to fluconazole.

Actividad molusquicida del Piquerol A aislado de Piqueria trinervia (compositae sobre ocho especies de caracoles pulmonados The molluscicide activity of Piquerol A isolated from Piqueria trinervia (Compositae against eight species of pulmonate snails

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Alejandro Cruz-Reys

1989-03-01

Full Text Available De las partes aéreas de la planta Piqueria trinervia (Compositae colectada en diveresas áereas de México, se aisló el Piquerol A. Este compuesto se probó como agente molusquicida contra ocho especies de caracoles pulmonados: Fossaria (Fossaria humilis, F. (Bakerilymnae sp., Pseudosuccinea columella, Stagnicola attenuata, de México; F. (B. cubensis y Physacubensis, de Cuba; P. Columella y Biomphalaria glabrata, de Brasil; B glabrata, de Puerto Rico; S. elodes, de Estados Unidos. Se utilizaron tres concentraciones 50, 25 y 5 ppm para cada una de las especies y 2 períodos de exposición, 6 y 24 horas, a 20-22ºC. En 50 ppm, después de 6 horas, y 25 ppm, después de 24 horas los ejemplares de todas las especies murieron. En 5 ppm después de 24 horas, se observaron mortalidades de 60 a 100%. En ningún caso se observó recuperación después de la exposición por 24 horas. El piquerol A es un terpeno biodegradable que presenta otras actividades biológicas. No se han hecho pruebas de toxicidad en otros animales ni pruebas de campo. Sin embargo, es una substacia con alto potencial de uso como molusquicida en zonas de transmisión focal. Es la primera que en México se hacen estudios sistemáticos sobre molusquicidas de origen vegetal.In laboratory trials an aqueous solution of Piquerol A from Piqueria trinervia, collected in several regions of Mexico, showed a molluscicide action on the adults of eight different pulmonates snails species. Fossaria (Fossaria humilis, F. (Bakerilymnaea sp., Pseudosuccinea columella and Stagnicola attenuata from Mexico; F. (B. cubensis and Physa cubensis from Cuba; P. columella and Biomphalaria glabrata from Brazil; B. glabrata from Puerto Rico; and S. elodes from USA. The solution was tested at 50, 25 and 5 ppm concentration, for two periods of 6 and 24 hours, at room temperature (20-22ºC. A 100% mortality was obtained for all species at 50 ppm concentration after 6 hours of exposure; the same percentage at 25

Morphology and anatomy of leaf miners in two species of Commelinaceae (Commelina diffusa Burm. f. and Floscopa glabrata (Kunth Hassk Morfologia e anatomia de minas foliares em duas espécies de Commelinaceae Commelina diffusa Burm. f. e Floscopa glabrata (Kunth Hassk

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Paula Maria Elb

2010-03-01

Full Text Available In specialized literature, reports on anatomy of miners in host plants are few in number. These agents trigger excavations, or paths, by consumption of plant inner tissues by larvae of several insects. The aim of this work was to investigate leaf miner occurrence in Commelina diffusa (a cosmopolitan plant and Floscopa glabrata (an amphibious plant using anatomical techniques. The place where the plants were collected is subjected to seasonal floods, consequently both the species were exposed to the same weather conditions and seasonal floods. This study showed that members of Agromyzidae and Chironomidae families, which are Diptera endophytophagous larvae types, were responsible for the tunnels. Moreover, in Commelina diffusa Agromyzidae larvae were found, while in Floscopa glabrata three Chironomidae cephalic exuviae were found. The miners, as can be seen from anatomical studies, used only mesophyll parenchyma tissues for feeding, causing the formation of linear mines. In addition, in both the species, the epidermis and the medium-sized vascular units were kept intact, showing no structural modification, such as neoformation of tissues.Existem poucos relatos na literatura sobre anatomia de plantas parasitadas por agentes minadores, os quais promovem escavações ou caminhos através do consumo dos tecidos internos das plantas por larvas de diversos insetos. A proposta deste trabalho foi analisar anatomicamente a ocorrência de minas foliares em Commelina diffusa (planta cosmopolita e Floscopa glabrata (planta anfíbia causadas por espécies de larvas endofitófagas de dípteros, pertencentes a duas famílias: Agromyzidae e Chironomidae. O local onde as plantas foram coletas está sujeito a inundações sazonais, e as duas espécies foram submetidas às mesmas condições climáticas. Em Commelina diffusa foram encontradas larvas da família Agromyzidae e, em Floscopa glabrata observaram-se três exuvias cefálicas de Chironomidae. Os dados anat

[Phylogenetic analysis of CO I gene of Oncomelania snails from project of afforestation for schistosomiasis control in marshland endemic regions].

Science.gov (United States)

Xu, Yu-Mei; Zhang, Shi-Qing; Zhu, Chuan-Gang

2012-04-01

To investigate the genetic difference of cytochrome oxidase I (CO I ) of Oncomelania snails from the project of afforestation for schistosomiasis control in marshland regions, so as to explore the effects of different ecological environments. The snails were collected from 3 different areas, Anqing, Tongling, Wuwei, i.e. the upstream, midstream and downstream regions along the Yangtz River in Anhui Province. Genomic DNA was extracted from the snails, and CO I gene fragments were amplified by PCR, then purified and sequenced. The sequences were edited by using Blast. The CO I genes of O. h. minima and Biomphalaria glabrata were used as the reference of exogenous gene. The genetic distances of the various regions were calculated by the Kimura method and phylogenetic trees were constructed with UPGMA and the NJ method of MEGA (3.1) software. The amplified CO I gene of the snail was a fragment about 700 bp including 2 primers in length. There were little genetic diversity among the different areas, the identities were higher than or equal to 98%. The genetic distances indicated that the distance between the projects of afforestation and woodland in Anqing was 0.003, while Tongling was 0.019, Wuwei was 0.007. The distances among the three projects of afforestation were 0.003-0.012. The two phylogenetic trees were constructed by the methods of UPGMA and NJ respectively, which took on very similar topo-structure in which isolates of Biomphalaria glabrata located in one clade and all the others in the other one. In the other one clade, O. H. minima located in one clade. There was little genetic diversity among Anqing, Tongling, Wuwei clusters. The afforestations of Anqing and Wuwei clustered into one group, while the woodlands of Anqing and Wuwei appeared as another group. There is a little genetic diversity of the snail cytochrome oxidase I (CO I ) in different ecological environments among the upstream, midstream and downstream regions along the Yangtz River in Anhui

Micronuclei as biomarkers of genotoxicity of gamma radiation in aquatic environments

Energy Technology Data Exchange (ETDEWEB)

Silva, Luanna R.S.; Silva, Edvane B.; Melo, Ana M.M.A. [Universidade Federal de Pernambuco (GERAR/DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear. Grupo de Estudos em Radioprotecao e Radioecologia; Silva, Ronaldo C. da [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Genetica; Amancio, Francisco F. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Biofisica e Radiobiologia. Lab. de Radiobiologia

2011-07-01

Ionizing radiation is a genotoxic agent, inducing gene mutations and cellular death. Several efforts have been defendants in the development of techniques for measurement of radiation damage in biological systems. Among these techniques, micronuclei test has been showing as a great bio marker of DNA damage, being used in environmental monitoring to detect genotoxic agents in the environment. Additionally, organisms as Biomphalaria glabrata, freshwater molluscs, presents itself as an excellent model to assess damage caused by physical and chemical agents, due their biological and environmental characteristics. The snails were divided into groups of 5 individuals exposed to doses of 0 (control), 25, 35, 45 and 55 Gy of {sup 60}Co. After 48 hours of irradiation, the hemo lymph was collected and prepared the slides, which were stained with Giemsa and analyzed the cellular changes in haemocytes Statistical analysis was accomplished through chi-square test, ANOVA and Tukey test (p< 0,05). The results indicated that B. glabrata showed to be sensitive to gamma radiation. The snails irradiated with 35 Gy showed a decrease of haemocytes, while that of 55 Gy increased. Cellular and morphological changes were observed at doses of 35, 45 and 55 Gy and the dose of 55 Gy, the most radiotoxic. (author)

Micronuclei as biomarkers of genotoxicity of gamma radiation in aquatic environments

International Nuclear Information System (INIS)

Silva, Luanna R.S.; Silva, Edvane B.; Melo, Ana M.M.A.; Silva, Ronaldo C. da; Amancio, Francisco F.

2011-01-01

Ionizing radiation is a genotoxic agent, inducing gene mutations and cellular death. Several efforts have been defendants in the development of techniques for measurement of radiation damage in biological systems. Among these techniques, micronuclei test has been showing as a great bio marker of DNA damage, being used in environmental monitoring to detect genotoxic agents in the environment. Additionally, organisms as Biomphalaria glabrata, freshwater molluscs, presents itself as an excellent model to assess damage caused by physical and chemical agents, due their biological and environmental characteristics. The snails were divided into groups of 5 individuals exposed to doses of 0 (control), 25, 35, 45 and 55 Gy of 60 Co. After 48 hours of irradiation, the hemo lymph was collected and prepared the slides, which were stained with Giemsa and analyzed the cellular changes in haemocytes Statistical analysis was accomplished through chi-square test, ANOVA and Tukey test (p< 0,05). The results indicated that B. glabrata showed to be sensitive to gamma radiation. The snails irradiated with 35 Gy showed a decrease of haemocytes, while that of 55 Gy increased. Cellular and morphological changes were observed at doses of 35, 45 and 55 Gy and the dose of 55 Gy, the most radiotoxic. (author)

Study of the radiomodifier effect of Pityrocarpa moniliformis extract

International Nuclear Information System (INIS)

Moraes, Joao V.T.; Luna Filho, Ricardo L.C.; Siqueira, Williams N.; Silva, Hianna A.M.F.; Pereira, Dewson R.; Melo, Ana M.M.A.

2017-01-01

Ionizing radiation has been applied in several areas of knowledge, among them the study of the radiomodifier activity of natural substances. These substances can modify the cellular response to the damage induced by the radiation. Therefore, this work aimed to evaluate the radiomodifier action of Pityrocarpa moniliformis extract on Biomphalaria glabrata embryos exposed to "6"0Co gamma radiation. Initially, toxicity tests were performed on the extract against the B. glabrata embryos for the choice of concentration that did not cause death and embryonic malformation. Then, the antioxidant activity of the P. moniliformis extract with flavonoids and phenolic compounds was evaluated by means of the ABTS method. To evaluate the radiomodifier activity of the extract, embryos were selected in the blastula stage and irradiated with 7.5 Gy in a "6"0Co source (Gammacell-Co"6"0). Then, the embryos were exposed for 24 h to the extract of P. moniliformis at a concentration of 250 μg/mL. The results showed that the extract of P. moniliformis presents flavonoids and enzymatic inhibition by ABTS, which demonstrates the presence of antioxidant compounds. However, the tests of the radiomodifier activity did not present radioprotective effect for embryos exposed to ionizing radiation. (author)

Study of the radiomodifier effect of Pityrocarpa moniliformis extract

Energy Technology Data Exchange (ETDEWEB)

Moraes, Joao V.T.; Luna Filho, Ricardo L.C.; Siqueira, Williams N.; Silva, Hianna A.M.F.; Pereira, Dewson R.; Melo, Ana M.M.A., E-mail: joaotorres16@gmail.com, E-mail: ricardolclf@hotmail.com, E-mail: williams.wns@gmail.com, E-mail: hiannaamfs@gmail.com, E-mail: dewson.rocha@gmail.com, E-mail: amdemelo@hotmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Biofisica e Radiobiologia

2017-11-01

Ionizing radiation has been applied in several areas of knowledge, among them the study of the radiomodifier activity of natural substances. These substances can modify the cellular response to the damage induced by the radiation. Therefore, this work aimed to evaluate the radiomodifier action of Pityrocarpa moniliformis extract on Biomphalaria glabrata embryos exposed to {sup 60}Co gamma radiation. Initially, toxicity tests were performed on the extract against the B. glabrata embryos for the choice of concentration that did not cause death and embryonic malformation. Then, the antioxidant activity of the P. moniliformis extract with flavonoids and phenolic compounds was evaluated by means of the ABTS method. To evaluate the radiomodifier activity of the extract, embryos were selected in the blastula stage and irradiated with 7.5 Gy in a {sup 60}Co source (Gammacell-Co{sup 60}). Then, the embryos were exposed for 24 h to the extract of P. moniliformis at a concentration of 250 μg/mL. The results showed that the extract of P. moniliformis presents flavonoids and enzymatic inhibition by ABTS, which demonstrates the presence of antioxidant compounds. However, the tests of the radiomodifier activity did not present radioprotective effect for embryos exposed to ionizing radiation. (author)

The South-American distribution and southernmost record of Biomphalaria peregrina—a potential intermediate host of schistosomiasis

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Alejandra Rumi

2017-05-01

Full Text Available Schistosomiasis remains a major parasitic disease, endemic in large parts of South America. Five neotropical species of Biomphalaria have been found to act as intermediate hosts of Schistosoma mansoni in natural populations, while others have been shown to be susceptible in experimental infections, although not found infected in the field. Among these potential intermediate hosts, Biomphalaria peregrina represents the most widespread species in South America, with confirmed occurrence records from Venezuela to northern Patagonia. In this study, we report the southernmost record for the species at the Pinturas River, in southern Patagonia, which finding implies a southward reassessment of the limit for the known species of this genus. The identities of the individuals from this population were confirmed through morphological examination, and by means of two mitochondrial genes, cytochrome oxidase subunit I (COI and 16S-rRNA. With both markers, phylogenetic analyses were conducted in order to compare the genetic background of individuals from the Pinturas River with previously genetically characterized strains of B. peregrina from various South-American locations. In addition, we produced a potential distribution model of B. peregrina in South America and identified the environmental variables that best predict that distribution. The model was estimated through a maximum entropy algorithm and run with occurrence points obtained from several sources, including the scientific literature and international databases, along with climatic and hydrographic variables. Different phylogenetic analyses with either the COI or 16S-rRNA sequences did not conflict, but rather gave very similar topological organizations. Two major groups were identified, with sequences from the Pinturas River grouping together with haplotypes from subtropical and temperate regions. The model developed had a satisfactory performance for the study area. We observed that the areas

Effects of Snail Density on Growth, Reproduction and Survival of Biomphalaria alexandrina Exposed to Schistosoma mansoni

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T. D. Mangal

2010-01-01

Full Text Available The effects of snail density on Biomphalaria alexandrina parasitized with Schistosoma mansoni were investigated. Laboratory experiments were used to quantify the impact of high density on snail growth, fecundity, and survival. Density-dependent birth rates of snails were determined to inform mathematical models, which, until now, have assumed a linear relationship between density and fecundity. The experiments show that the rate of egg-laying followed a negative exponential distribution with increasing density and this was significantly affected by exposure to parasitic infection. High density also affected the weight of snails and survival to a greater degree than exposure to parasitic infection. Although snail growth rates were initially constrained by high density, they retained the potential for growth suggesting a reversible density-dependent mechanism. These experimental data can be used to parameterise models and confirm that snail populations are regulated by nonlinear density-dependent mechanisms.

Acute extrarenal kidney damage in the course of infection with fungal strain of Candida glabrata in a patient with type 2 diabetes

International Nuclear Information System (INIS)

Szarejko-Paradowska, A.; Bartnicki, P.; Pietrzak, B.; Wilk, R.; Serwa-Stepien, E.; Rysz, J.; Jablonowski, Z.

2010-01-01

Background: Acute renal injury is becoming a significant epidemiological problem among patients requiring hospital treatment. Extrarenal aetiology of the kidney injury is recognized in 5 % to 10 % of hospitalized patients; however, the identification of the mycelium of the Candida glabrata as the direct factor causing the acute urinary obstruction is extremely rare. Case Report: A 64-year-old woman was admitted to the clinic because of progressing weakness, nausea and vomiting, poor appetite and reduced urination. On admission, laboratory findings revealed pyuria, inflammatory changes, acute renal failure (eGFR-MDRD 6 ml/min), and hyperglycemia. The patient underwent USG of the abdominal cavity, which showed bilateral hydronephrosis, with lithiasis on the right site. Cystoscopy done the next day revealed that the mucous membrane of the bladder was reddened and had a white coating. During the next several days, a renal fistula was created on the left and right sides. Candida glabrata was isolated from urine, and was sensitive only to voriconazole. V-fend (voriconazole) treatment resulted in increase of diuresis and decrease in creatinine and urea levels. Conclusions: Urinary tract infection caused by Candida glabrata causes significant therapeutic problems. In most cases, these yeasts are resistant to triazole anti-fungal drugs such as fluconazole, which translates into significantly increased mortality of patients. To date, a similar case was described only by one group of doctors, however, due to the intensity of the currently used immunosuppression and multiantibiotic therapy, increased incidence of diabetes and the aging of the population, it is expected that the prevalence of this clinical problem will increase. (authors)

Suscetibilidade de Biomphalaria tenagophila do Estado de São Paulo à infecção por linhagens de Schistosoma mansoni da Baixada Maranhense (Maranhão, Brasil Susceptibility of Biomphalaria tenagophila, from S. Paulo State, to infection by Schistosoma mansoni, from the State of Maranhão

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Othon de Carvalho Bastos

1984-10-01

Full Text Available Exemplares de Biomphalaria tenagophila, provenientes do Vale do Rio Paraíba do Sul (São Paulo, Brasil, foram expostos às linhagens humana (H e silvestre (S de Schistosoma mansoni, oriundos da Região da Baixada Maranhense, ao noroeste do Estado do Maranhão. As linhagens H e S apresentaram comportamento distinto quando colocadas à infectar os moluscos paulistas. As B. tenagophila infectadas com a linhagem S apresentaram índice de mortalidade inferior ao observado nas infectadas com a linhagem H. No molusco paulista a linhagem silvestre maranhense completou seu desenvolvimento, fato que não ocorreu com a linhagem humana. Estas observações foram comparadas com os resultados anteriormente obtidos, quando estudou-se o comportamento das linhagens H e S do Vale do Rio Paraíba do Sul no molusco simpátrico. Foi verificado que as linhagens maranhenses e paulistas quando comparadas apresentavam comportamento similar frente a B. tenogophila do Vale do Rio Paraíba do Sul, SP.Wild (W and human (H strains of Schistosoma mansoni were isolated in the lowland region of Maranhão State (northeastern Brazil. Snail progenies of Biomphalaria tenagophila collected from Paraiba do Sul River valley (Southeastern Brazil were exposed to W miracidia, obtained from livers of wild rodents,and to H miracidia, from eggs in human stools. The date of elimination of cercariae, the quantity of eliminated larvae, the infection index of the moluscs and the mortality rate of the snails were recorded. This data suggest better adaptation of the W strain than of the H strain to B. tenagophila. These results were compared with published data of H and W strains from the Paraiba do Sul River valley and similar parasitological behavior was found.

The dual role of Candida glabrata Drug:H+ Antiporter CgAqr1 (ORF CAGL0J09944g in antifungal drug and acetic acid resistance

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Catarina eCosta

2013-06-01

Full Text Available Opportunistic Candida species often have to cope with inhibitory concentrations of acetic acid, in the acidic environment of the vaginal mucosa. Given that the ability of these yeast species to tolerate stress induced by weak acids and antifungal drugs appears to be a key factor in their persistence and virulence, it is crucial to understand the underlying mechanisms.In this study, the Drug:H+ Antiporter CgAqr1 (ORF CAGL0J09944g, from Candida glabrata, was identified as a determinant of resistance to acetic acid, and also to the antifungal agents flucytosine and, less significantly, clotrimazole. These antifungals were found to act synergistically with acetic acid against this pathogen. The action of CgAqr1 in this phenomenon was analyzed. Using a GFP fusion, CgAqr1 was found to localize to the plasma membrane and to membrane vesicles when expressed in C. glabrata or, heterologously, in Saccharomyces cerevisiae. Given its ability to complement the susceptibility phenotype of its S. cerevisiae homolog, ScAqr1, CgAqr1 was proposed to play a similar role in mediating the extrusion of chemical compounds. Significantly, the expression of this gene was found to reduce the intracellular accumulation of 3H-flucytosine and, to a moderate extent, of 3H-clotrimazole, consistent with a direct role in antifungal drug efflux. Interestingly, no effect of CgAQR1 deletion could be found on the intracellular accumulation of 14C-acetic acid, suggesting that its role in acetic acid resistance may be indirect, presumably through the transport of a still unidentified physiological substrate. Although neither of the tested chemicals induces changes in CgAQR1 expression, pre-exposure to flucytosine or clotrimazole was found to make C. glabrata cells more sensitive to acetic acid stress. Results from this study show that CgAqr1 is an antifungal drug resistance determinant and raise the hypothesis that it may play a role in C. glabrata persistent colonization and

Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Science.gov (United States)

Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

2015-07-01

Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Molluscicidal saponins from Phytolacca dodecandra

DEFF Research Database (Denmark)

Thiilborg, S. T.; Christensen, S. B.; Cornett, Claus

1993-01-01

Two new monodesmosidic saponins were isolated from an aqueous extract of the Ethiopian strain 44 of Phytolacca dodecandra. Their structures were established as 3-0-alpha-L-rhamnopyranosyl-(1-->2)-O-[beta-D-galactopyranosyl-(1-->3)] -beta-D-glucopyranosyloleanolic acid and 3-O-beta-D-xylopyranosyl......Two new monodesmosidic saponins were isolated from an aqueous extract of the Ethiopian strain 44 of Phytolacca dodecandra. Their structures were established as 3-0-alpha-L-rhamnopyranosyl-(1-->2)-O-[beta-D-galactopyranosyl-(1-->3)] -beta-D-glucopyranosyloleanolic acid and 3-O......-beta-D-xylopyranosyl-(1-->6)-O-beta-D-gluco-pyranosyl-(1-->3)]-beta -D-glucopyranosyloleanolic acid mainly by spectroscopic methods (LSIMS, H-1 NMR, COSY, NOESY, TOCSY, J-resolved H-1 NMR, C-13 NMR, HETCOR). The saponins are potent molluscicides against the schistosomiasis transmitting snail Biomphalaria glabrata with LC...

Identification of planorbids from Venezuela by polymerase chain reaction amplification and restriction fragment length polymorphism of internal transcriber spacer of the RNA ribosomal gene

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Caldeira Roberta L

2000-01-01

Full Text Available Snails of the genus Biomphalaria from Venezuela were subjected to morphological assessment as well as polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP analysis. Morphological identification was carried out by comparison of characters of the shell and the male and female reproductive apparatus. The PCR-RFLP involved amplification of the internal spacer region ITS1 and ITS2 of the RNA ribosomal gene and subsequent digestion of this fragment by the restriction enzymes DdeI, MnlI, HaeIII and MspI. The planorbids were compared with snails of the same species and others reported from Venezuela and present in Brazil, Cuba and Mexico. All the enzymes showed a specific profile for each species, that of DdeI being the clearest. The snails were identified as B. glabrata, B. prona and B. kuhniana.

Candida glabrata prosthetic joint infection, successfully treated with anidulafungin: A case report and review of the literature.

Science.gov (United States)

Koutserimpas, Christos; Samonis, George; Velivassakis, Emmanouil; Iliopoulou-Kosmadaki, Stylliani; Kontakis, Georgios; Kofteridis, Diamantis P

2018-04-01

Non-albicans Candida prosthetic joint infection (PJI) is extremely rare. A case of a Candida glabrata knee PJI is a 68-year-old splenectomised female smoker, suffering from chronic obstructive pulmonary disease (COPD) and alcoholism is reported. The patient presented with a peri-prosthetic fracture, 15 years after total knee replacement surgery. Cultures of the intraoperative peri-prosthetic tissue and materials yielded C. glabrata, as well as a methicillin-resistant S. epidermitis. The patient was treated with anidulafungin and vancomycin. The knee prosthetic joint was removed and cement-spacer with vancomycin and gentamycin was placed. Additionally, an external fixation was performed. A second stage revision surgery was planned, after completion of the antimicrobial and antifungal treatment. The patient is followed up for 4 months without signs, symptoms or findings of infection. PJI Candida infections require a high clinical suspicion index. It is of utmost importance to report these cases, since there is no consensus yet of the proper antifungal treatment. Furthermore, a literature review regarding treatment of those cases is provided. First-line treatment with an echinocandin seems most proper, due to their fungicidal properties, their effectiveness against biofilm, as well as their minimal toxicity, making them ideal for long-term use. Further experience is needed, for better understanding the disease's pathogenesis and optimal treatment. © 2017 Blackwell Verlag GmbH.

Web services for transcriptomics

NARCIS (Netherlands)

Neerincx, P.

2009-01-01

Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as

KRE5 Suppression Induces Cell Wall Stress and Alternative ER Stress Response Required for Maintaining Cell Wall Integrity in Candida glabrata

Science.gov (United States)

Sasaki, Masato; Ito, Fumie; Aoyama, Toshio; Sato-Okamoto, Michiyo; Takahashi-Nakaguchi, Azusa; Chibana, Hiroji; Shibata, Nobuyuki

2016-01-01

The maintenance of cell wall integrity in fungi is required for normal cell growth, division, hyphae formation, and antifungal tolerance. We observed that endoplasmic reticulum stress regulated cell wall integrity in Candida glabrata, which possesses uniquely evolved mechanisms for unfolded protein response mechanisms. Tetracycline-mediated suppression of KRE5, which encodes a predicted UDP-glucose:glycoprotein glucosyltransferase localized in the endoplasmic reticulum, significantly increased cell wall chitin content and decreased cell wall β-1,6-glucan content. KRE5 repression induced endoplasmic reticulum stress-related gene expression and MAP kinase pathway activation, including Slt2p and Hog1p phosphorylation, through the cell wall integrity signaling pathway. Moreover, the calcineurin pathway negatively regulated cell wall integrity, but not the reduction of β-1,6-glucan content. These results indicate that KRE5 is required for maintaining both endoplasmic reticulum homeostasis and cell wall integrity, and that the calcineurin pathway acts as a regulator of chitin-glucan balance in the cell wall and as an alternative mediator of endoplasmic reticulum stress in C. glabrata. PMID:27548283

Assessment of toxicity and genotoxicity of the reactive azo dyes Remazol Black B and Remazol Orange 3R and effectiveness of electron beam irradiation in the reduction of color and toxic effects

International Nuclear Information System (INIS)

Pinheiro, Alessandro de Sa

2011-01-01

The textile industries play an important role in national and global economy. But, their activities are considered potentially polluting. The use of large volumes of water and the production of colored wastewater with high organic matter are among the main issues raised, especially during the stage of dyeing and washing of the textile process. The reactive azo dyes are the main colors used in the industry for dyeing of cotton in Brazil and worldwide. Because of its low setting and variations in the fiber production process, about 30% of the initial concentration used in the dyeing baths are lost and will compose the final effluent. These compounds have a low biodegradability, are highly soluble in water and therefore are not completely removed by conventional biological processes. In addition, other processes do not promote degradation but the transference to solid environment. The dyes discarded without treatment in the water body can cause aesthetic modifications, alter photosynthesis and gas solubility, as well as being toxic and genotoxic. The main objectives of this study were to evaluate the toxicity and genotoxicity of two reactive azo dyes (Remazol Black B - RPB and Remazol Orange 3R - R3AR) and the percentage of color and toxicity reduction after the use of electron beam radiation. The acute toxicity assays performed with Vibrio fischeri, Daphnia similis and Biomphalaria glabrata showed different response patterns for dyes. The different chemical forms of dyes were slightly toxic to Vibrio fischeri and only the RPB dye (vinylsulphone) was toxic (EC50 15min = 6,23 mg L-1). In tests with Daphnia similis, the dye RPB was slightly toxic in its pattern form, sulphatoethylsulphone, (CE50 48h = 91,25 mg L -1 ) and showed no toxicity in other chemical forms. However, the RA3R dye was toxic to the dafnids and the vinylsulphone form very toxic (EC50 48h = 0,54 mg L-1). No toxicity was observed in Biomphalaria glabrata assays. Chronic toxicity was assessed with the

Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment

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Li Qingdi

2012-06-01

Full Text Available Abstract Background The selection of stable and suitable reference genes for real-time quantitative PCR (RT-qPCR is a crucial prerequisite for reliable gene expression analysis under different experimental conditions. The present study aimed to identify reference genes as internal controls for gene expression studies by RT-qPCR in azole-stimulated Candida glabrata. Results The expression stability of 16 reference genes under fluconazole stress was evaluated using fold change and standard deviation computations with the hkgFinder tool. Our data revealed that the mRNA expression levels of three ribosomal RNAs (RDN5.8, RDN18, and RDN25 remained stable in response to fluconazole, while PGK1, UBC7, and UBC13 mRNAs showed only approximately 2.9-, 3.0-, and 2.5-fold induction by azole, respectively. By contrast, mRNA levels of the other 10 reference genes (ACT1, EF1α, GAPDH, PPIA, RPL2A, RPL10, RPL13A, SDHA, TUB1, and UBC4 were dramatically increased in C. glabrata following antifungal treatment, exhibiting changes ranging from 4.5- to 32.7-fold. We also assessed the expression stability of these reference genes using the 2-ΔΔCT method and three other software packages. The stability rankings of the reference genes by geNorm and the 2-ΔΔCT method were identical to those by hkgFinder, whereas the stability rankings by BestKeeper and NormFinder were notably different. We then validated the suitability of six candidate reference genes (ACT1, PGK1, RDN5.8, RDN18, UBC7, and UBC13 as internal controls for ten target genes in this system using the comparative CT method. Our validation experiments passed for all six reference genes analyzed except RDN18, where the amplification efficiency of RDN18 was different from that of the ten target genes. Finally, we demonstrated that the relative quantification of target gene expression varied according to the endogenous control used, highlighting the importance of the choice of internal controls in such

Comparison of genome engineering using the CRISPR-Cas9 system in C. glabrata wild-type and lig4 strains.

Science.gov (United States)

Cen, Yuke; Timmermans, Bea; Souffriau, Ben; Thevelein, Johan M; Van Dijck, Patrick

2017-10-01

Candida glabrata is reported as the second most prevalent human opportunistic fungal pathogen in North America and is threatening patients all over the world. Its incidence is rising, while it has developed resistance to the most widely used antifungal drugs, necessitating new approaches based on better insight into the biology of the organism. Despite its close phylogenetic relationship with Saccharomyces cerevisiae, generating precise genomic alterations in this species is problematic. Previously we have shown that deletion of LIG4, which encodes an enzyme involved in Non-Homologous End Joining (NHEJ), strongly enhances the probability of obtaining correctly modified transformants. In this work we used the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated protein 9 (Cas9) system to genetically engineer the C. glabrata genome, targeting the genes ADE2, MET15 and SOK2, located on different chromosomes. We used the CRISPR-Cas9 technology to replace the open reading frame (ORF) by the SAT1 selective marker or introduced a premature stop codon in ADE2 and MET15, as they are easily scored by their adenine or methionine auxotrophy, respectively. The SOK2 gene was modified by insertion of a triple HA-tag sequence and the transformants were verified in a western blot. The CRISPR-Cas9 mediated targeting efficiency varies depending on the gene targeted and the genetic modification performed. We show that CRISPR-Cas9 mediated genome editing is more efficient than the conventional method in the wild-type strain, moreover it has the big advantage being marker-free. In previous work, we showed that the targeting efficiency is highly increased in the lig4Δ strain using the conventional way to delete genes in C. glabrata. Using the CRISPR-Cas9 system in this strain, the percentage of correct transformants is consistently higher compared to the wild-type strain. This indicates that using the lig4 mutant as such is already a strong

Schistosoma mansoni mucin gene (SmPoMuc expression: epigenetic control to shape adaptation to a new host.

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Cecile Perrin

Full Text Available The digenetic trematode Schistosoma mansoni is a human parasite that uses the mollusc Biomphalaria glabrata as intermediate host. Specific S. mansoni strains can infect efficiently only certain B. glabrata strains (compatible strain while others are incompatible. Strain-specific differences in transcription of a conserved family of polymorphic mucins (SmPoMucs in S. mansoni are the principle determinants for this compatibility. In the present study, we investigated the bases of the control of SmPoMuc expression that evolved to evade B. glabrata diversified antigen recognition molecules. We compared the DNA sequences and chromatin structure of SmPoMuc promoters of two S. mansoni strains that are either compatible (C or incompatible (IC with a reference snail host. We reveal that although sequence differences are observed between active promoter regions of SmPoMuc genes, the sequences of the promoters are not diverse and are conserved between IC and C strains, suggesting that genetics alone cannot explain the evolution of compatibility polymorphism. In contrast, promoters carry epigenetic marks that are significantly different between the C and IC strains. Moreover, we show that modifications of the structure of the chromatin of the parasite modify transcription of SmPoMuc in the IC strain compared to the C strain and correlate with the presence of additional combinations of SmPoMuc transcripts only observed in the IC phenotype. Our results indicate that transcription polymorphism of a gene family that is responsible for an important adaptive trait of the parasite is epigenetically encoded. These strain-specific epigenetic marks are heritable, but can change while the underlying genetic information remains stable. This suggests that epigenetic changes may be important for the early steps in the adaptation of pathogens to new hosts, and might be an initial step in adaptive evolution in general.

A paralogue of the phosphomutase-like gene family in Candida glabrata, CgPmu2, gained broad-range phosphatase activity due to a small number of clustered substitutions.

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Orlando, Kelly A; Iosue, Christine L; Leone, Sarah G; Davies, Danielle L; Wykoff, Dennis D

2015-10-15

Inorganic phosphate is required for a range of cellular processes, such as DNA/RNA synthesis and intracellular signalling. The phosphate starvation-inducible phosphatase activity of Candida glabrata is encoded by the gene CgPMU2 (C. glabrata phosphomutase-like protein). CgPMU2 is part of a three-gene family (∼75% identical) created through gene duplication in the C. glabrata clade; only CgPmu2 is a PHO-regulated broad range acid phosphatase. We identified amino acids that confer broad range phosphatase activity on CgPmu2 by creating fusions of sections of CgPMU2 with CgPMU1, a paralogue with little broad range phosphatase activity. We used site-directed mutagenesis on various fusions to sequentially convert CgPmu1 to CgPmu2. Based on molecular modelling of the Pmu proteins on to a histidine phosphatase crystal structure, clusters of amino acids were found in two distinct regions that were able to confer phosphatase activity. Substitutions in these two regions together conferred broad phosphatase activity on CgPmu1. Interestingly, one change is a histidine adjacent to the active site histidine of CgPmu2 and it exhibits a novel ability to partially replace the conserved active site histidine in CgPmu2. Additionally, a second amino acid change was able to confer nt phosphatase activity to CgPmu1, suggesting single amino acid changes neofunctionalize CgPmu2. © 2015 Authors; published by Portland Press Limited.

Cnh1 Na+/H+ antiporter and Ena1 Na+-ATPase play different roles in cation homeostasis and cell physiology of Candida glabrata

Czech Academy of Sciences Publication Activity Database

Krauke, Yannick; Sychrová, Hana

2011-01-01

Roč. 11, č. 1 (2011), s. 29-41 ISSN 1567-1356 R&D Projects: GA MŠk(CZ) LC531 Grant - others:EC(XE) MRTN-CT-2004-512481 Institutional research plan: CEZ:AV0Z50110509 Keywords : Candida glabrata * potassium homeostasis * podium detoxification * Ena 1 ATPase * Cnh1 antiporter Subject RIV: EE - Microbiology, Virology Impact factor: 2.403, year: 2011

Aspectos imunológicos e parasitológicos em Biomphalaria tenagophila infectadas por Schistosoma mansoni e outros Digenea

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Balan Doralice de Souza Luro

1993-01-01

Full Text Available Estudou-se o comportamento de amebócitos de Biomphalaria tenagophila infectadas por Schistosoma mansoni, por outros Digenea e a resistência à superinfecção, presente em infecções mistas. Foi verificada a atividade fagocitária dos amebócitos, o número destas células circulantes, a reação amebocitária nos tecidos, o perfil eletroforético da hemolinfa, além da reação de imunodifusão. Concluiu-se que moluscos infectados por outros Digenea apresentam resistência à superinfecção por S. mansoni, sendo que os amebócitos parecem não ter participação direta na destruição dos esporocistos de S. mansoni nesta eventualidade. Nos moluscos infectados observou-se maior número de amebócitos circulantes e aumento de capacidade fagocitária destas células.

Antidiarrheal Thymol Derivatives from Ageratina glabrata. Structure and Absolute Configuration of 10-Benzoyloxy-8,9-epoxy-6-hydroxythymol Isobutyrate

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Celia Bustos-Brito

2016-09-01

Full Text Available Chemical investigation of the leaves from Ageratina glabrata yielded four new thymol derivatives, namely: 10-benzoyloxy-8,9-dehydro-6-hydroxythymol isobutyrate (4, 10-benzoyloxy-8,9-dehydrothymol (5, 10-benzoyloxythymol (6 and 10-benzoyloxy-6,8-dihydroxy-9-isobutyryl-oxythymol (7. In addition, (8S-10-benzoyloxy-8,9-epoxy-6-hydroxythymol isobutyrate (1, together with other two already known thymol derivatives identified as 10-benzoyloxy-8,9-epoxy-6-methoxythymol isobutyrate (2 and 10-benzoyloxy-8,9-epoxythymol isobutyrate (3 were also obtained. In this paper, we report the structures and complete assignments of the 1H and 13C-NMR data of compounds 1–7, and the absolute configuration for compound 1, unambiguously established by single crystal X-ray diffraction, and evaluation of the Flack parameter. The in vitro antiprotozoal assay showed that compound 1 and its derivative 1a were the most potent antiamoebic and antigiardial compounds. Both compounds showed selectivity and good antiamoebic activity comparable to emetine and metronidazole, respectively, two antiprotozoal drugs used as positive controls. In relation to anti-propulsive effect, compound 1 and 1a showed inhibitory activity, with activities comparable to quercetin and compound 9, two natural antipropulsive compounds used as positive controls. These data suggest that compound 1 may play an important role in antidiarrheal properties of Ageratina glabrata.

Aspectos da ecologia reprodutiva de Pera glabrata (Schott Poepp. ex Baill. (Euphorbiaceae em uma área de Cerrado no estado de São Paulo

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Juliana Ribeirão de Freitas

2011-12-01

Full Text Available Pera glabrata é uma árvore que apresenta ampla distribuição no Brasil. A espécie vegetal é de importância para a conservação e recuperação de áreas degradadas, pois está presente em áreas impactadas, produz e dispersa grande quantidade de sementes e constitui-se em fonte alimentar para elevado número de espécies animais. Apesar da importância fitossociológica da espécie, ainda não existem estudos que abordem a sua ecologia reprodutiva. Este trabalho teve como objetivo caracterizar aspectos da fenologia reprodutiva, da morfologia floral, dos sistemas reprodutivo e de polinização e da dispersão de sementes da espécie. O estudo foi realizado em uma área de Cerrado no município de São Carlos, SP. Verificou-se que Pera glabrata é dioica e apresenta floração massiva e as flores dos dois sexos são pequenas, involucradas, amarelas e de antese diurna. As flores masculinas apresentam néctar e emitem odor adocicado, e as femininas não oferecem recursos perceptíveis aos visitantes florais. As flores foram visitadas por 32 espécies de Diptera e Hymenoptera de pequeno porte. Ocorre a formação de frutos e sementes por autogamia. Foram identificadas 25 espécies de aves visitando indivíduos com frutos maduros, das quais 16 ingeriram as sementes ariladas. Pera glabrata é autogâmica, com síndrome de polinização por diversos pequenos insetos e com dispersão ornitocórica de suas sementes.

Chimeras between C. glabrata Cnh1 and S. cerevisiae Nha1 Naplus/Hplus-antiporters are functional proteins increasing the salt tolerance of yeast cells

Czech Academy of Sciences Publication Activity Database

Krauke, Yannick; Sychrová, Hana

2010-01-01

Roč. 55, č. 5 (2010), s. 435-441 ISSN 0015-5632 R&D Projects: GA MŠk(CZ) LC531 Grant - others:EC(XE) MRTN-CT-2004-512481 Institutional research plan: CEZ:AV0Z50110509 Keywords : C. glabrata * S. cerevisiae * Nha1 antiporter Subject RIV: EE - Microbiology, Virology Impact factor: 0.977, year: 2010

Evaluation of Chemical and Physical-morphological Factors as Potential Determinants of Biomphalaria pfeifferi (Krauss, 1848 Distribution

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Utzinger Jürg

1997-01-01

Full Text Available This study was carried out in five sites along a small perennial river system in south-central Tanzania, which had been identified as the focus for transmission of intestinal schistosomiasis in the area. Malacological surveys preceding the study showed a focal distribution of Biomphalaria pfeifferi, intermediate host snail of Schistosoma mansoni, the snails being present in three sites but absent from the other two sites. The objective of this study was to evaluate to what extent chemical and/or physical-morphological factors determine the distribution of B. pfeifferi between these five sites. It was found that none of the chemical constituents in the waters examined were outside the tolerance range of B. pfeifferi snails. Moreover, the composition of water from B. pfeifferi-free sites was not different from that in those sites where snails occurred. Furthermore, none of the physical-morphological constituents seemed likely to be a determinant for the absence of B. pfeifferi. In view of these findings, and those of previous studies, it is concluded that the focal distribution of B. pfeifferi cannot be associated with a single environmental factor and is rather the result of more complex interactions of habitat factors

Evaluation of chemotherapy in the control of Schistosoma mansoni in Marquis Valley, Saint Lucia. II. Biological results.

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Barnish, G

1982-01-01

Following the final chemotherapy campaign of a 4-year program, the biological assessment of transmission of Schistosoma mansoni was evaluated for 5 years. No infected Biomphalaria glabrata were found amongst 28,791 and 13,550 snails examined from flowing and static index sites, respectively. However, 89 infected snails of 16,602 examined (0.54%) were found from additional sites. Sentinel snails examined between March 1974 and October 1977 revealed no infections and their use was discontinued. Following an increase in transmission, routine focal mollusciciding at 4-weekly intervals was introduced in March 1980. The cost for eight applications was US $641, representing a cost per caput of $0.21. These figures, extrapolated to a full year's control, become $1,042 and $0.35, respectively. The maximum cost was for the molluscicide, which absorbed 71.5% of the total. The data suggest that the main transmission of S. mansoni occurs in the dry season, in flowing habitats, as it does elsewhere in St. Lucia.

Facultative Sterol Uptake in an Ergosterol-Deficient Clinical Isolate of Candida glabrata Harboring a Missense Mutation in ERG11 and Exhibiting Cross-Resistance to Azoles and Amphotericin B

NARCIS (Netherlands)

Hull, Claire M.; Parker, Josie E.; Bader, Oliver; Weig, Michael; Gross, Uwe; Warrilow, Andrew G. S.; Kelly, Diane E.; Kelly, Steven L.

We identified a clinical isolate of Candida glabrata (CG156) exhibiting flocculent growth and cross-resistance to fluconazole (FLC), voriconazole (VRC), and amphotericin B (AMB), with MICs of >256, >256, and 32 mu g ml(-1), respectively. Sterol analysis using gas chromatography-mass spectrometry

Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii

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Stahl Ulf

2010-05-01

Full Text Available Abstract Background The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 → 3-β-linked glucose with a (1 → 6-β-glycosyl branch on every third unit. Although the physicochemical properties of scleroglucan are well understood, almost nothing is known about the genetics of scleroglucan biosynthesis. Similarly, the biosynthetic pathway of oxalate, the main by-product during scleroglucan production, has not been elucidated yet. In order to provide a basis for genetic and metabolic engineering approaches, we studied scleroglucan and oxalate biosynthesis in S. rolfsii using different transcriptomic approaches. Results Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified ~800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions. From these, candidate genes were identified which could represent potential leads for targeted modification of the S. rolfsii metabolism for increased scleroglucan yields. Conclusions The results presented in this paper provide for the first time genomic and transcriptomic data about S. rolfsii and demonstrate the power and usefulness of combined transcriptome sequencing and comparative microarray analysis. The data obtained allowed us to predict the biosynthetic pathways of scleroglucan and

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies.

Science.gov (United States)

Sun, Ying; Huang, Yu; Li, Xiaofeng; Baldwin, Carole C; Zhou, Zhuocheng; Yan, Zhixiang; Crandall, Keith A; Zhang, Yong; Zhao, Xiaomeng; Wang, Min; Wong, Alex; Fang, Chao; Zhang, Xinhui; Huang, Hai; Lopez, Jose V; Kilfoyle, Kirk; Zhang, Yong; Ortí, Guillermo; Venkatesh, Byrappa; Shi, Qiong

2016-01-01

Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in 'omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the "Transcriptomes of 1,000 Fishes" (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far.

Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis

OpenAIRE

Jones, Beryl M.; Wcislo, William T.; Robinson, Gene E.

2015-01-01

Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome fo...

Endoscopic Endonasal Transsphenoidal Drainage of a Spontaneous Candida glabrata Pituitary Abscess.

Science.gov (United States)

Strickland, Ben A; Pham, Martin; Bakhsheshian, Joshua; Carmichael, John; Weiss, Martin; Zada, Gabriel

2018-01-01

Noniatrogenic pituitary abscess remains a rare clinical entity, and is the indication for surgery in abscess caused by Candida species, and also provide an intraoperative video showing the endoscopic management of this pathology. A 33-year-old woman presented with headache, hypopituitarism, and vision loss in the setting of diabetic ketoacidosis, and was found to have multiple abscesses in the liver, lung, kidney, and uterus. Brain magnetic resonance imaging revealed a 15-mm cystic sellar mass with restricted diffusion. The patient underwent urgent evacuation of the abscess via an endoscopic endonasal transsphenoidal route, with obvious purulent material filling the sella, later identified as Candida glabrata. Antimicrobial therapy was refined appropriately, and she exhibited significant improvement in neurologic function, although endocrinopathy has persisted. With timely management, including a combination of surgical drainage and appropriate antimicrobial therapy, neurologic outcomes are good in most cases of pituitary abscess; however, endocrinopathy often does not improve. Although most reported cases with identified causative organisms speciate bacteria, some cases are of fungal etiology and require different antimicrobial agents. This further underscores the importance of identifying the causative agent. Copyright © 2017 Elsevier Inc. All rights reserved.

Amphotericin B and caspofungin resistance in Candida glabrata isolates recovered from a critically ill patient

DEFF Research Database (Denmark)

Krogh-Madsen, Mikkel; Arendrup, Maiken Cavling; Heslet, Lars

2006-01-01

BACKGROUND: Consecutive Candida glabrata isolates recovered from a patient in an intensive care unit were resistant to amphotericin B (minimum inhibitory concentration, up to 32 mu g/mL; determined by Etest [AB Biodisk]). Analyses at the national reference laboratory showed that some isolates were...... also resistant to azoles and caspofungin. In this study, 4 isolates were studied thoroughly using susceptibility assays and a mouse model and to determine clonality. METHODS: Different broth microdilution tests, Etests, and time-kill studies for antifungals were performed in different media. Three...... isolates obtained from nonrelated patients, and a reference strain. RESULTS: The murine model indicated that 1 isolate was resistant to amphotericin B, 1 had intermediate susceptibility, and 1 was fully susceptible. Two of the 3 isolates were resistant to caspofungin. Microdilution methods did not reliably...

The Escherichia coli transcriptome linked to growth fitness

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Bei-Wen Ying

2016-03-01

Full Text Available A series of Escherichia coli strains with varied genomic sequences were subjected to high-density microarray analyses to elucidate the fitness-correlated transcriptomes. Fitness, which is commonly evaluated by the growth rate during the exponential phase, is not only determined by the genome but is also linked to growth conditions, e.g., temperature. We previously reported genetic and environmental contributions to E. coli transcriptomes and evolutionary transcriptome changes in thermal adaptation. Here, we describe experimental details on how to prepare microarray samples that truly represent the growth fitness of the E. coli cells. A step-by-step record of sample preparation procedures that correspond to growing cells and transcriptome data sets that are deposited at the GEO database (GSE33212, GSE52770, GSE61739 are also provided for reference. Keywords: Transcriptome, Growth fitness, Escherichia coli, Microarray

Integrative investigation of metabolic and transcriptomic data

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Önsan Z İlsen

2006-04-01

Full Text Available Abstract Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions was investigated using linear modelling, and open reading-frames (ORFs whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.

TRAM (Transcriptome Mapper: database-driven creation and analysis of transcriptome maps from multiple sources

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Danieli Gian

2011-02-01

Full Text Available Abstract Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays, implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile, useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene

Processing of predicted substrates of fungal Kex2 proteinases from Candida albicans, C. glabrata, Saccharomyces cerevisiae and Pichia pastoris

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Bader Oliver

2008-07-01

Full Text Available Abstract Background Kexin-like proteinases are a subfamily of the subtilisin-like serine proteinases with multiple regulatory functions in eukaryotes. In the yeast Saccharomyces cerevisiae the Kex2 protein is biochemically well investigated, however, with the exception of a few well known proteins such as the α-pheromone precursors, killer toxin precursors and aspartic proteinase propeptides, very few substrates are known. Fungal kex2 deletion mutants display pleiotropic phenotypes that are thought to result from the failure to proteolytically activate such substrates. Results In this study we have aimed at providing an improved assembly of Kex2 target proteins to explain the phenotypes observed in fungal kex2 deletion mutants by in vitro digestion of recombinant substrates from Candida albicans and C. glabrata. We identified CaEce1, CA0365, one member of the Pry protein family and CaOps4-homolog proteins as novel Kex2 substrates. Conclusion Statistical analysis of the cleavage sites revealed extended subsite recognition of negatively charged residues in the P1', P2' and P4' positions, which is also reflected in construction of the respective binding pockets in the ScKex2 enzyme. Additionally, we provide evidence for the existence of structural constrains in potential substrates prohibiting proteolysis. Furthermore, by using purified Kex2 proteinases from S. cerevisiae, P. pastoris, C. albicans and C. glabrata, we show that while the substrate specificity is generally conserved between organisms, the proteinases are still distinct from each other and are likely to have additional unique substrate recognition.

Transcriptome complexity in a genome-reduced bacterium

DEFF Research Database (Denmark)

Güell, Marc; van Noort, Vera; Yus, Eva

2009-01-01

To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previousl...

Comportamento da cepa LE de Schistosoma mansoni, após passagem em hospedeiro humano infectado acidentalmente

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Neusa Araújo

1986-12-01

Full Text Available Uma auxiliar de laboratório infectou-se acidentalmente, com cercárias de Schistosoma mansoni, cepa LE, mantida rotineiramente em nossos laboratórios. Decorridos 5 meses, o exame parasitológico de fezes revelou 108 ovos/g . A pacientefoi tratada com oxamniquine, porém a infecção continuou ativa (6 ovos/g. Foi então obtido o isolado SSF mantido no modelo Biomphalaria glabrata - camundongo albino. Os resultados obtidos no estudo comparativo, entre o isolado SSF e a cepa LE, que lhe deu origem, mostraram que a duração do período pré-patente e o índice de infectividade em camundongos, bem como a resposta aos agentes esquistossomicidas (hycanthone, oxamniquine epraziquantel não apresentaram diferenças estatisticamente significativas. Por outro lado, o número de miracídios obtidos dos intestinos e fígados dos camundongos infectados foi o dobro com a cepa LE, quando comparados com aquele do isolado SSF. Também a variação do peso dos animais foi bastante diferente. Concluiu-se que apenas uma passagem pelo hospedeiro humano não mudou substancialmente as características da cepa estudada.A laboratory technician was accidentally infected with the LE strain of Schistosoma mansoni cercariae maintained in our laboratories. After 5 months infection parasitological examination revealed 108 eggs/g faeces. Althrough treated with oxamniquine, the infection still persisted (6 eggs/g of faeces. An isolate (SSF was obtained from that person and maintained in Biomphalaria glabrata - Swiss mouse by alternate passage. The experimental comparative results between the newly obtained SSF isolate and the original LE strain showed that the differences in pre-patent period, the mice infectivity level and the schistosomicidal response to hycanthone, oxamniquine and praziquantel was not statistically significant. On the other hand the number of miracidia recovered from intestines and livers of equally infected mice was twice as miich in the LE strain than

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

Science.gov (United States)

Li, Xinguo; Wu, Harry X; Southerton, Simon G

2010-06-21

Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

Overcoming the heterologous bias: An in vivo functional analysis of multidrug efflux transporter, CgCdr1p in matched pair clinical isolates of Candida glabrata

International Nuclear Information System (INIS)

Puri, Nidhi; Manoharlal, Raman; Sharma, Monika; Sanglard, Dominique; Prasad, Rajendra

2011-01-01

Research highlights: → First report to demonstrate an in vivo expression system of an ABC multidrug transporter CgCdr1p of C. glabrata. → First report on the structure and functional characterization of CgCdr1p. → Functional conservation of divergent but typical residues of CgCdr1p. → CgCdr1p elicits promiscuity towards substrates and has a large drug binding pocket with overlapping specificities. -- Abstract: We have taken advantage of the natural milieu of matched pair of azole sensitive (AS) and azole resistant (AR) clinical isolates of Candida glabrata for expressing its major ABC multidrug transporter, CgCdr1p for structure and functional analysis. This was accomplished by tagging a green fluorescent protein (GFP) downstream of ORF of CgCDR1 and integrating the resultant fusion protein at its native chromosomal locus in AS and AR backgrounds. The characterization confirmed that in comparison to AS isolate, CgCdr1p-GFP was over-expressed in AR isolates due to its hyperactive native promoter and the GFP tag did not affect its functionality in either construct. We observed that in addition to Rhodamine 6 G (R6G) and Fluconazole (FLC), a recently identified fluorescent substrate of multidrug transporters Nile Red (NR) could also be expelled by CgCdr1p. Competition assays with these substrates revealed the presence of overlapping multiple drug binding sites in CgCdr1p. Point mutations employing site directed mutagenesis confirmed that the role played by unique amino acid residues critical to ATP catalysis and localization of ABC drug transporter proteins are well conserved in C. glabrata as in other yeasts. This study demonstrates a first in vivo novel system where over-expression of GFP tagged MDR transporter protein can be driven by its own hyperactive promoter of AR isolates. Taken together, this in vivo system can be exploited for the structure and functional analysis of CgCdr1p and similar proteins wherein the arte-factual concerns encountered in using

Overcoming the heterologous bias: An in vivo functional analysis of multidrug efflux transporter, CgCdr1p in matched pair clinical isolates of Candida glabrata

Energy Technology Data Exchange (ETDEWEB)

Puri, Nidhi; Manoharlal, Raman; Sharma, Monika [Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067 (India); Sanglard, Dominique [Institut de Microbiologie, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne (Switzerland); Prasad, Rajendra, E-mail: rp47jnu@gmail.com [Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067 (India)

2011-01-07

Research highlights: {yields} First report to demonstrate an in vivo expression system of an ABC multidrug transporter CgCdr1p of C. glabrata. {yields} First report on the structure and functional characterization of CgCdr1p. {yields} Functional conservation of divergent but typical residues of CgCdr1p. {yields} CgCdr1p elicits promiscuity towards substrates and has a large drug binding pocket with overlapping specificities. -- Abstract: We have taken advantage of the natural milieu of matched pair of azole sensitive (AS) and azole resistant (AR) clinical isolates of Candida glabrata for expressing its major ABC multidrug transporter, CgCdr1p for structure and functional analysis. This was accomplished by tagging a green fluorescent protein (GFP) downstream of ORF of CgCDR1 and integrating the resultant fusion protein at its native chromosomal locus in AS and AR backgrounds. The characterization confirmed that in comparison to AS isolate, CgCdr1p-GFP was over-expressed in AR isolates due to its hyperactive native promoter and the GFP tag did not affect its functionality in either construct. We observed that in addition to Rhodamine 6 G (R6G) and Fluconazole (FLC), a recently identified fluorescent substrate of multidrug transporters Nile Red (NR) could also be expelled by CgCdr1p. Competition assays with these substrates revealed the presence of overlapping multiple drug binding sites in CgCdr1p. Point mutations employing site directed mutagenesis confirmed that the role played by unique amino acid residues critical to ATP catalysis and localization of ABC drug transporter proteins are well conserved in C. glabrata as in other yeasts. This study demonstrates a first in vivo novel system where over-expression of GFP tagged MDR transporter protein can be driven by its own hyperactive promoter of AR isolates. Taken together, this in vivo system can be exploited for the structure and functional analysis of CgCdr1p and similar proteins wherein the arte-factual concerns

Avaliação do tipo de substrato e do período de armazenamento para a germinação de sementes de Cordia glabrata (Mart. DC. = Evaluation of substrate type and storage period for the germination of Cordia glabrata (Mart. DC seeds

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Juliana Gadum

2009-07-01

Full Text Available Informações sobre a viabilidade e substratos adequados para a germinação de sementes de espécies arbóreas nativas são escassas. Cordia glabrata (louro-preto, espécie pioneira e de ampla distribuição, está incluída entre essas espécies. Suas característicaspermitem a utilização em ornamentação, na prática apícola e na medicina popular. Levando em conta seu potencial de utilização, este trabalho teve por objetivo avaliar as taxas de germinação, em diferentes substratos, de sementes recém-colhidas e armazenadas até 120 dias em laboratório, as quais foram coletadas no Pantanal do Rio Negro, Estado do Mato Grosso do Sul. Foram realizados testes com sementes recém-colhidas e após 30, 60, 90 e 120 dias de armazenamento, em três tipos de substrato (papel-filtro, solo arenoso e solo arenoso + matéria orgânica. Os resultados revelaram que C. glabrata possui pequena porcentagem de água (1,55% nas sementes, que decai com o período de armazenamento. Seu período de viabilidade é curto (90 dias e os melhores resultados foram obtidos com sementes recém-colhidas germinadas em papel-filtro (34%, com índice de velocidade de germinação de 10.Information about the feasibility and adequate substrates for the germination of seeds from native arboreous species are scarce. Cordiaglabrata (louro preto, a pioneering species with wide distribution, is included among these species. Its characteristics allow its use in ornamentation, apiculture and popular medicine. Considering its potential of utilization, this work had as objective to evaluate thegermination rates, in different substrates, of recently reaped seeds stored for up to 120 days in laboratory, which were collected in Pantanal of the Rio Negro, Mato Grosso do Sul State. Tests were done with recently reaped seeds and after 30, 60, 90 and 120 days ofstorage, in three kinds of substrate (paper filter, sandy soil and sandy soil + organic matter. The results revealed that C

β-Glucan induces reactive oxygen species production in human neutrophils to improve the killing of Candida albicans and Candida glabrata isolates from vulvovaginal candidiasis.

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Patricia de Souza Bonfim-Mendonça

Full Text Available Vulvovaginal candidiasis (VVC is among the most prevalent vaginal diseases. Candida albicans is still the most prevalent species associated with this pathology, however, the prevalence of other Candida species, such as C. glabrata, is increasing. The pathogenesis of these infections has been intensely studied, nevertheless, no consensus has been reached on the pathogenicity of VVC. In addition, inappropriate treatment or the presence of resistant strains can lead to RVVC (vulvovaginal candidiasis recurrent. Immunomodulation therapy studies have become increasingly promising, including with the β-glucans. Thus, in the present study, we evaluated microbicidal activity, phagocytosis, intracellular oxidant species production, oxygen consumption, myeloperoxidase (MPO activity, and the release of tumor necrosis factor α (TNF-α, interleukin-8 (IL-8, IL-1β, and IL-1Ra in neutrophils previously treated or not with β-glucan. In all of the assays, human neutrophils were challenged with C. albicans and C. glabrata isolated from vulvovaginal candidiasis. β-glucan significantly increased oxidant species production, suggesting that β-glucan may be an efficient immunomodulator that triggers an increase in the microbicidal response of neutrophils for both of the species isolated from vulvovaginal candidiasis. The effects of β-glucan appeared to be mainly related to the activation of reactive oxygen species and modulation of cytokine release.

Inactivation of Candida glabrata by a humid DC argon discharge afterglow: dominant contributions of short-lived aqueous active species

Science.gov (United States)

Xiong, Qing; Liu, Hongbin; Lu, Weiping; Chen, Qiang; Xu, Le; Wang, Xia; Zhu, Qunlin; Zeng, Xue; Yi, Ping

2017-05-01

Plasma medicine applications are currently attracting significant interest all over the world. Bactericidal treatments of Candida glabrata cultured in saline suspension are performed in this study by a room-temperature reactive afterglow of a DC-driven argon discharge. Water vapor was added to the discharge to study the inactivation contributions of reactive hydrolytic species including OH and H2O2 transporting along the gas flow to the treated solutions. The inactivation results indicate that the dominant roles in the bactericidal treatments are played by the short-lived aqueous active species, but not the stable species like H2O2aq (aq indicates an aqueous species). Further analysis shows that the ·OHaq radicals play an important role in the inactivation process. The ·OHaq radicals in the suspension are mostly produced from the direct dissolution of the OH species in the reactive afterglow. With the increase of added water vapor content, the ·OHaq production increases and enhances the inactivation efficiency of C. glabrata. Furthermore, it is found that the ambient air diffusion shows essential effects on the bactericidal activity of the remote humid argon discharge. Higher bactericidal effects can be obtained in open-space treatments compared to in a controlled Ar + H2O gas atmosphere. Key active air-byproduct species are believed to be generated in the suspension during the treatments and contributing to the inactivation process. Based on chemical analysis, the peroxynitrous acid ONOOHaq is considered as the key antimicrobial air-byproduct species. These results indicate the important dependence of plasma biomedical effects on the processing environment, which finally relates to the critical contributions of the key reactive species formed therein.

Facultative Sterol Uptake in an Ergosterol-Deficient Clinical Isolate of Candida glabrata Harboring a Missense Mutation in ERG11 and Exhibiting Cross-Resistance to Azoles and Amphotericin B

Science.gov (United States)

Hull, Claire M.; Parker, Josie E.; Bader, Oliver; Weig, Michael; Gross, Uwe; Warrilow, Andrew G. S.; Kelly, Diane E.

2012-01-01

We identified a clinical isolate of Candida glabrata (CG156) exhibiting flocculent growth and cross-resistance to fluconazole (FLC), voriconazole (VRC), and amphotericin B (AMB), with MICs of >256, >256, and 32 μg ml−1, respectively. Sterol analysis using gas chromatography-mass spectrometry (GC-MS) revealed that CG156 was a sterol 14α-demethylase (Erg11p) mutant, wherein 14α-methylated intermediates (lanosterol was >80% of the total) were the only detectable sterols. ERG11 sequencing indicated that CG156 harbored a single-amino-acid substitution (G315D) which nullified the function of native Erg11p. In heterologous expression studies using a doxycycline-regulatable Saccharomyces cerevisiae erg11 strain, wild-type C. glabrata Erg11p fully complemented the function of S. cerevisiae sterol 14α-demethylase, restoring growth and ergosterol synthesis in recombinant yeast; mutated CG156 Erg11p did not. CG156 was culturable using sterol-free, glucose-containing yeast minimal medium (glcYM). However, when grown on sterol-supplemented glcYM (with ergosta 7,22-dienol, ergosterol, cholestanol, cholesterol, Δ7-cholestenol, or desmosterol), CG156 cultures exhibited shorter lag phases, reached higher cell densities, and showed alterations in cellular sterol composition. Unlike comparator isolates (harboring wild-type ERG11) that became less sensitive to FLC and VRC when cultured on sterol-supplemented glcYM, facultative sterol uptake by CG156 did not affect its azole-resistant phenotype. Conversely, CG156 grown using glcYM with ergosterol (or with ergosta 7,22-dienol) showed increased sensitivity to AMB; CG156 grown using glcYM with cholesterol (or with cholestanol) became more resistant (MICs of 2 and >64 μg AMB ml−1, respectively). Our results provide insights into the consequences of sterol uptake and metabolism on growth and antifungal resistance in C. glabrata. PMID:22615281

Lab-scale preparations of Candida albicans and dual Candida albicans-Candida glabrata biofilms on the surface of medical-grade polyvinyl chloride (PVC) perfusion tube using a modified gravity-supported free-flow biofilm incubator (GS-FFBI).

Science.gov (United States)

Shao, Jing; Lu, KeQiao; Tian, Ge; Cui, YanYan; Yan, YuanYuan; Wang, TianMing; Zhang, XinLong; Wang, ChangZhong

2015-02-01

The assembly of a man-made gravity-supported free-flow biofilm incubator (GS-FFBI) was described, which was composed of a gas cushion injector and four incubators. The GS-FFBI had the characteristics of (i) a bottom-up flow direction, and (ii) lab-scale biofilm preparation without the use of a multichannel pump. Two opportunistic fungal strains, namely Candida albicans and Candida glabrata, were employed to incubate C. albicans and dual C. albicans-C. glabrata biofilms on the surface of medical-grade polyvinyl chloride perfusion tube. In terms of the results from {2, 3-bis (2-methoxy-4-nitro-5-sulfo-phenyl)-2H-tetrazolium-5-carboxanilide} (XTT) assay, dry weight measurement, colony-forming unit counting, susceptibility test, and scanning electron microscopy, it was demonstrated that GS-FFBI could form both stable single and dual Candida biofilms with no significant variations among the four incubators or the three daily incubations within 21h, and could operate for at least 96h smoothly with no contamination of stock medium. The results also indicated, for the first time, that C. albicans and C. glabrata might be co-existent competitively and symbiotically in the dual biofilms with flowing media. GS-FFBI would be a useful device to study in vitro morphological and physiological features of microbial biofilms in the medical settings. Copyright © 2014 Elsevier B.V. All rights reserved.

Dispersão de Biomphalaria straminea, hospedeira intermediária do Schistosoma mansoni, através da distribuição de peixes The spreading of Biomphalaria straminea, intermediate host of Schistosoma mansoni through the distribution of fishes

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Renato de R. Corrêa

1970-12-01

Full Text Available Foi focalizado, pela primeira vez o encontro de B. straminea no Estado de São Paulo. Esta espécie vem juntar-se aos planorbídeos já assinalados em nosso Estado. Foram descritos os criadouros, onde a B. straminea foi coletada, localizados em tanques de criação de peixes nas Estações de Piscicultura de Barra Bonita e Americana, Estado de São Paulo, e em um aquário particular na capital dêsse Estado. Fêz-se referência ao transporte de peixes oriundos de zonas do país onde ocorre aquela espécie, Amazonas e Ceará, como responsável pela introdução daquele molusco no Estado. Destacou-se êsse achado pelo perigo que representa a distribuição de peixes da maneira como vem sendo feita atualmente em nosso país, tendo sido julgado necessário o estabelecimento de quarentena para aquêles vindos de zonas infestadas por espécies hospedeiras intermediárias do S. mansoni. Foram relatadas as medidas de combate aos caramujos efetuadas imediatamente após aquela descoberta e os resultados obtidos. Conclui-se que a dispersão passiva da B. straminea pelo transporte de peixes, deve ampliar a distribuição geográfica dêsse planorbídeo, já assinalado na Venezuela, Guianas e no Brasil, sendo que neste último ocorre em tôdas as Unidades Federativas, exceto, no Rio Grande do Sul, Santa Catarina, Rio de Janeiro e Territórios.Up the present, the works of collecting planorbids done in 226 municipalities for the elaboration of the geographical distribution chart in the State of São Paulo (Brazil, showed the presence of two intermediate host species of Schistosoma mansoni: Biomphalaria tenagophila and Biompralaria glabrata. Although the technicians from the Psiculture Stations, have not found snails in the water inside the containers used for the transportation of fishes, the ecological conditions of B. straminea in the latest researches are such as to indicate that they have been introduced, in our State through fish transportation imported

Plant transcriptomics and responses to environmental stress: an ...

Indian Academy of Sciences (India)

3Centre for Environmental Research, Near East University, 33010, Lefkosha, Turkish Republic of the Northern Cyprus. 4Department of ...... Transcriptomic analysis of sense and antisense strands of .... 2008 Stem cell transcriptome profiling via.

Redistribution of carbon flux in Torulopsis glabrata by altering vitamin and calcium level.

Science.gov (United States)

Liu, Liming; Li, Yin; Zhu, Yang; Du, Guocheng; Chen, Jian

2007-01-01

Manipulation of cofactor (thiamine, biotin and Ca(2+)) levels as a potential tool to redistribute carbon flux was studied in Torulopsis glabrata. With sub-optimization of vitamin in fermentation medium, the carbon flux was blocked at the key node of pyruvate, and 69 g/L pyruvate was accumulated. Increasing the concentrations of thiamine and biotin could selectively open the valve of carbon flux from pyruvate to pyruvate dehydrogenase complex, the pyruvate carboxylase (PC) pathway and the channel into the TCA cycle, leading to the over-production of alpha-ketoglutarate. In addition, the activity of PC was enhanced with Ca(2+) present in fermentation medium. By combining high concentration's vitamins and CaCO(3) as the pH buffer, a batch culture was conducted in a 7-L fermentor, with the pyruvate concentration decreased to 21.8 g/L while alpha-ketoglutarate concentration increased to 43.7 g/L. Our study indicated that the metabolic flux could be redistributed to overproduce desired metabolites with manipulating the cofactor levels. Furthermore, the manipulation of vitamin level provided an alternative tool to realize metabolic engineering goals.

Strategic and Operational Plan for Integrating Transcriptomics ...

Science.gov (United States)

Plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT; the details are in the attached slide presentation presentation on plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT, given at the OECD meeting on June 23, 2016

Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

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Rodd F Helen

2011-04-01

Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

Invading freshwater snails and biological control in Martinique Island, French West Indies.

Science.gov (United States)

Pointier, J P

2001-01-01

Eight alien freshwater snail species were introduced into Martinique Island during the last 50 years. The introduced snails include four planorbids (Biomphalaria straminea, Helisoma duryi, Amerianna carinata and Gyraulus sp.), three thiarids (Melanoides tuberculata, M. amabilis and Tarebia granifera) and one ampullarid (Marisa cornuarietis). Four of these species rapidly colonized the whole Martinican hydrographic system whereas the other four remained restricted to some particular sites. The invasion processes were documented during the last 20 years and showed (i) a rapid invasion of the island by several morphs of M. tuberculata at the beginning of the 80's; (ii) the introduction of T. granifera in 1991 and M. amabilis in 1997; and (iii) the rapid spread of these last two species throughout the island. In the years following its introduction, M. tuberculata was used in biological control experiments against the snail hosts of schistosomiasis, B. glabrata and B. straminea. Experiments were conducted with success in several groups of water-cress beds which constituted the latest transmission sites for schistosomiasis at the beginning of the 80's. A malacological survey carried out in 2000 all over the island showed the absence of B. glabrata but the presence of some residual populations of B. straminea. Long-term studies carried out in Martinique have shown that the thiarids are able to maintain relatively stable populations over a long period of time, thus preventing recolonization by the snail hosts. Within this context the invasion of the hydrographic system of Martinique by thiarid snails has resulted in an efficient and sustainable control of the intermediate hosts of schistosomiasis.

Transcriptome sequences resolve deep relationships of the grape family.

Science.gov (United States)

Wen, Jun; Xiong, Zhiqiang; Nie, Ze-Long; Mao, Likai; Zhu, Yabing; Kan, Xian-Zhao; Ickert-Bond, Stefanie M; Gerrath, Jean; Zimmer, Elizabeth A; Fang, Xiao-Dong

2013-01-01

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

Avaliação do tipo de substrato e do período de armazenamento para a germinação de sementes de Cordia glabrata (Mart. DC. - DOI: 10.4025/actascibiolsci.v31i3.1013 Evaluation of substrate type and storage period for the germination of Cordia glabrata (Mart. DC seeds - DOI: 10.4025/actascibiolsci.v31i3.1013

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Juliana Gadum

2009-07-01

Full Text Available Informações sobre a viabilidade e substratos adequados para a germinação de sementes de espécies arbóreas nativas são escassas. Cordia glabrata (louro-preto, espécie pioneira e de ampla distribuição, está incluída entre essas espécies. Suas características permitem a utilização em ornamentação, na prática apícola e na medicina popular. Levando em conta seu potencial de utilização, este trabalho teve por objetivo avaliar as taxas de germinação, em diferentes substratos, de sementes recém-colhidas e armazenadas até 120 dias em laboratório, as quais foram coletadas no Pantanal do Rio Negro, Estado do Mato Grosso do Sul. Foram realizados testes com sementes recém-colhidas e após 30, 60, 90 e 120 dias de armazenamento, em três tipos de substrato (papel-filtro, solo arenoso e solo arenoso + matéria orgânica. Os resultados revelaram que C. glabrata possui pequena porcentagem de água (1,55% nas sementes, que decai com o período de armazenamento. Seu período de viabilidade é curto (90 dias e os melhores resultados foram obtidos com sementes recém-colhidas germinadas em papel-filtro (34%, com índice de velocidade de germinação de 10.Information about the feasibility and adequate substrates for the germination of seeds from native arboreous species are scarce. Cordia glabrata (louro preto, a pioneering species with wide distribution, is included among these species. Its characteristics allow its use in ornamentation, apiculture and popular medicine. Considering its potential of utilization, this work had as objective to evaluate the germination rates, in different substrates, of recently reaped seeds stored for up to 120 days in laboratory, which were collected in Pantanal of the Rio Negro, Mato Grosso do Sul State. Tests were done with recently reaped seeds and after 30, 60, 90 and 120 days of storage, in three kinds of substrate (paper filter, sandy soil and sandy soil + organic matter. The results revealed that C

The utility of transcriptomics in fish conservation.

Science.gov (United States)

Connon, Richard E; Jeffries, Ken M; Komoroske, Lisa M; Todgham, Anne E; Fangue, Nann A

2018-01-29

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers. © 2018. Published by The Company of Biologists Ltd.

3rd International Conference on Transcriptomics

OpenAIRE

John A Daniel

2017-01-01

Conference Series has been instrumental in conducting international Biochemistry meetings for seven years, and very excited to expand Europe, America and Asia Pacific continents. Previous meetings were held in major cities like Philadelphia, Orlando with success the meetings again scheduled in three continents. 3rd International Conference on Transcriptomics to be held during October 30 - November 01, 2017 at Bangkok, Thailand The Global Transcriptomics business sector to develop at a C...

Transcriptome sequences resolve deep relationships of the grape family.

Directory of Open Access Journals (Sweden)

Jun Wen

Full Text Available Previous phylogenetic studies of the grape family (Vitaceae yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

The Human Transcriptome: An Unfinished Story

Directory of Open Access Journals (Sweden)

Mihaela Pertea

2012-06-01

Full Text Available Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

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Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

Inactivation of Candida glabrata by a humid DC argon discharge afterglow: dominant contributions of short-lived aqueous active species

International Nuclear Information System (INIS)

Xiong, Qing; Liu, Hongbin; Xu, Le; Wang, Xia; Zhu, Qunlin; Lu, Weiping; Chen, Qiang; Zeng, Xue; Yi, Ping

2017-01-01

Plasma medicine applications are currently attracting significant interest all over the world. Bactericidal treatments of Candida glabrata cultured in saline suspension are performed in this study by a room-temperature reactive afterglow of a DC-driven argon discharge. Water vapor was added to the discharge to study the inactivation contributions of reactive hydrolytic species including OH and H 2 O 2 transporting along the gas flow to the treated solutions. The inactivation results indicate that the dominant roles in the bactericidal treatments are played by the short-lived aqueous active species, but not the stable species like H 2 O 2aq (aq indicates an aqueous species). Further analysis shows that the ·OH aq radicals play an important role in the inactivation process. The ·OH aq radicals in the suspension are mostly produced from the direct dissolution of the OH species in the reactive afterglow. With the increase of added water vapor content, the ·OH aq production increases and enhances the inactivation efficiency of C. glabrata . Furthermore, it is found that the ambient air diffusion shows essential effects on the bactericidal activity of the remote humid argon discharge. Higher bactericidal effects can be obtained in open-space treatments compared to in a controlled Ar + H 2 O gas atmosphere. Key active air-byproduct species are believed to be generated in the suspension during the treatments and contributing to the inactivation process. Based on chemical analysis, the peroxynitrous acid ONOOH aq is considered as the key antimicrobial air-byproduct species. These results indicate the important dependence of plasma biomedical effects on the processing environment, which finally relates to the critical contributions of the key reactive species formed therein. (paper)

Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis.

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Jones, Beryl M; Wcislo, William T; Robinson, Gene E

2015-08-14

Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome for analysis of gene expression profiles throughout development. Gene Ontology analysis indicates that stage-specific genes are involved in ion transport, cell-cell signaling, and metabolism. A number of distinct biological processes are upregulated in each life stage, and transitions between life stages involve shifts in dominant functional processes, including shifts from transcriptional regulation in embryos to metabolism in larvae, and increased lipid metabolism in adults. We expect that this transcriptome will provide a useful resource for future analyses to better understand the molecular basis of the evolution of eusociality and, more generally, phenotypic plasticity. Copyright © 2015 Jones et al.

Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse

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Lauren L. Kordonowy

2016-10-01

Full Text Available Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens of Peromyscus eremicus (Cactus mouse, a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss.

Control of schistosomiasis in Guayama and Arroyo, Puerto Rico*

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Jobin, William R.; Ferguson, Frederick F.; Palmer, Juan R.

1970-01-01

In 1953, a programme to control schistosomiasis mansoni was started in Guayama and Arroyo, Puerto Rico, employing, first, chemical and, later, both biological and chemical methods to control Biomphalaria glabrata, the snail host of Schistosoma mansoni. Sodium pentachlorophenate was the molluscicide, and an ampullarid snail, Marisa cornuarietis, was used for biological control in ponds and reservoirs. In addition some chemotherapy was given to infected persons. The prevalence of intestinal schistosomiasis was measured annually, sampling about one-third of the 6-year-old population in Guayama and Arroyo and in Caguas, an untreated area. Costs of the programme and the results are discussed in relation to similar projects in other parts of Puerto Rico. In Guayama and Arroyo the prevalence of schistosomiasis reached zero in 6-year-olds by 1966 despite the persistence of the disease in a nearby untreated area. Although this decline appeared related to the control effort, it is noted that a large decline also occurred in the untreated area, suggesting the influence of other factors such as economic development or improvements in sanitation. PMID:5309511

Control of schistosomiasis in Guayama and Arroyo, Puerto Rico.

Science.gov (United States)

Jobin, W R; Ferguson, F F; Palmer, J R

1970-01-01

In 1953, a programme to control schistosomiasis mansoni was started in Guayama and Arroyo, Puerto Rico, employing, first, chemical and, later, both biological and chemical methods to control Biomphalaria glabrata, the snail host of Schistosoma mansoni. Sodium pentachlorophenate was the molluscicide, and an ampullarid snail, Marisa cornuarietis, was used for biological control in ponds and reservoirs. In addition some chemotherapy was given to infected persons. The prevalence of intestinal schistosomiasis was measured annually, sampling about one-third of the 6-year-old population in Guayama and Arroyo and in Caguas, an untreated area. Costs of the programme and the results are discussed in relation to similar projects in other parts of Puerto Rico. In Guayama and Arroyo the prevalence of schistosomiasis reached zero in 6-year-olds by 1966 despite the persistence of the disease in a nearby untreated area. Although this decline appeared related to the control effort, it is noted that a large decline also occurred in the untreated area, suggesting the influence of other factors such as economic development or improvements in sanitation.

Activity of praziquantel on in vitro transformed Schistosoma mansoni sporocysts

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ACA Mattos

2006-10-01

Full Text Available Praziquantel (PZQ is effective against all the evolutive phases of Schistosoma mansoni. Infected Biomphalaria glabrata snails have their cercarial shedding interrupted when exposed to PZQ. Using primary in vitro transformed sporocysts, labeled with the probe Hoechst 33258 (indicator of membrane integrity, and lectin of Glycine max (specific for carbohydrate of N-acetylgalactosamine membrane, we evaluated the presence of lysosomes at this evolutive phase of S. mansoni, as well as the influence of PZQ on these acidic organelles and on the tegument of the sporocyst. Although the sporocyst remained alive, it was observed that there was a marked contraction of its musculature, and there occurred a change in the parasite's structure. Also, the acidic vesicles found in the sporocysts showed a larger delimited area after contact of the parasites with PZQ. Damages to the tegument was also observed, as show a well-marked labeling either with Hoechst 33258 or with lectin of Glycine max after contact of sporocysts with the drug. These results could partially explain the interruption/reduction mechanism of cercarial shedding in snails exposed to PZQ.

The Primary Role of Fibrinogen-Related Proteins in Invertebrates Is Defense, Not Coagulation

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Hanington, Patrick C.; Zhang, Si-Ming

2010-01-01

In vertebrates, the conversion of fibrinogen into fibrin is an essential process that underlies the establishment of the supporting protein framework required for coagulation. In invertebrates, fibrinogen-domain-containing proteins play a role in the defense response generated against pathogens; however, they do not function in coagulation, suggesting that this role has been recently acquired. Molecules containing fibrinogen motifs have been identified in numerous invertebrate organisms, and most of these molecules known to date have been linked to defense. Moreover, recent genome projects of invertebrate animals have revealed surprisingly high numbers of fibrinogen-like loci in their genomes, suggesting important and perhaps diverse functions of fibrinogen-like proteins in invertebrates. The ancestral role of molecules containing fibrinogen-related domains (FReDs) with immunity is the focus of this review, with emphasis on specific FReDs called fibrinogen-related proteins (FREPs) identified from the schistosome-transmitting mollusc Biomphalaria glabrata. Herein, we outline the range of invertebrate organisms FREPs can be found in, and detail the roles these molecules play in defense and protection against infection. PMID:21063081

Sobre um foco urbano de esquistossomose em área metropolitana da região sudeste do Brasil

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Guimarães Carlos Tito

1993-01-01

Full Text Available Descreve-se foco de transmissão ativa de esquistossomose mansoni em Belo Horizonte, MG, Brasil, localizado no Parque "Julien Rien", uma área de lazer com 48.500 m², criada pela Prefeitura Municipal, em 1980, na zona sul da cidade. Em capturas feitas durante 10 anos (1983-1992 foram coletados 3.361 exemplares de Biomphalaria glabrata (diâmetro médio= 9,3 mm, dos quais 23 (0,7% estavam infectados pelo Schistosoma mansoni. O encontro de moluscos hospedeiros intermediários do S. mansoni em áreas urbanizadas (pequenos lagos artificiais cimentados de parques, jardins, prédios públicos, e outros pode estar relacionado com a introdução de peixes e plantas aquáticas. É sugerida, como medida profilática, a não introdução de peixes e plantas aquáticas nesses locais, a não ser após período de quarentena de, no mínimo, 30 dias.

[Schistosomiasis in an ecotourism area in Minas Gerais State, Brazil].

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Massara, Cristiano Lara; Amaral, Graciela Larissa; Caldeira, Roberta Lima; Drummond, Sandra Costa; Enk, Martin Johannes; Carvalho, Omar dos Santos

2008-07-01

This paper discusses schistosomiasis transmission in São José da Serra, a village with a population of 500 in the county of Jaboticatubas, Minas Gerais State, Brazil. The area receives thousands of visitors a year for ecotourism. The study was motivated by a case of acute schistosomiasis involving a couple that spent the 2007 Carnival (Mardi Gras) holiday in the area. Stool tests from 268 local residents (53.6% of the population) showed that 35 (13%) were positive for the infection. A comparison with a previous survey (2005) in the same location showed an increase in the schistosomiasis-positive rate from 9.6% to 12.5%, among the 56 individuals who participated in both surveys. A malacological survey of 65 Biomphalaria glabrata snails showed one specimen (1.5%) eliminating cercariae. In a similar survey in 2005, no positive snail specimens were found. The study indicates that active schistosomiasis transmission is occurring in the area, and that integrated educational programs are needed for both the local community and tourists.

Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum transcriptome.

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Silvan Oulion

Full Text Available BACKGROUND: The basally divergent phylogenetic position of amphioxus (Cephalochordata, as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae. RESULTS: Starting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode. Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp. Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species. CONCLUSION: We obtained a high-quality amphioxus (B. lanceolatum reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation

TCW: transcriptome computational workbench.

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Carol Soderlund

Full Text Available BACKGROUND: The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. METHODOLOGY: The Transcriptome Computational Workbench (TCW provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms. The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina or assembling long sequences (e.g. Sanger, 454, transcripts, annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. CONCLUSION: It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the

TCW: transcriptome computational workbench.

Science.gov (United States)

Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

2013-01-01

The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

High Throughput Transcriptomics @ USEPA (Toxicology ...

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The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

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Xianwen Ren

Full Text Available Next generation sequencing (NGS technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.

Clinical characteristics of the first cases of invasive candidiasis in China due to pan-echinocandin-resistant Candida tropicalis and Candida glabrata isolates with delineation of their resistance mechanisms

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Xiao M

2018-01-01

Full Text Available Meng Xiao,1,2,* Xin Fan,1–3,* Xin Hou,1,2,4,* Sharon CA Chen,5 He Wang,1,2 Fanrong Kong,5 Zi-Yong Sun,6,* Yun-Zhuo Chu,7 Ying-Chun Xu1,2 1Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China; 2Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, People’s Republic of China; 3Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital, Beijing, People’s Republic of China; 4Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China; 5Center for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, NSW, Australia; 6Department of Clinical Laboratory, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, People’s Republic of China; 7Department of Clinical Laboratory, The First Affiliated Hospital of Chinese Medical University, Shenyang, People’s Republic of China *These authors contributed equally to this work Abstract: Echinocandin antifungal agents have become the first-line therapy for invasive candidiasis (IC in many countries. Despite their increasing use, resistance to this class of drug is, overall, still uncommon. Here, we report two patients from the People’s Republic of China with IC, one with infection caused by pan-echinocandin-resistant Candida tropicalis and the other by pan-echinocandin-resistant Candida glabrata. We also describe the mechanisms of drug resistance of these isolates. The echinocandin-resistant C. glabrata isolate was cultured from ascitic fluid of a 46-year-old male patient with intra-abdominal IC developing after surgery in 2012. This patient had had no prior antifungal exposure. The echinocandin-resistant C. tropicalis isolate was cultured from chest drainage

The testes transcriptome derived from the New World Screwworm, Cochliomyia hominivorax TSA

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In a collaboration with National Center for Genome Resources researchers, we sequenced and assembled the testes transcriptome derived from the Pacora, Panama, production plant strain of the New World Screwworm, Cochliomyia hominivorax. This transcriptome contains 4,149 unigenes and the Transcriptome...

Principle considerations for the use of transcriptomics in doping research.

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Neuberger, Elmo W I; Moser, Dirk A; Simon, Perikles

2011-10-01

Over the course of the past decade, technical progress has enabled scientists to investigate genome-wide RNA expression using microarray platforms. This transcriptomic approach represents a promising tool for the discovery of basic gene expression patterns and for identification of cellular signalling pathways under various conditions. Since doping substances have been shown to influence mRNA expression, it has been suggested that these changes can be detected by screening the blood transcriptome. In this review, we critically discuss the potential but also the pitfalls of this application as a tool in doping research. Transcriptomic approaches were considered to potentially provide researchers with a unique gene expression signature or with a specific biomarker for various physiological and pathophysiological conditions. Since transcriptomic approaches are considerably prone to biological and technical confounding factors that act on study subjects or samples, very strict guidelines for the use of transcriptomics in human study subjects have been developed. Typical field conditions associated with doping controls limit the feasibility of following these strict guidelines as there are too many variables counteracting a standardized procedure. After almost a decade of research using transcriptomic tools, it still remains a matter of future technological progress to identify the ultimate biomarker using technologies and/or methodologies that are sufficiently robust against typical biological and technical bias and that are valid in a court of law. Copyright © 2011 John Wiley & Sons, Ltd.

Biological control of the snail hosts of schistosomiasis in areas of low transmission: the example of the Caribbean area.

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Pointier, J P; Jourdane, J

2000-10-23

The biological control of schistosomiasis has already proven its efficiency in several habitats in the Caribbean area. Two main types of biological control agents, either trematode parasites or competitor snails have been studied and tested against the snail hosts of schistosomiasis in this region. The first one, Ribeiroia guadeloupensis, a trematode sterilizing Biomphalaria glabrata was successfully tested in a Guadeloupean pond housing a natural population of B. glabrata. The second agent involves several species of competitor snails belonging to the Ampullariidae (Pomacea glauca, Marisa cornuarietis) and Thiaridae (Tarebia granifera, Melanoides tuberculata) families. Ampullarid snails were tested with success in several West Indian islands such as Guadeloupe. Thiarid snails have also proven their efficiency but also their limits in several types of habitats in Guadeloupe, Martinique, St. Lucia and Venezuela. Competitor snails have also proven to be useful in preventing the recolonization by the snail hosts after molluscicide treatments. The case of the rivers of the littoral central part of Venezuela is particularly relevant to this issue. The island of Martinique also constitutes a good example of the importance of competitor snails in a post-transmission phase of schistosomiasis control. This island is a well-developed country where schistosomiasis transmission was interrupted in the 1970s. However, the reactivation of some transmission sites was observed in the 1980s. The introduction of M. tuberculata into these sites resulted in the interruption of transmission and the near total disappearance of the snail hosts. Presently, the thiarid snails have colonized the whole Martinican hydrographic system and maintain dense populations preventing an eventual recolonization by the planorbid snails and thus are maintaining a sustainable control.

Invading freshwater snails and biological control in Martinique Island, French West Indies

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Jean-Pierre Pointier

2001-09-01

Full Text Available Eight alien freshwater snail species were introduced into Martinique Island during the last 50 years. The introduced snails include four planorbids (Biomphalaria straminea, Helisoma duryi, Amerianna carinata and Gyraulus sp., three thiarids (Melanoides tuberculata, M. amabilis and Tarebia granifera and one ampullarid (Marisa cornuarietis. Four of these species rapidly colonized the whole Martinican hydrographic system whereas the other four remained restricted to some particular sites. The invasion processes were documented during the last 20 years and showed (i a rapid invasion of the island by several morphs of M. tuberculata at the beginning of the 80's; (ii the introduction of T. granifera in 1991 and M. amabilis in 1997; and (iii the rapid spread of these last two species throughout the island. In the years following its introduction, M. tuberculata was used in biological control experiments against the snail hosts of schistosomiasis, B. glabrata and B. straminea. Experiments were conducted with success in several groups of water-cress beds which constituted the latest transmission sites for schistosomiasis at the beginning of the 80's. A malacological survey carried out in 2000 all over the island showed the absence of B. glabrata but the presence of some residual populations of B. straminea. Long-term studies carried out in Martinique have shown that the thiarids are able to maintain relatively stable populations over a long period of time, thus preventing recolonization by the snail hosts. Within this context the invasion of the hydrographic system of Martinique by thiarid snails has resulted in an efficient and sustainable control of the intermediate hosts of schistosomiasis.

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

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Zhang, Jin; Ruhlman, Tracey A; Mower, Jeffrey P; Jansen, Robert K

2013-12-29

Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition

Avaliação da esquistossomose e de outras parasitoses intestinais, em escolares do município de Bambuí, Minas Gerais, Brasil Evaluation of the schistosomiasis and others intestinal parasitosis in the school children of Bambuí county, Minas Gerais, Brazil

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Roberto Sena Rocha

2000-10-01

Full Text Available O objetivo desse trabalho foi determinar a prevalência das parasitoses em escolares de Bambuí, através de exames coprológicos (direto e Kato-Katz e reavaliar os criadouros de moluscos descritos no município. Dos 2.901 escolares examinados, 20,1% estavam parasitados, sendo que Giardia lamblia, Entamoeba coli, Ascaris lumbricoides e ancilostomídeos foram os parasitas mais freqüentes, com prevalências de 6,2%, 6,2%, 4,8% e 1,4%, respectivamente. Os ancilostomídeos foram significativamente mais freqüentes na zona rural e nos alunos com mais de 14 anos, enquanto a prevalência da E. coli foi maior na zona urbana e a G. lamblia mais freqüente na faixa etária de 0-6 anos. Somente três crianças eliminavam ovos de Schistosoma mansoni. O único hospedeiro intermediário encontrado foi a Biomphalaria glabrata e nenhuma delas estava eliminando cercárias de S. mansoni . Comparando-se estes dados a de levantamentos realizados anteriormente no município, observou-se uma queda na prevalência de todos os parasitas. Algumas hipóteses para tentar explicar esta queda são discutidas tais como: processo intenso de urbanização e a melhoria das condições sócio-sanitárias do município.This work was carried out with the purpose of determining the prevalence of intestinal parasitoses in the school children of Bambuí, through parasitological examinations (direct and Kato-Katz methods and reevaluating the snails' breeding places described in the county. Of the 2,091 school children examined, 20.1% had at least one parasitic infection. Giardia lamblia, Entamoeba coli, Ascaris lumbricoides and hookworm are the most frequent parasites, with a prevalence of 6.2%, 6.2%, 4.8% and 1.4%, respectively. The hookworms were significantly more frequent among students from the rural area and in those aged over 14 years, while the prevalence of E. coli was greater in the urban area and the G. lamblia was more frequent in children under 6 years old. Only three

Blood transcriptomics and metabolomics for personalized medicine.

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Li, Shuzhao; Todor, Andrei; Luo, Ruiyan

2016-01-01

Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine.

Carboxymethylated ɩ-carrageenan conjugated amphotericin B loaded gelatin nanoparticles for treating intracellular Candida glabrata infections.

Science.gov (United States)

Aparna, V; Melge, Anu Rohit; Rajan, V K; Biswas, Raja; Jayakumar, R; Gopi Mohan, C

2018-04-15

Intercellular Candida glabrata infections are difficult to treat due to poor penetration of drugs into the fungal niche. Delivering amphotericin B (Amp B) into the macrophages where the pathogen inhabits is an effective solution. We are studying the macrophage targeting proficiency of ɩ-carrageenan for the delivery of Amp B using gelatin A nanoparticles (GNPs). The choice of gelatin A was the outcome of in silico inspections where the amino functionalized polymer having the best docking score with Amp B was selected. We prepared a sustained release formulation of amp B loaded carboxymethyl ɩ-carrageenan conjugated gelatin nanoparticles (CMC-Amp B-GNPs) with size 343±12nm and -25±5.3mV zeta potential. The formulations were found to be stable, biocompatible and non-haemolytic. Flow cytometry analysis showed 3 fold higher uptake of CMC-GNPs compared to the GNPs by RAW 264.7 cells. CMC-Amp B-GNPs showed enhanced antifungal activity than bare Amp B and Amp B-GNPs. Copyright © 2017 Elsevier B.V. All rights reserved.

Transcriptome dynamics-based operon prediction in prokaryotes.

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Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri; Tagliaferri, Roberto; Greco, Dario

2014-05-16

Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.

Transcriptome profiling of Elettaria cardamomum (L. Maton (small cardamom

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F. Nadiya

2017-03-01

Full Text Available Elettaria cardamomum (L. Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base and 24,889,197 (75 base raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild and SRX1141276 (cultivars. The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

The Embryonic Transcriptome of the Red-Eared Slider Turtle (Trachemys scripta.

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Nicholas J Kaplinsky

Full Text Available The bony shell of the turtle is an evolutionary novelty not found in any other group of animals, however, research into its formation has suggested that it has evolved through modification of conserved developmental mechanisms. Although these mechanisms have been extensively characterized in model organisms, the tools for characterizing them in non-model organisms such as turtles have been limited by a lack of genomic resources. We have used a next generation sequencing approach to generate and assemble a transcriptome from stage 14 and 17 Trachemys scripta embryos, stages during which important events in shell development are known to take place. The transcriptome consists of 231,876 sequences with an N50 of 1,166 bp. GO terms and EC codes were assigned to the 61,643 unique predicted proteins identified in the transcriptome sequences. All major GO categories and metabolic pathways are represented in the transcriptome. Transcriptome sequences were used to amplify several cDNA fragments designed for use as RNA in situ probes. One of these, BMP5, was hybridized to a T. scripta embryo and exhibits both conserved and novel expression patterns. The transcriptome sequences should be of broad use for understanding the evolution and development of the turtle shell and for annotating any future T. scripta genome sequences.

The Embryonic Transcriptome of the Red-Eared Slider Turtle (Trachemys scripta).

Science.gov (United States)

Kaplinsky, Nicholas J; Gilbert, Scott F; Cebra-Thomas, Judith; Lilleväli, Kersti; Saare, Merly; Chang, Eric Y; Edelman, Hannah E; Frick, Melissa A; Guan, Yin; Hammond, Rebecca M; Hampilos, Nicholas H; Opoku, David S B; Sariahmed, Karim; Sherman, Eric A; Watson, Ray

2013-01-01

The bony shell of the turtle is an evolutionary novelty not found in any other group of animals, however, research into its formation has suggested that it has evolved through modification of conserved developmental mechanisms. Although these mechanisms have been extensively characterized in model organisms, the tools for characterizing them in non-model organisms such as turtles have been limited by a lack of genomic resources. We have used a next generation sequencing approach to generate and assemble a transcriptome from stage 14 and 17 Trachemys scripta embryos, stages during which important events in shell development are known to take place. The transcriptome consists of 231,876 sequences with an N50 of 1,166 bp. GO terms and EC codes were assigned to the 61,643 unique predicted proteins identified in the transcriptome sequences. All major GO categories and metabolic pathways are represented in the transcriptome. Transcriptome sequences were used to amplify several cDNA fragments designed for use as RNA in situ probes. One of these, BMP5, was hybridized to a T. scripta embryo and exhibits both conserved and novel expression patterns. The transcriptome sequences should be of broad use for understanding the evolution and development of the turtle shell and for annotating any future T. scripta genome sequences.

Global meta-analysis of transcriptomics studies.

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José Caldas

Full Text Available Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy, based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields multiple independent phenotype comparisons, and connections are established not between studies, but rather between subsets of the studies corresponding to phenotype comparisons. We propose a rank-based statistical meta-analysis framework that establishes global connections between transcriptomics studies without breaking down studies into sets of phenotype comparisons. By using a rank product method, our framework extracts global features from each study, corresponding to genes that are consistently among the most expressed or differentially expressed genes in that study. Those features are then statistically modelled via a term-frequency inverse-document frequency (TF-IDF model, which is then used for connecting studies. Our framework is fast and parameter-free; when applied to large collections of Homo sapiens and Streptococcus pneumoniae transcriptomics studies, it performs better than similarity-based approaches in retrieving related studies, using a Medical Subject Headings gold standard. Finally, we highlight via case studies how the framework can be used to derive novel biological hypotheses regarding related studies and the genes that drive those connections. Our proposed statistical framework shows that it is possible to perform a meta-analysis of transcriptomics studies with arbitrary experimental designs by deriving global expression features rather than decomposing studies into multiple phenotype comparisons.

Transcriptome signature of the adult mouse choroid plexus

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Marques Fernanda

2011-01-01

Full Text Available Abstract Background Although the gene expression profile of several tissues in humans and in rodent animal models has been explored, analysis of the complete choroid plexus (CP transcriptome is still lacking. A better characterization of the CP transcriptome can provide key insights into its functions as one of the barriers that separate the brain from the periphery and in the production of cerebrospinal fluid. Methods This work extends further what is known about the mouse CP transcriptome through a microarray analysis of CP tissue from normal mice under physiological conditions. Results We found that the genes most highly expressed are those implicated in energy metabolism (oxidative phosphorylation, glycolysis/gluconeogenesis and in ribosomal function, which is in agreement with the secretory nature of the CP. On the other hand, genes encoding for immune mediators are among those with lower expression in basal conditions. In addition, we found genes known to be relevant during brain development, and not previously identified to be expressed in the CP, including those encoding for various axonal guidance and angiogenesis molecules and for growth factors. Some of these are known to influence the neural stem cell niche in the subventricular zone, highlighting the involvement of the CP as a likely modulator of neurogenesis. Interestingly, our observations confirm that the CP transcriptome is unique, displaying low homology with that of other tissues. Of note, we describe here that the closest similarity is with the transcriptome of the endothelial cells of the blood-brain barrier. Conclusions Based on the data presented here, it will now be possible to further explore the function of particular proteins of the CP secretome in health and in disease.

Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures.

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Moon Young Lee

Full Text Available Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC, which serve as slow-wave electrical pacemakers for gastrointestinal (GI smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

Developmental transcriptome of Aplysia californica'

KAUST Repository

Heyland, Andreas; Vue, Zer; Voolstra, Christian R.; Medina, Mó nica; Moroz, Leonid L.

2010-01-01

developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms

Biomphalaria obstructa (Morelet, 1849: a study of topotypic specimens (Mollusca: pulmonata: planorbidae

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W. Lobato Paraense

1990-12-01

Full Text Available A description of Biomphalaria obstructa (Morelet, 1849, based on specimens collected at its type locality - isla del carmen, state of Campeche, Mexico - is presented. The Shell is small, 13 mm in diameter, 3.5 mm in width and with 5.75 whorls in the largest specimen, thin, moderately lustrous and translucent, horn-colored. Whorls increasing regularly (neither slowly nor rapidly in diameter, rounded on the periphery side, bluntly angular on the left. Suture well-marked, deeper on the left. Right side widely concave, with first whorl deeply situated and partly hidden by the next. Left side shallower than right one, largely flattened, with first whorl plaintly visible. Aperture roundly heart-shaped, usually in the same plane as the body whorl but somewhat deflected to the left (less frequently to the right in some specimens. Peristome sharp, seldom blunt; a distinct callus on the parietal wall. A number of young shells develop one set (seldom more of apertural lamellae which tend to be resorbed as the shell grows. Absence of renal ridge. Ovotestis with about 70 mostly unbrached diverticula. Seminal vesicle beset with well-developed knoblike to fingerlike diverticula. Vaginal pouch more or less developed. Spermatheca club-shaped when empty, egg-shaped when full, and with intermediate forms between those extremes. Spermathecal body usually somewhat longer than the duct. Prostate with 7 to 20 (mean 12.06 ± 2.51 usually short diverticula which give off plumpish branches spreading out in a fan shape and overlapping to some extent their immediate neighbors. Foremost prostatic diverticulum nearly always partially or completely inserted between the spermathecal body and the uterine wall. Penial sheath consistently narrower and shorter than the prepuce. Muscular coat of the penis consisting of an inner longitudinal and an outer circular layers. Ratios between organ lengths: caudal to cephalic parts of female duct = 0.55 to 1.37 (mean 0.85 +- 0.17; cephalic

Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867.

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Huixia Du

Full Text Available BACKGROUND: Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus. RESULTS: In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs and 54,000 single nucleotide polymorphisms (SNPs were detected in the A. japonicus transcriptome. CONCLUSION: Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic

Genome Annotation and Transcriptomics of Oil-Producing Algae

Science.gov (United States)

2015-03-16

AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

De novo transcriptome assembly of shrimp Palaemon serratus

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Alejandra Perina

2017-03-01

Full Text Available The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000 to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.

Single cell transcriptome profiling of developing chick retinal cells.

Science.gov (United States)

Laboissonniere, Lauren A; Martin, Gregory M; Goetz, Jillian J; Bi, Ran; Pope, Brock; Weinand, Kallie; Ellson, Laura; Fru, Diane; Lee, Miranda; Wester, Andrea K; Liu, Peng; Trimarchi, Jeffrey M

2017-08-15

The vertebrate retina is a specialized photosensitive tissue comprised of six neuronal and one glial cell types, each of which develops in prescribed proportions at overlapping timepoints from a common progenitor pool. While each of these cells has a specific function contributing to proper vision in the mature animal, their differential representation in the retina as well as the presence of distinctive cellular subtypes makes identifying the transcriptomic signatures that lead to each retinal cell's fate determination and development challenging. We have analyzed transcriptomes from individual cells isolated from the chick retina throughout retinogenesis. While we focused our efforts on the retinal ganglion cells, our transcriptomes of developing chick cells also contained representation from multiple retinal cell types, including photoreceptors and interneurons at different stages of development. Most interesting was the identification of transcriptomes from individual mixed lineage progenitor cells in the chick as these cells offer a window into the cell fate decision-making process. Taken together, these data sets will enable us to uncover the most critical genes acting in the steps of cell fate determination and early differentiation of various retinal cell types. © 2017 Wiley Periodicals, Inc.

Transcriptome Profiling in Human Diseases: New Advances and Perspectives.

Science.gov (United States)

Casamassimi, Amelia; Federico, Antonio; Rienzo, Monica; Esposito, Sabrina; Ciccodicola, Alfredo

2017-07-29

In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements) and TCGA (The Cancer Genome Atlas), to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

Analysis of the Citrullus colocynthis transcriptome during water deficit stress.

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Zhuoyu Wang

Full Text Available Citrullus colocynthis is a very drought tolerant species, closely related to watermelon (C. lanatus var. lanatus, an economically important cucurbit crop. Drought is a threat to plant growth and development, and the discovery of drought inducible genes with various functions is of great importance. We used high throughput mRNA Illumina sequencing technology and bioinformatic strategies to analyze the C. colocynthis leaf transcriptome under drought treatment. Leaf samples at four different time points (0, 24, 36, or 48 hours of withholding water were used for RNA extraction and Illumina sequencing. qRT-PCR of several drought responsive genes was performed to confirm the accuracy of RNA sequencing. Leaf transcriptome analysis provided the first glimpse of the drought responsive transcriptome of this unique cucurbit species. A total of 5038 full-length cDNAs were detected, with 2545 genes showing significant changes during drought stress. Principle component analysis indicated that drought was the major contributing factor regulating transcriptome changes. Up regulation of many transcription factors, stress signaling factors, detoxification genes, and genes involved in phytohormone signaling and citrulline metabolism occurred under the water deficit conditions. The C. colocynthis transcriptome data highlight the activation of a large set of drought related genes in this species, thus providing a valuable resource for future functional analysis of candidate genes in defense of drought stress.

Comparison of four species of snails as potential decoys to intercept schistosome miracidia.

Science.gov (United States)

Laracuente, A; Brown, R A; Jobin, W

1979-01-01

Preliminary studies have shown that various species of aquatic snails may be used as decoys or "sponges" to intercept schistosome miracidia, thereby preventing the miracidia from reaching the snails which normally serve as their intermediate host. In this study, four species of snails were evaluated as candidate decoys for field trials: Marisa cornuarietis, Pomacea australis, Helisoma caribaeum, and Tarebia granifera. In the laboratory all four species caused considerable reductions in the proportion of Biomphalaria glabrata infected by miracidia of Schistosoma mansoni. The most effective decoys were M. cornuarietis and H. caribaeum, both of which caused experimental infection levels of 90% to decrease to 25% when five decoy snails were present for each target snail. When ten decoy snails were present for each target snail, the proportion infected decreased to 1%. M. cornuarietis was chosen as the candidate for field trials because it was found more frequently in Puerto Rico than was H. caribaeum. Initial field trials in two ponds showed that M. cornuarietis blocked infections at a ratio of 6 decoys to 1 target snail, confirming the laboratory results. Further studies in flowing water are needed before the technique can be generally evaluated in an endemic area.

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

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Sanz Libia

2011-05-01

Full Text Available Abstract Background A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects. Results The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27% were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements and class II (DNA transposons mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large

De novo transcriptome assembly of two different peach cultivars grown in Korea

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Yeonhwa Jo

2015-12-01

Full Text Available Peach (Prunus persica is one of the most popular stone fruits worldwide. Next generation sequencing (NGS has facilitated genome and transcriptome analyses of several stone fruit trees. In this study, we conducted de novo transcriptome analyses of two peach cultivars grown in Korea. Leaves of two cultivars, referred to as Jangtaek and Mibaek, were harvested and used for library preparation. The two prepared libraries were paired-end sequenced by the HiSeq2000 system. We obtained 8.14 GB and 9.62 GB sequence data from Jangtaek and Mibaek (NCBI accession numbers: SRS1056585 and SRS1056587, respectively. The Trinity program was used to assemble two transcriptomes de novo, resulting in 110,477 (Jangtaek and 136,196 (Mibaek transcripts. TransDecoder identified possible coding regions in assembled transcripts. The identified proteins were subjected to BLASTP search against NCBI's non-redundant database for functional annotation. This study provides transcriptome data for two peach cultivars, which might be useful for genetic marker development and comparative transcriptome analyses.

Low-cost motility tracking system (LOCOMOTIS for time-lapse microscopy applications and cell visualisation.

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Adam E Lynch

Full Text Available Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6×. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8×. In preliminary cell culture experiments using our system, velocities (mean µm/min ± SE of 0.81 ± 0.01 (Biomphalaria glabrata hemocytes on uncoated plates, 1.17 ± 0.004 (MDA-MB-231 breast cancer cells, 1.24 ± 0.006 (SC5 mouse Sertoli cells and 2.21 ± 0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates, were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers.

Low-cost motility tracking system (LOCOMOTIS) for time-lapse microscopy applications and cell visualisation.

Science.gov (United States)

Lynch, Adam E; Triajianto, Junian; Routledge, Edwin

2014-01-01

Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6×. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8×). In preliminary cell culture experiments using our system, velocities (mean µm/min ± SE) of 0.81 ± 0.01 (Biomphalaria glabrata hemocytes on uncoated plates), 1.17 ± 0.004 (MDA-MB-231 breast cancer cells), 1.24 ± 0.006 (SC5 mouse Sertoli cells) and 2.21 ± 0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates), were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers.

Low-Cost Motility Tracking System (LOCOMOTIS) for Time-Lapse Microscopy Applications and Cell Visualisation

Science.gov (United States)

Lynch, Adam E.; Triajianto, Junian; Routledge, Edwin

2014-01-01

Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6×. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8×). In preliminary cell culture experiments using our system, velocities (mean µm/min ± SE) of 0.81±0.01 (Biomphalaria glabrata hemocytes on uncoated plates), 1.17±0.004 (MDA-MB-231 breast cancer cells), 1.24±0.006 (SC5 mouse Sertoli cells) and 2.21±0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates), were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers. PMID:25121722

Transcriptomics resources of human tissues and organs

DEFF Research Database (Denmark)

Uhlén, Mathias; Hallström, Björn M.; Lindskog, Cecilia

2016-01-01

a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome......Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide...

Transcriptome architecture across tissues in the pig

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Folch Josep M

2008-04-01

Full Text Available Abstract Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes and between sexes (19 genes. The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

DEFF Research Database (Denmark)

Nicolas, Pierre; Mäder, Ulrike; Dervyn, Etienne

2012-01-01

Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutrition...

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

NARCIS (Netherlands)

Nicolas, Pierre; Maeder, Ulrike; Dervyn, Etienne; Rochat, Tatiana; Leduc, Aurelie; Pigeonneau, Nathalie; Bidnenko, Elena; Marchadier, Elodie; Hoebeke, Mark; Aymerich, Stephane; Becher, Doerte; Bisicchia, Paola; Botella, Eric; Delumeau, Olivier; Doherty, Geoff; Denham, Emma L.; Fogg, Mark J.; Fromion, Vincent; Goelzer, Anne; Hansen, Annette; Haertig, Elisabeth; Harwood, Colin R.; Homuth, Georg; Jarmer, Hanne; Jules, Matthieu; Klipp, Edda; Le Chat, Ludovic; Lecointe, Francois; Lewis, Peter; Liebermeister, Wolfram; March, Anika; Mars, Ruben A. T.; Nannapaneni, Priyanka; Noone, David; Pohl, Susanne; Rinn, Bernd; Ruegheimer, Frank; Sappa, Praveen K.; Samson, Franck; Schaffer, Marc; Schwikowski, Benno; Steil, Leif; Stuelke, Joerg; Wiegert, Thomas; Devine, Kevin M.; Wilkinson, Anthony J.; van Dijl, Jan Maarten; Hecker, Michael; Voelker, Uwe; Bessieres, Philippe; Noirot, Philippe

2012-01-01

Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional

Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish

NARCIS (Netherlands)

Palstra, A.P.; Beltran, S.; Burgerhout, E.; Brittijn, S.A.; Magnoni, L.J.; Henkel, C.V.; Jansen, A.; Thillart, G.E.E.J.M.; Spaink, H.P.; Planas, J.V.

2013-01-01

Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of

Transposable elements in the Anopheles funestus transcriptome.

Science.gov (United States)

Fernández-Medina, Rita D; Carareto, Claudia M A; Struchiner, Cláudio J; Ribeiro, José M C

2017-06-01

Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements.The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

Directory of Open Access Journals (Sweden)

Jacqueline D Farrell

Full Text Available Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.De novo transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.Our study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.

Transcriptome Profiling in Human Diseases: New Advances and Perspectives

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Amelia Casamassimi

2017-07-01

Full Text Available In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements and TCGA (The Cancer Genome Atlas, to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome.

Science.gov (United States)

Weisberg, Alexandra J; Kim, Gunjune; Westwood, James H; Jelesko, John G

2017-11-10

Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is "leaves of three, let it be", which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology. As a means of gaining a more molecular-oriented understanding of poison ivy physiology and ecology, Next Generation DNA sequencing technology was used to develop poison ivy root and leaf RNA-seq transcriptome resources. De novo assembled transcriptomes were analyzed to generate a core set of high quality expressed transcripts present in poison ivy tissue. The predicted protein sequences were evaluated for similarity to SwissProt homologs and InterProScan domains, as well as assigned both GO terms and KEGG annotations. Over 23,000 simple sequence repeats were identified in the transcriptome, and corresponding oligo nucleotide primer pairs were designed. A pan-transcriptome analysis of existing Anacardiaceae transcriptomes revealed conserved and unique transcripts among these species.

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

2010-03-22

Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis

Science.gov (United States)

Vukmirovic, Milica; Kaminski, Naftali

2018-01-01

Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by aberrant remodeling of the lung parenchyma with extensive changes to the phenotypes of all lung resident cells. The introduction of transcriptomics, genome scale profiling of thousands of RNA transcripts, caused a significant inversion in IPF research. Instead of generating hypotheses based on animal models of disease, or biological plausibility, with limited validation in humans, investigators were able to generate hypotheses based on unbiased molecular analysis of human samples and then use animal models of disease to test their hypotheses. In this review, we describe the insights made from transcriptomic analysis of human IPF samples. We describe how transcriptomic studies led to identification of novel genes and pathways involved in the human IPF lung such as: matrix metalloproteinases, WNT pathway, epithelial genes, role of microRNAs among others, as well as conceptual insights such as the involvement of developmental pathways and deep shifts in epithelial and fibroblast phenotypes. The impact of lung and transcriptomic studies on disease classification, endotype discovery, and reproducible biomarkers is also described in detail. Despite these impressive achievements, the impact of transcriptomic studies has been limited because they analyzed bulk tissue and did not address the cellular and spatial heterogeneity of the IPF lung. We discuss new emerging technologies and applications, such as single-cell RNAseq and microenvironment analysis that may address cellular and spatial heterogeneity. We end by making the point that most current tissue collections and resources are not amenable to analysis using the novel technologies. To take advantage of the new opportunities, we need new efforts of sample collections, this time focused on access to all the microenvironments and cells in the IPF lung. PMID:29670881

Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

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Hawdon John

2010-05-01

Full Text Available Abstract Background Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism, the present study generated a near complete transcriptome of the canine hookworm Ancylostoma caninum to a very high coverage using high throughput technology, and compared it to those of the free-living nematode Caenorhabditis elegans and the parasite Brugia malayi. Results The generated transcripts from four developmental stages, infective L3, serum stimulated L3, adult male and adult female, covered 93% of the A. caninum transcriptome. The broad diversity among nematode transcriptomes was confirmed, and an impact of parasitic adaptation on transcriptome diversity was inferred. Intra-population analysis showed that A. caninum has higher coding sequence diversity than humans. Examining the developmental expression profiles of A. caninum revealed major transitions in gene expression from larval stages to adult. Adult males expressed the highest number of selectively expressed genes, but adult female expressed the highest number of selective parasitism-related genes. Genes related to parasitism adaptation and A. caninum specific genes exhibited more expression selectivity while those conserved in nematodes tend to be consistently expressed. Parasitism related genes were expressed more selectively in adult male and female worms. The comprehensive analysis of digital expression profiles along with transcriptome comparisons enabled identification of a set of parasitism genes encoding secretory proteins in animal parasitic nematode. Conclusions This study validated the usage of deep sequencing for gene expression profiling. Parasitic adaptation of the canine hookworm is related to its diversity and developmental dynamics. This comprehensive comparative genomic and expression study substantially improves our understanding of

DOGMA: domain-based transcriptome and proteome quality assessment.

Science.gov (United States)

Dohmen, Elias; Kremer, Lukas P M; Bornberg-Bauer, Erich; Kemena, Carsten

2016-09-01

Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Major differences between human atopic dermatitis and murine models as determined by global transcriptomic profiling

DEFF Research Database (Denmark)

Ewald, David Adrian; Noda, Shinji; Oliva, Margeaux

2017-01-01

, and a comparison of these models with the human AD transcriptomic fingerprint is lacking. We sought to evaluate the transcriptomic profiles of six common murine models and determine how they relate to human AD skin. Transcriptomic profiling was performed using microarrays and qRT-PCR on biopsies from NC/Nga, flaky...

Transcriptomic network analysis of micronuclei-related genes: a case study

DEFF Research Database (Denmark)

van Leeuwen, D. M.; Pedersen, Marie; Knudsen, Lisbeth E.

2011-01-01

checkpoint and aneuploidy. The MN-related gene network was tested against a transcriptomics case study associated with MN measurements. In this case study, transcriptomic data from children and adults differentially exposed to ambient air pollution in the Czech Republic were analysed and visualised......Mechanistically relevant information on responses of humans to xenobiotic exposure in relation to chemically induced biological effects, such as micronuclei (MN) formation can be obtained through large-scale transcriptomics studies. Network analysis may enhance the analysis and visualisation...... of such data. Therefore, this study aimed to develop a 'MN formation' network based on a priori knowledge, by using the pathway tool MetaCore. The gene network contained 27 genes and three gene complexes that are related to processes involved in MN formation, e.g. spindle assembly checkpoint, cell cycle...

Transcriptome Dynamics during Maize Endosperm Development.

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Jianzhou Qu

Full Text Available The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP. We found that more than 11,000 protein-coding genes underwent alternative splicing (AS events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs, were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.

The floral transcriptome of Eucalyptus grandis

CSIR Research Space (South Africa)

Vining, KJ

2015-10-01

Full Text Available As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages...

Deletion of the Candida glabrata ERG3 and ERG11 genes: effect on cell viability, cell growth, sterol composition, and antifungal susceptibility.

Science.gov (United States)

Geber, A; Hitchcock, C A; Swartz, J E; Pullen, F S; Marsden, K E; Kwon-Chung, K J; Bennett, J E

1995-01-01

We have cloned and sequenced the structural genes encoding the delta 5,6 sterol desaturase (ERG3 gene) and the 14 alpha-methyl sterol demethylase (ERG11 gene) from Candida glabrata L5 (leu2). Single and double mutants of these genes were created by gene deletion. The phenotypes of these mutants, including sterol profiles, aerobic viabilities, antifungal susceptibilities, and generation times, were studied. Strain L5D (erg3 delta::LEU2) accumulated mainly ergosta-7,22-dien-3 beta-ol, was aerobically viable, and remained susceptible to antifungal agents but had a slower generation time than its parent strain. L5LUD (LEU2 erg11 delta::URA3) strains required medium supplemented with ergosterol and an anaerobic environment for growth. A spontaneous aerobically viable mutant, L5LUD40R (LEU erg11 delta::URA3), obtained from L5LUD (LEU2 erg11 delta::URA3), was found to accumulate lanosterol and obtusifoliol, was resistant to azole antifungal agents, demonstrated some increase in resistance to amphotericin B, and exhibited a 1.86-fold increase in generation time in comparison with L5 (leu2). The double-deletion mutant L5DUD61 (erg3 delta::LEU2 erg11 delta::URA3) was aerobically viable, produced mainly 14 alpha-methyl fecosterol, and had the same antifungal susceptibility pattern as L5LUD40R (LEU2 erg11 delta::URA3), and its generation time was threefold greater than that of L5 (leu2). Northern (RNA) analysis revealed that the single-deletion mutants had a marked increase in message for the undeleted ERG3 and ERG11 genes. These results indicate that differences in antifungal susceptibilities and the restoration of aerobic viability exist between the C. glabrata ergosterol mutants created in this study and those sterol mutants with similar genetic lesions previously reported for Saccharomyces cerevisiae. PMID:8593007

Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine

Science.gov (United States)

Xin, Jie; Zhang, Rong-chao; Wang, Lei

2017-01-01

Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers. PMID:28900463

ALTERATIONS IN THE DEVELOPING TESTIS TRANSCRIPTOME FOLLOWING EMBRYONIC VINCLOZOLIN EXPOSURE

OpenAIRE

Clement, Tracy M.; Savenkova, Marina I.; Settles, Matthew; Anway, Matthew D.; Skinner, Michael K.

2010-01-01

The current study investigates the direct effects of in utero vinclozolin exposure on the developing F1 generation rat testis transcriptome. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic day 13, 14 and 16. A total of 576 di...

The renal transcriptome in experimental hypertension

NARCIS (Netherlands)

Wesseling, S.

2007-01-01

The renal transcriptome in experimental hypertension The kidneys importantly determine blood pressure. Kidney dysfunction can result in hypertension, which in turn leads to renal damage. In primary hypertension the cause is unknown. The condition is polygenic, however, which genetic defects cause

Brain transcriptome atlases : A computational perspective

NARCIS (Netherlands)

Mahfouz, A.M.E.T.A.; Huisman, S.M.H.; Lelieveldt, B.P.F.; Reinders, M.J.T.

2017-01-01

The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases

Transcriptome Analysis of Barbarea vulgaris Infested with Diamondback Moth (Plutella xylostella) Larvae

Science.gov (United States)

Shen, Di; Wang, Haiping; Wu, Qingjun; Lu, Peng; Qiu, Yang; Song, Jiangping; Zhang, Youjun; Li, Xixiang

2013-01-01

Background The diamondback moth (DBM, Plutella xylostella) is a crucifer-specific pest that causes significant crop losses worldwide. Barbarea vulgaris (Brassicaceae) can resist DBM and other herbivorous insects by producing feeding-deterrent triterpenoid saponins. Plant breeders have long aimed to transfer this insect resistance to other crops. However, a lack of knowledge on the biosynthetic pathways and regulatory networks of these insecticidal saponins has hindered their practical application. A pyrosequencing-based transcriptome analysis of B. vulgaris during DBM larval feeding was performed to identify genes and gene networks responsible for saponin biosynthesis and its regulation at the genome level. Principal Findings Approximately 1.22, 1.19, 1.16, 1.23, 1.16, 1.20, and 2.39 giga base pairs of clean nucleotides were generated from B. vulgaris transcriptomes sampled 1, 4, 8, 12, 24, and 48 h after onset of P. xylostella feeding and from non-inoculated controls, respectively. De novo assembly using all data of the seven transcriptomes generated 39,531 unigenes. A total of 37,780 (95.57%) unigenes were annotated, 14,399 of which were assigned to one or more gene ontology terms and 19,620 of which were assigned to 126 known pathways. Expression profiles revealed 2,016–4,685 up-regulated and 557–5188 down-regulated transcripts. Secondary metabolic pathways, such as those of terpenoids, glucosinolates, and phenylpropanoids, and its related regulators were elevated. Candidate genes for the triterpene saponin pathway were found in the transcriptome. Orthological analysis of the transcriptome with four other crucifer transcriptomes identified 592 B. vulgaris-specific gene families with a P-value cutoff of 1e−5. Conclusion This study presents the first comprehensive transcriptome analysis of B. vulgaris subjected to a series of DBM feedings. The biosynthetic and regulatory pathways of triterpenoid saponins and other DBM deterrent metabolites in this plant were

Cell type-specific responses to salinity - the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum.

Science.gov (United States)

Oh, Dong-Ha; Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar; Lee, Sang-Yeol; Bohnert, Hans J; Dassanayake, Maheshi

2015-08-01

Mesembryanthemum crystallinum (ice plant) exhibits extreme tolerance to salt. Epidermal bladder cells (EBCs), developing on the surface of aerial tissues and specialized in sodium sequestration and other protective functions, are critical for the plant's stress adaptation. We present the first transcriptome analysis of EBCs isolated from intact plants, to investigate cell type-specific responses during plant salt adaptation. We developed a de novo assembled, nonredundant EBC reference transcriptome. Using RNAseq, we compared the expression patterns of the EBC-specific transcriptome between control and salt-treated plants. The EBC reference transcriptome consists of 37 341 transcript-contigs, of which 7% showed significantly different expression between salt-treated and control samples. We identified significant changes in ion transport, metabolism related to energy generation and osmolyte accumulation, stress signalling, and organelle functions, as well as a number of lineage-specific genes of unknown function, in response to salt treatment. The salinity-induced EBC transcriptome includes active transcript clusters, refuting the view of EBCs as passive storage compartments in the whole-plant stress response. EBC transcriptomes, differing from those of whole plants or leaf tissue, exemplify the importance of cell type-specific resolution in understanding stress adaptive mechanisms. No claim to original US government works. New Phytologist © 2015 New Phytologist Trust.

Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

Czech Academy of Sciences Publication Activity Database

Pantalacci, S.; Gueguen, L.; Petit, C.; Lambert, A.; Peterková, Renata; Sémon, E.

2017-01-01

Roč. 18, feb (2017), s. 29 ISSN 1474-760X R&D Projects: GA ČR(CZ) GB14-37368G Institutional support: RVO:68378041 Keywords : comparative transcriptomics * developmental biology * transcriptomic signature Subject RIV: EA - Cell Biology OBOR OECD: Developmental biology Impact factor: 11.908, year: 2016

De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data

Directory of Open Access Journals (Sweden)

Yeonhwa Jo

2017-10-01

Full Text Available Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV, infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking

NARCIS (Netherlands)

Huan, T. (Tianxiao); R. Joehanes (Roby); C. Schurmann (Claudia); K. Schramm (Katharina); L.C. Pilling (Luke); M.J. Peters (Marjolein); R. Mägi (Reedik); D.L. Demeo (Dawn L.); G.T. O'Connor (George); L. Ferrucci (Luigi); A. Teumer (Alexander); G. Homuth (Georg); R. Biffar (Reiner); U. Völker (Uwe); C. Herder (Christian); M. Waldenberger (Melanie); A. Peters (Annette); S. Zeilinger (Sonja); A. Metspalu (Andres); A. Hofman (Albert); A.G. Uitterlinden (André); D.G. Hernandez (Dena); A. Singleton (Andrew); S. Bandinelli (Stefania); P.J. Munson (Peter); H. Lin (Honghuang); E.J. Benjamin (Emelia); T. Esko (Tõnu); H.J. Grabe (Hans Jörgen); H. Prokisch (Holger); J.B.J. van Meurs (Joyce); D. Melzer (David); D. Levy (Daniel)

2016-01-01

textabstractCigarette smoking is a leading modifiable cause of death worldwide. We hypothesized that cigarette smoking induces extensive transcriptomic changes that lead to target-organ damage and smoking-related diseases. We performed a metaanalysis of transcriptome-wide gene expression using whole

A comparison of the Giardia lamblia trophozoite and cyst transcriptome using microarrays

Directory of Open Access Journals (Sweden)

Widmer Giovanni

2011-05-01

Full Text Available Abstract Background Compared with many protists, Giardia lamblia has a simple life cycle alternating between cyst and trophozoite. Most research on the molecular biology of Giardia parasites has focused on trophozoites and the processes of excystation and encystation, whereas cysts have attracted less interest. The striking morphological differences between the dormant cyst and the rapidly dividing and motile trophozoite implies profound changes in the metabolism as the parasite encysts in the host's intestine and excysts upon ingestion by a new host. Results To investigate the magnitude of the transcriptional changes occurring during the G. lamblia life cycle we compared the transcriptome of G. lamblia trophozoites and cysts using single-color oligonucleotide microarrays. Cysts were found to possess a much smaller transcriptome, both in terms of mRNA diversity and abundance. Genes encoding proteins related to ribosomal functions are highly over-represented. The comparison of the transcriptome of cysts generated in culture or extracted from feces revealed little overlap, raising the possibility of significant biological differences between the two types of cysts. Conclusions The comparison of the G. lamblia cyst and trophozoite transcriptome showed that transcripts of most genes are present at a lower level in cysts. This global view of the cyst and trophozoite transcriptome complements studies focused on the expression of selected genes during trophozoite multiplication, encystation and excystation.

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.

Science.gov (United States)

Richardson, Mark F; Sequeira, Fernando; Selechnik, Daniel; Carneiro, Miguel; Vallinoto, Marcelo; Reid, Jack G; West, Andrea J; Crossland, Michael R; Shine, Richard; Rollins, Lee A

2018-01-01

Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers. © The Authors 2017. Published by Oxford University Press.

Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.

Science.gov (United States)

Gao, Chen; Wang, Yibin

2014-01-01

With the advancement of transcriptome profiling by micro-arrays and high-throughput RNA-sequencing, transcriptome complexity and its dynamics are revealed at different levels in cardiovascular development and diseases. In this review, we will highlight the recent progress in our knowledge of cardiovascular transcriptome complexity contributed by RNA splicing, RNA editing and noncoding RNAs. The emerging importance of many of these previously under-explored aspects of gene regulation in cardiovascular development and pathology will be discussed.

Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome.

Science.gov (United States)

Azim, M Kamran; Khan, Ishtaiq A; Zhang, Yong

2014-05-01

We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80% of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37%) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.

Comparative de novo transcriptome analysis of male and female Sea buckthorn.

Science.gov (United States)

Bansal, Ankush; Salaria, Mehul; Sharma, Tashil; Stobdan, Tsering; Kant, Anil

2018-02-01

Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism. The current study showed 63,904 and 62,272 coding sequences (CDS) in female and male transcriptome data sets, respectively. 16,831 common CDS were screened out from both transcriptomes, out of which 625 were upregulated and 491 were found to be downregulated. To understand the potential regulatory roles of differentially expressed genes in metabolic networks and biosynthetic pathways: KEGG mapping, gene ontology, and co-expression network analysis were performed. Comparison with Flowering Interactive Database (FLOR-ID) resulted in eight differentially expressed genes viz. CHD3-type chromatin-remodeling factor PICKLE ( PKL ), phytochrome-associated serine/threonine-protein phosphatase ( FYPP ), protein TOPLESS ( TPL ), sensitive to freezing 6 ( SFR6 ), lysine-specific histone demethylase 1 homolog 1 ( LDL1 ), pre-mRNA-processing-splicing factor 8A ( PRP8A ), sucrose synthase 4 ( SUS4 ), ubiquitin carboxyl-terminal hydrolase 12 ( UBP12 ), known to be broadly involved in flowering, photoperiodism, embryo development, and cold response pathways. Male and female flower bud transcriptome data of Sea buckthorn may provide comprehensive information at genomic level for the identification of genetic regulation involved in sex determination.

Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models

International Nuclear Information System (INIS)

Rogers, Simon; Girolami, Mark; Kolch, Walter; Waters, Katrina M.; Liu, Tao; Thrall, Brian D.; Wiley, H. S.

2008-01-01

Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analyzed separately, there is an increasing interest in comparing and co-analyzing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated. Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. By providing probabilistic assignments this approach sits between the two extremes of concatenating the data on the assumption that mRNA and protein clusters would have a one-to-one relationship, and independent clustering where the mRNA profile provides no information on the protein profile and vice-versa. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC) stimulated by epidermal growth factor (EGF) over a series of timepoints corresponding to one cell cycle. The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the gene ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding. Conclusions: The dynamic regulation of the transcriptome and proteome in mammalian cells in response to an acute mitogenic stimulus appears largely independent with very little

Comparing de novo assemblers for 454 transcriptome data.

Science.gov (United States)

Kumar, Sujai; Blaxter, Mark L

2010-10-16

Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible

Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers

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Johanna F.B. Pagano

2016-09-01

Full Text Available Maternal mRNA that is present in the mature oocyte plays an important role in the proper development of the early embryo. To elucidate the role of the maternal transcriptome we recently reported a microarray study on individual zebrafish eggs from five different clutches from sibling mothers and showed differences in maternal RNA abundance between and within clutches, “Mother-specific signature in the maternal transcriptome composition of mature, unfertilized Eggs” [1]. Here we provide in detail the applied preprocessing method as well as the R-code to identify expressed and non-expressed genes in the associated transcriptome dataset. Additionally, we provide a website that allows a researcher to search for the expression of their gene of interest in this experiment. Keywords: Zebrafish, Danio rerio, Egg transcriptome, Single egg

The developmental transcriptome of Drosophila melanogaster

Energy Technology Data Exchange (ETDEWEB)

University of Connecticut; Graveley, Brenton R.; Brooks, Angela N.; Carlson, Joseph W.; Duff, Michael O.; Landolin, Jane M.; Yang, Li; Artieri, Carlo G.; van Baren, Marijke J.; Boley, Nathan; Booth, Benjamin W.; Brown, James B.; Cherbas, Lucy; Davis, Carrie A.; Dobin, Alex; Li, Renhua; Lin, Wei; Malone, John H.; Mattiuzzo, Nicolas R.; Miller, David; Sturgill, David; Tuch, Brian B.; Zaleski, Chris; Zhang, Dayu; Blanchette, Marco; Dudoit, Sandrine; Eads, Brian; Green, Richard E.; Hammonds, Ann; Jiang, Lichun; Kapranov, Phil; Langton, Laura; Perrimon, Norbert; Sandler, Jeremy E.; Wan, Kenneth H.; Willingham, Aarron; Zhang, Yu; Zou, Yi; Andrews, Justen; Bicke, Peter J.; Brenner, Steven E.; Brent, Michael R.; Cherbas, Peter; Gingeras, Thomas R.; Hoskins, Roger A.; Kaufman, Thomas C.; Oliver, Brian; Celniker, Susan E.

2010-12-02

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. Drosophila melanogaster is an important non-mammalian model system that has had a critical role in basic biological discoveries, such as identifying chromosomes as the carriers of genetic information and uncovering the role of genes in development. Because it shares a substantial genic content with humans, Drosophila is increasingly used as a translational model for human development, homeostasis and disease. High-quality maps are needed for all functional genomic elements. Previous studies demonstrated that a rich collection of genes is deployed during the life cycle of the fly. Although expression profiling using microarrays has revealed the expression of, 13,000 annotated genes, it is difficult to map splice junctions and individual base modifications generated by RNA editing using such approaches. Single-base resolution is essential to define precisely the elements that comprise the Drosophila transcriptome. Estimates of the number of transcript isoforms are less accurate than estimates of the number of genes

Ciclo Vital de Schistosoma mansoni através do Holochilus brasiliensis (Desmarest, 1818 em ambiente semi-natural (Trematoda, Shistosomatidae; Rodentia, Cricetidae

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Omar dos Santos Carvalho

1976-10-01

Full Text Available Junto ao Lago da Pampulha, Belo Horizonte, MG, foram capturados (julho/72-novembro/73 28 exemplares de Holochilus brasiliensis, dos quais 11 (39,3% eliminavam nas fezes ovos viáveis de S. mansoni. Miracídios da cepa mencionada ("H" infectaram Biomphalaria glabrata e as cercárias obtidas também infectaram camundongos albinos, recuperando-se, ao final do experimento, 35,3% de vermes adultos. Por outro lado, cercárias de cepa humana ("LE" de S. mansoni infectaram sete exemplares de H. brasiliensis, nascidos em laboratório, recuperando-se no fim de 60 dias, 30,5% de vermes adultos. Estudos anatomapatológicos de H. brasiliensis demonstraram infecção generalizada, encontrando-se granuloma no esôfago, estômago, intestino (delgado e grosso, fígado, baço, pâncreas e linfonodos abdominais. Espessamentos fibrosos da íntima da veia porta, granulomas em espaços porta e fibrose incipiente dos espaços porta e interlobular foram lesões decorrentes da presença de ovos de S. mansoni encontrados no fígado. Em ambiente semi-natural, foi possível fechar o ciclo do S. mansoni sem direta participação humana, utilizando-se B. glabrata experimentalmente infectadas com trematódeos da cepa "LE", H. brasiliensis nascidos em laboratório e B. glabrata nascida no ambiente semi-natural estabelecido. Verificou-se que ambas as cepas ("H" e "LE" comportaram-se de maneira análoga, não sendo verificadas, também, diferenças morfológicas entre os ovos e vermes adultos de ambas. As observações, realizadas no campo e no laboratório demonstraram que o Holochilus brasiliensis é bom hospedeiro de Schistosoma mansoni. Assim, em determinadas áreas e sob certas condições ecológicas, o cricetídeo em questão poderá, efetivamente, integrar-se ao ciclo do trematódeo na natureza, independente ou paralelamente à presença do homem. Assinala-se, finalmente, que o presente trabalho relata o segundo fechamento do ciclo biológico de S. mansoni em condi

Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

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Li Shen

2013-06-01

Full Text Available A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE, recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.

Unique transcriptomic response to sepsis is observed among patients of different age groups.

Science.gov (United States)

Raymond, Steven L; López, María Cecilia; Baker, Henry V; Larson, Shawn D; Efron, Philip A; Sweeney, Timothy E; Khatri, Purvesh; Moldawer, Lyle L; Wynn, James L

2017-01-01

Sepsis is a major cause of morbidity and mortality, especially at the extremes of age. To understand the human age-specific transcriptomic response to sepsis, a multi-cohort, pooled analysis was conducted on adults, children, infants, and neonates with and without sepsis. Nine public whole-blood gene expression datasets (636 patients) were employed. Age impacted the transcriptomic host response to sepsis. Gene expression from septic neonates and adults was more dissimilar whereas infants and children were more similar. Neonates showed reductions in inflammatory recognition and signaling pathways compared to all other age groups. Likewise, adults demonstrated decreased pathogen sensing, inflammation, and myeloid cell function, as compared to children. This may help to explain the increased incidence of sepsis-related organ failure and death in adults. The number of dysregulated genes in septic patients was proportional to age and significantly differed among septic adults, children, infants, and neonates. Overall, children manifested a greater transcriptomic intensity to sepsis as compared to the other age groups. The transcriptomic magnitude for adults and neonates was dramatically reduced as compared to children and infants. These findings suggest that the transcriptomic response to sepsis is age-dependent, and diagnostic and therapeutic efforts to identify and treat sepsis will have to consider age as an important variable.

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing.

Science.gov (United States)

Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

2010-08-01

Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons and upstream open reading frames, which provide remarkable insight into the A. oryzae transcriptome. We were also able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes and pathways that might be involved in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae is much more complex than previously anticipated, and these results may provide a blueprint for further study of the A. oryzae transcriptome.

CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

OpenAIRE

Verma, Mohit; Kumar, Vinay; Patel, Ravi K.; Garg, Rohini; Jain, Mukesh

2015-01-01

Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB), which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database fea...

De novo transcriptome assembly of mangosteen (Garcinia mangostana L. fruit

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Deden Derajat Matra

2016-12-01

Full Text Available Garcinia mangostana L. (Mangosteen, of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

Histological chorioamnionitis shapes the neonatal transcriptomic immune response.

Science.gov (United States)

Weitkamp, Jörn-Hendrik; Guthrie, Scott O; Wong, Hector R; Moldawer, Lyle L; Baker, Henry V; Wynn, James L

2016-07-01

Histologic chorioamnionitis (HCA) is commonly associated with preterm birth and deleterious post-natal outcomes including sepsis and necrotizing enterocolitis. Transcriptomic analysis has been used to uncover gene signatures that permit diagnosis and prognostication, show new therapeutic targets, and reveal mechanisms that underlie differential outcomes with other complex disease states in neonates such as sepsis. To define the transcriptomic and inflammatory protein response in peripheral blood among infants with exposure to histologic chorioamnionitis. Prospective, observational study. Uninfected preterm neonates retrospectively categorized based on placental pathology with no HCA exposure (n=18) or HCA exposure (n=15). We measured the transcriptomic and inflammatory mediator response in prospectively collected whole blood. We found 488 significant (p<0.001), differentially expressed genes in whole blood samples among uninfected neonates with HCA exposure that collectively represented activated innate and adaptive immune cellular pathways and revealed a potential regulatory role for the pleotropic microRNA molecule miR-155. Differentially secreted plasma cytokines in patients with HCA exposure compared to patients without HCA included MCP-1, MPO, and MMP-9 (p<0.05). Exposure to HCA distinctively activates the neonatal immune system in utero with potentially long-term health consequences. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Coevolutionary genetic variation in the legume-rhizobium transcriptome.

Science.gov (United States)

Heath, Katy D; Burke, Patricia V; Stinchcombe, John R

2012-10-01

Coevolutionary change requires reciprocal selection between interacting species, where the partner genotypes that are favoured in one species depend on the genetic composition of the interacting species. Coevolutionary genetic variation is manifested as genotype × genotype (G × G) interactions for fitness in interspecific interactions. Although quantitative genetic approaches have revealed abundant evidence for G × G interactions in symbioses, the molecular basis of this variation remains unclear. Here we study the molecular basis of G × G interactions in a model legume-rhizobium mutualism using gene expression microarrays. We find that, like quantitative traits such as fitness, variation in the symbiotic transcriptome may be partitioned into additive and interactive genetic components. Our results suggest that plant genetic variation had the largest influence on nodule gene expression and that plant genotype and the plant genotype × rhizobium genotype interaction determine global shifts in rhizobium gene expression that in turn feedback to influence plant fitness benefits. Moreover, the transcriptomic variation we uncover implicates regulatory changes in both species as drivers of symbiotic gene expression variation. Our study is the first to partition genetic variation in a symbiotic transcriptome and illuminates potential molecular routes of coevolutionary change. © 2012 Blackwell Publishing Ltd.

Comparative whole genome transcriptome and metabolome analyses of five Klebsiella pneumonia strains.

Science.gov (United States)

Lee, Soojin; Kim, Borim; Yang, Jeongmo; Jeong, Daun; Park, Soohyun; Shin, Sang Heum; Kook, Jun Ho; Yang, Kap-Seok; Lee, Jinwon

2015-11-01

The integration of transcriptomics and metabolomics can provide precise information on gene-to-metabolite networks for identifying the function of novel genes. The goal of this study was to identify novel gene functions involved in 2,3-butanediol (2,3-BDO) biosynthesis by a comprehensive analysis of the transcriptome and metabolome of five mutated Klebsiella pneumonia strains (∆wabG = SGSB100, ∆wabG∆budA = SGSB106, ∆wabG∆budB = SGSB107, ∆wabG∆budC = SGSB108, ∆wabG∆budABC = SGSB109). First, the transcriptomes of all five mutants were analyzed and the genes exhibiting reproducible changes in expression were determined. The transcriptome was well conserved among the five strains, and differences in gene expression occurred mainly in genes coding for 2,3-BDO biosynthesis (budA, budB, and budC) and the genes involved in the degradation of reactive oxygen, biosynthesis and transport of arginine, cysteine biosynthesis, sulfur metabolism, oxidoreductase reaction, and formate dehydrogenase reaction. Second, differences in the metabolome (estimated by carbon distribution, CO2 emission, and redox balance) among the five mutant strains due to gene alteration of the 2,3-BDO operon were detected. The functional genomics approach integrating metabolomics and transcriptomics in K. Pneumonia presented here provides an innovative means of identifying novel gene functions involved in 2,3-BDO biosynthesis metabolism and whole cell metabolism.

Transcriptomic signatures in cartilage ageing

Science.gov (United States)

2013-01-01

Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome. PMID:23971731

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

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Loren A Honaas

Full Text Available Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1 proportion of reads mapping to an assembly 2 recovery of conserved, widely expressed genes, 3 N50 length statistics, and 4 the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.

Spatial distribution of schistosomiasis foci on Itamaracá Island, Pernambuco, Brazil

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CS Barbosa

2004-08-01

Full Text Available Acute cases of schistosomiasis have been found on the coastal area of Pernambuco, Brazil, due to environmental disturbances and disorderly occupation of the urban areas. This study identifies and spatially marks the main foci of the snail host species, Biomphalaria glabrata on Itamaracá Island. The chaotic occupation of the beach resorts has favoured the emergence of transmission foci, thus exposing residents and tourists to the risk of infection. A database covering five years of epidemiological investigation on snails infected by Schistosoma mansoni in the island was produced with information from the geographic positioning of the foci, number of snails collected, number of snails tested positive, and their infection rate. The spatial position of the foci were recorded through the Global Positioning System (GPS, and the geographical coordinates were imported by AutoCad. The software packages ArcView and Spring were used for data processing and spatial analysis. AutoCad 2000 was used to plot the pairs of coordinates obtained from GPS. Between 1998 and 2002 5009 snails, of which 12.2% were positive for S. mansoni, were collected in Forte Beach. A total of 27 foci and areas of environmental risk were identified and spatially analyzed allowing the identification of the areas exposed to varying degrees of risk.

Acute schistosomiasis outbreak in the metropolitan area of Belo Horizonte, Minas Gerais: alert about the risk of unnoticed transmission increased by growing rural tourism

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Martin J Enk

2003-09-01

Full Text Available The present article describes the occurrence of 17 cases of acute schistosomiasis in the metropolitan area of Belo Horizonte, state of Minas Gerais, Brazil. All individuals affected took a bath in a swimming pool of a holiday resort that was provided with water from a nearby brook. The apparently clean water and the absence of snails in the pool gave the wrong impression that there was no risk for infection. During a malacological survey at the site snails of the species Biomphalaria glabrata were found and tested positive for Schistosoma mansoni. All the patients live in the middle-class area of Barreiro, metropolitan area of Belo Horizonte and have medium grade school education. The difficulties in establishing the right diagnosis is expressed by the search for medical attention in 17 different medical facilities, the wide range of laboratory test and the inadequate treatment administration. A lack of knowledge about the disease was found in all groups studied. The booming rural tourism in endemic areas is identified as a probable risk factor for infection, especially for individuals of the non-immune middle and upper class parts of the society in urban centers. Special attention is given to a multidisciplinary approach to the complex issue of disease control and prevention.

Comparative Transcriptomics to Identify Novel Genes and Pathways in Dinoflagellates

Science.gov (United States)

Ryan, D.

2016-02-01

The unarmored dinoflagellate Karenia brevis is among the most prominent harmful, bloom-forming phytoplankton species in the Gulf of Mexico. During blooms, the polyketides PbTx-1 and PbTx-2 (brevetoxins) are produced by K. brevis. Brevetoxins negatively impact human health and the Gulf shellfish harvest. However, the genes underlying brevetoxin synthesis are currently unknown. Because the K. brevis genome is extremely large ( 1 × 1011 base pairs long), and with a high proportion of repetitive, non-coding DNA, it has not been sequenced. In fact, large, repetitive genomes are common among the dinoflagellate group. High-throughput RNA sequencing technology enabled us to assemble Karenia transcriptomes de novo and investigate potential genes in the brevetoxin pathway through comparative transcriptomics. The brevetoxin profile varies among K. brevis clonal cultures. For example, well-documented Wilson-CCFWC268 typically produces 8-10 pg PbTx per cell, whereas SP1 produces differences in gene expression. Of the 85,000 transcripts in the K. brevis transcriptome, 4,600 transcripts, including novel unannotated orthologs and putative polyketide synthases (PKSs), were only expressed by brevetoxin-producing K. brevis and K. papilionacea, not K. mikimotoi. Examination of gene expression between the typical- and low-toxin Wilson clones identified about 3,500 genes with significantly different expression levels, including 2 putative PKSs. One of the 2 PKSs was only found in the brevetoxin-producing Karenia species. These transcriptomes could not have been characterized without high-throughput RNA sequencing.

Characterizing the transcriptome and molecular markers information ...

Indian Academy of Sciences (India)

2008). Analyses of the genetic structure .... The annotations and classifications for the transcriptome ... Based on the Pfam classification, the predic- ..... J. Lipid. Res. 33, 251–262. Eckert C. G., Samis K. E. and Lougheed S. C. 2008 Genetic vari-.

Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome.

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Sumedha S Gunewardena

Full Text Available During development, liver undergoes a rapid transition from a hematopoietic organ to a major organ for drug metabolism and nutrient homeostasis. However, little is known on a transcriptome level of the genes and RNA-splicing variants that are differentially regulated with age, and which up-stream regulators orchestrate age-specific biological functions in liver. We used RNA-Seq to interrogate the developmental dynamics of the liver transcriptome in mice at 12 ages from late embryonic stage (2-days before birth to maturity (60-days after birth. Among 21,889 unique NCBI RefSeq-annotated genes, 9,641 were significantly expressed in at least one age, 7,289 were differently regulated with age, and 859 had multiple (> = 2 RNA splicing-variants. Factor analysis showed that the dynamics of hepatic genes fall into six distinct groups based on their temporal expression. The average expression of cytokines, ion channels, kinases, phosphatases, transcription regulators and translation regulators decreased with age, whereas the average expression of peptidases, enzymes and transmembrane receptors increased with age. The average expression of growth factors peak between Day-3 and Day-10, and decrease thereafter. We identified critical biological functions, upstream regulators, and putative transcription modules that seem to govern age-specific gene expression. We also observed differential ontogenic expression of known splicing variants of certain genes, and 1,455 novel splicing isoform candidates. In conclusion, the hepatic ontogeny of the transcriptome ontogeny has unveiled critical networks and up-stream regulators that orchestrate age-specific biological functions in liver, and suggest that age contributes to the complexity of the alternative splicing landscape of the hepatic transcriptome.

Transcriptome dynamics of the microRNA inhibition response

DEFF Research Database (Denmark)

Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto

2015-01-01

We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line-the first such dynamic study of the microRNA inhibition response-revealing both general and specific aspects of the physiological response. We show...... validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods...... of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies....

Scrimer: designing primers from transcriptome data

Czech Academy of Sciences Publication Activity Database

Mořkovský, Libor; Pačes, Jan; Rídl, Jakub; Reifová, R.

2015-01-01

Roč. 15, č. 6 (2015), s. 1415-1420 ISSN 1755-098X R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 ; RVO:68378050 Keywords : next-generation sequencing * primer design * SNaPshot * SNP genotyping * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.298, year: 2015

Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells

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Tebaldi Toma

2012-06-01

Full Text Available Abstract Background The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translation. Here we address this issue by simultaneously profiling with microarrays the total mRNAs (the transcriptome and the polysome-associated mRNAs (the translatome after EGF treatment of human cells, and extending the analysis to other 19 different transcriptome/translatome comparisons in mammalian cells following different stimuli or undergoing cell programs. Results Triggering of the EGF pathway results in an early induction of transcriptome and translatome changes, but 90% of the significant variation is limited to the translatome and the degree of concordant changes is less than 5%. The survey of other 19 different transcriptome/translatome comparisons shows that extensive uncoupling is a general rule, in terms of both RNA movements and inferred cell activities, with a strong tendency of translation-related genes to be controlled purely at the translational level. By different statistical approaches, we finally provide evidence of the lack of dependence between changes at the transcriptome and translatome levels. Conclusions We propose a model of diffused independency between variation in transcript abundances and variation in their engagement on polysomes, which implies the existence of specific mechanisms to couple these two ways of regulating gene expression.

Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence.

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Houshyani, Benyamin; van der Krol, Alexander R; Bino, Raoul J; Bouwmeester, Harro J

2014-06-19

Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types. In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis. Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.

Characterization of the heart transcriptome of the white shark (Carcharodon carcharias).

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Richards, Vincent P; Suzuki, Haruo; Stanhope, Michael J; Shivji, Mahmood S

2013-10-11

The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to interest in the genetic basis of its form and function, as a representative of the oldest extant jawed vertebrate lineage, white sharks are also of conservation concern due to their small population size and threat from overfishing. Despite this, surprisingly little is known about the biology of white sharks, and genomic resources are unavailable. To address this deficit, we combined Roche-454 and Illumina sequencing technologies to characterize the first transciptome of any tissue for this species. From white shark heart cDNA we generated 665,399 Roche 454 reads (median length 387-bp) that were assembled into 141,626 contigs (mean length 503-bp). We also generated 78,566,588 Illumina reads, which we aligned to the 454 contigs producing 105,014 454/Illumina consensus sequences. To these, we added 3,432 non-singleton 454 contigs. By comparing these sequences to the UniProtKB/Swiss-Prot database we were able to annotate 21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Of these, 19,277 were additionally assigned Gene Ontology (GO) functional annotations. While acknowledging the limitations of our single tissue transcriptome, Fisher tests showed the white shark transcriptome to be significantly enriched for numerous metabolic GO terms compared to the zebra fish and human transcriptomes, with white shark showing more similarity to human than to zebra fish (i.e. fewer terms were significantly different). We also compared the transcriptome to other available elasmobranch sequences, for signatures of positive selection and identified several genes of putative adaptive significance on the white shark lineage. The white shark transcriptome also contained 8,404 microsatellites (dinucleotide, trinucleotide, or tetranucleotide motifs ≥ five perfect

Integrated transcriptomic and proteomic evaluation of gentamicin nephrotoxicity in rats

International Nuclear Information System (INIS)

Com, Emmanuelle; Boitier, Eric; Marchandeau, Jean-Pierre; Brandenburg, Arnd; Schroeder, Susanne; Hoffmann, Dana; Mally, Angela; Gautier, Jean-Charles

2012-01-01

Gentamicin is an aminoglycoside antibiotic, which induces renal tubular necrosis in rats. In the context of the European InnoMed PredTox project, transcriptomic and proteomic studies were performed to provide new insights into the molecular mechanisms of gentamicin-induced nephrotoxicity. Male Wistar rats were treated with 25 and 75 mg/kg/day subcutaneously for 1, 3 and 14 days. Histopathology observations showed mild tubular degeneration/necrosis and regeneration and moderate mononuclear cell infiltrate after long-term treatment. Transcriptomic data indicated a strong treatment-related gene expression modulation in kidney and blood cells at the high dose after 14 days of treatment, with the regulation of 463 and 3241 genes, respectively. Of note, the induction of NF-kappa B pathway via the p38 MAPK cascade in the kidney, together with the activation of T-cell receptor signaling in blood cells were suggestive of inflammatory processes in relation with the recruitment of mononuclear cells in the kidney. Proteomic results showed a regulation of 163 proteins in kidney at the high dose after 14 days of treatment. These protein modulations were suggestive of a mitochondrial dysfunction with impairment of cellular energy production, induction of oxidative stress, an effect on protein biosynthesis and on cellular assembly and organization. Proteomic results also provided clues for potential nephrotoxicity biomarkers such as AGAT and PRBP4 which were strongly modulated in the kidney. Transcriptomic and proteomic data turned out to be complementary and their integration gave a more comprehensive insight into the putative mode of nephrotoxicity of gentamicin which was in accordance with histopathological findings. -- Highlights: ► Gentamicin induces renal tubular necrosis in rats. ► The mechanisms of gentamicin nephrotoxicity remain still elusive. ► Transcriptomic and proteomic analyses were performed to study this toxicity in rats. ► Transcriptomic and proteomic

Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.

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Dianelys Gonzalez-Pena

Full Text Available Depression symptoms following immune response to a challenge have been reported after the recovery from sickness. A RNA-Seq study of the dysregulation of the microglia transcriptome in a model of inflammation-associated depressive behavior was undertaken. The transcriptome of microglia from mice at day 7 after Bacille Calmette Guérin (BCG challenge was compared to that from unchallenged Control mice and to the transcriptome from peripheral macrophages from the same mice. Among the 562 and 3,851 genes differentially expressed between BCG-challenged and Control mice in microglia and macrophages respectively, 353 genes overlapped between these cells types. Among the most differentially expressed genes in the microglia, serum amyloid A3 (Saa3 and cell adhesion molecule 3 (Cadm3 were over-expressed and coiled-coil domain containing 162 (Ccdc162 and titin-cap (Tcap were under-expressed in BCG-challenged relative to Control. Many of the differentially expressed genes between BCG-challenged and Control mice were associated with neurological disorders encompassing depression symptoms. Across cell types, S100 calcium binding protein A9 (S100A9, interleukin 1 beta (Il1b and kynurenine 3-monooxygenase (Kmo were differentially expressed between challenged and control mice. Immune response, chemotaxis, and chemokine activity were among the functional categories enriched by the differentially expressed genes. Functional categories enriched among the 9,117 genes differentially expressed between cell types included leukocyte regulation and activation, chemokine and cytokine activities, MAP kinase activity, and apoptosis. More than 200 genes exhibited alternative splicing events between cell types including WNK lysine deficient protein kinase 1 (Wnk1 and microtubule-actin crosslinking factor 1(Macf1. Network visualization revealed the capability of microglia to exhibit transcriptome dysregulation in response to immune challenge still after resolution of sickness

Whole transcriptome organisation in the dehydrated supraoptic nucleus

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C.C.T. Hindmarch

2013-12-01

Full Text Available The supraoptic nucleus (SON is part of the central osmotic circuitry that synthesises the hormone vasopressin (Avp and transports it to terminals in the posterior lobe of the pituitary. Following osmotic stress such as dehydration, this tissue undergoes morphological, electrical and transcriptional changes to facilitate the appropriate regulation and release of Avp into the circulation where it conserves water at the level of the kidney. Here, the organisation of the whole transcriptome following dehydration is modelled to fit Zipf's law, a natural power law that holds true for all natural languages, that states if the frequency of word usage is plotted against its rank, then the log linear regression of this is -1. We have applied this model to our previously published euhydrated and dehydrated SON data to observe this trend and how it changes following dehydration. In accordance with other studies, our whole transcriptome data fit well with this model in the euhydrated SON microarrays, but interestingly, fit better in the dehydrated arrays. This trend was observed in a subset of differentially regulated genes and also following network reconstruction using a third-party database that mines public data. We make use of language as a metaphor that helps us philosophise about the role of the whole transcriptome in providing a suitable environment for the delivery of Avp following a survival threat like dehydration.

Crx broadly modulates the pineal transcriptome

DEFF Research Database (Denmark)

Rovsing, Louise; Clokie, Samuel; Bustos, Diego M

2011-01-01

Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use of micro......Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use......-type animals; only eight of these were also day/night expressed in the Crx-/- pineal gland. However, in the Crx-/- pineal gland 41 genes exhibited differential night/day expression that was not seen in wild-type animals. These findings indicate that Crx broadly modulates the pineal transcriptome and also...... influences differential night/day gene expression in this tissue. Some effects of Crx deletion on the pineal transcriptome might be mediated by Hoxc4 up-regulation....

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

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Stinus Lindgreen

2014-10-01

Full Text Available Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification. However, a major challenge is to robustly distinguish functional outputs from transcriptional noise. To establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available RNA-seq datasets spanning 37 different Archaea and Bacteria. Using comparative tools, we identify close to a thousand highly-expressed candidate noncoding RNAs. However, our analyses reveal that capacity to identify noncoding RNA outputs is strongly dependent on phylogenetic sampling. Surprisingly, and in stark contrast to protein-coding genes, the phylogenetic window for effective use of comparative methods is perversely narrow: aggregating public datasets only produced one phylogenetic cluster where these tools could be used to robustly separate unannotated noncoding RNAs from a null hypothesis of transcriptional noise. Our results show that for the full potential of transcriptomics data to be realized, a change in experimental design is paramount: effective transcriptomics requires phylogeny-aware sampling.

De Novo Assembly of the Pea (Pisum sativum L. Nodule Transcriptome

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Vladimir A. Zhukov

2015-01-01

Full Text Available The large size and complexity of the garden pea (Pisum sativum L. genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR.

Chicken hepatic response to chronic heat stress using integrated transcriptome and metabolome analysis.

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Sara F Jastrebski

Full Text Available The liver plays a central role in metabolism and is important in maintaining homeostasis throughout the body. This study integrated transcriptomic and metabolomic data to understand how the liver responds under chronic heat stress. Chickens from a rapidly growing broiler line were heat stressed for 8 hours per day for one week and liver samples were collected at 28 days post hatch. Transcriptome analysis reveals changes in genes responsible for cell cycle regulation, DNA replication, and DNA repair along with immune function. Integrating the metabolome and transcriptome data highlighted multiple pathways affected by heat stress including glucose, amino acid, and lipid metabolism along with glutathione production and beta-oxidation.

Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq

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Khatib Hasan

2010-12-01

Full Text Available Abstract Background Advances in sequencing technologies have opened a new era of high throughput investigations. Although RNA-seq has been demonstrated in many organisms, no study has provided a comprehensive investigation of the bovine transcriptome using RNA-seq. Results In this study, we provide a deep survey of the bovine embryonic transcriptomes, the first application of RNA-seq in cattle. Embryos cultured in vitro were used as models to study early embryonic development in cattle. RNA amplified from limited amounts of starting total RNA were sequenced and mapped to the reference genome to obtain digital gene expression at single base resolution. In particular, gene expression estimates from more than 1.6 million unannotated bases in 1785 novel transcribed units were obtained. We compared the transcriptomes of embryos showing distinct developmental statuses and found genes that showed differential overall expression as well as alternative splicing. Conclusion Our study demonstrates the power of RNA-seq and provides further understanding of bovine preimplantation embryonic development at a fine scale.

Comparing de novo assemblers for 454 transcriptome data

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Blaxter Mark L

2010-10-01

Full Text Available Abstract Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects, which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies

The transcriptome landscape of early maize meiosis

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Meiosis, particularly meiotic recombination, is a major factor affecting yield and breeding of plants. To gain insight into the transcriptome landscape during early initiation steps of meiotic recombination, we profiled early prophase I meiocytes from maize using RNA-seq. Our analyses of genes prefe...

Using transcriptomic profiles in the diatom Phaeodactylum tricornutum to identify and prioritize stressors

International Nuclear Information System (INIS)

Osborn, Hannah L.; Hook, Sharon E.

2013-01-01

Highlights: •Exposure to stressors with different modes of action generated unique gene expression profiles in the diatom Phaeodactylum tricornutum. •The gene expression profile generated by a multiple stressor exposure reflected exposure to individual components of the mixture. •Quantitative PCR assays were generated that could be used to identify exposure to individual stressors. -- Abstract: The transcriptomic profile of the marine diatom, Phaeodactylum tricornutum, exposed to several ecologically relevant stressors, was used to develop toxicity identification evaluation (TIE)-like gene expression assays. Algal growth inhibition was measured by flow cytometry to determine exposure concentrations that elicited a sublethal toxic response. P. tricornutum was exposed to concentrations of copper (2 μg L −1 ), cadmium (5 μg L −1 ), silver (20 μg L −1 ), simazine (75 μg L −1 ), the water accommodated fraction (WAF) of weathered crude oil (5 mg L −1 ), 50 μg L −1 ammonia, a decreased salinity treatment (15‰), and a mixture exposure of ammonia, decreased salinity and cadmium (10 μg L −1 ). Analysis of the gene expression via microarray indicated that unique transcriptomic signals were generated for each of the individual treatments. Transcriptomic profiles of ammonia and the mixture treatment overlapped substantially. Photosynthesis related transcripts were altered in the simazine (herbicide) treatment. A transcript involved in degrading hydrocarbons, dioxygenase, had increased abundance after crude oil exposure. Overall, transcriptomic responses in the different treatments were associated with stress responses, membrane transport, transcription and translation and could be linked to contaminant mode of action. The transcriptomic profiles were used to design real-time (quantitative) polymerase chain reaction (qPCR) assays that would link changes in transcript abundance to a particular stressor in a TIE-based approach. At least one transcript

Using transcriptomic profiles in the diatom Phaeodactylum tricornutum to identify and prioritize stressors

Energy Technology Data Exchange (ETDEWEB)

Osborn, Hannah L., E-mail: Hannah.Osborn@csiro.au; Hook, Sharon E., E-mail: Sharon.Hook@csiro.au

2013-08-15

Highlights: •Exposure to stressors with different modes of action generated unique gene expression profiles in the diatom Phaeodactylum tricornutum. •The gene expression profile generated by a multiple stressor exposure reflected exposure to individual components of the mixture. •Quantitative PCR assays were generated that could be used to identify exposure to individual stressors. -- Abstract: The transcriptomic profile of the marine diatom, Phaeodactylum tricornutum, exposed to several ecologically relevant stressors, was used to develop toxicity identification evaluation (TIE)-like gene expression assays. Algal growth inhibition was measured by flow cytometry to determine exposure concentrations that elicited a sublethal toxic response. P. tricornutum was exposed to concentrations of copper (2 μg L{sup −1}), cadmium (5 μg L{sup −1}), silver (20 μg L{sup −1}), simazine (75 μg L{sup −1}), the water accommodated fraction (WAF) of weathered crude oil (5 mg L{sup −1}), 50 μg L{sup −1} ammonia, a decreased salinity treatment (15‰), and a mixture exposure of ammonia, decreased salinity and cadmium (10 μg L{sup −1}). Analysis of the gene expression via microarray indicated that unique transcriptomic signals were generated for each of the individual treatments. Transcriptomic profiles of ammonia and the mixture treatment overlapped substantially. Photosynthesis related transcripts were altered in the simazine (herbicide) treatment. A transcript involved in degrading hydrocarbons, dioxygenase, had increased abundance after crude oil exposure. Overall, transcriptomic responses in the different treatments were associated with stress responses, membrane transport, transcription and translation and could be linked to contaminant mode of action. The transcriptomic profiles were used to design real-time (quantitative) polymerase chain reaction (qPCR) assays that would link changes in transcript abundance to a particular stressor in a TIE

Silver colloidal nanoparticles: effect on matrix composition and structure of Candida albicans and Candida glabrata biofilms.

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Monteiro, D R; Silva, S; Negri, M; Gorup, L F; de Camargo, E R; Oliveira, R; Barbosa, D B; Henriques, M

2013-04-01

The aim of this study was to assess the effect of different silver nanoparticles (SN) concentrations on the matrix composition and structure of Candida albicans and Candida glabrata biofilms. Candida biofilms were developed in 6-well microtiter plates during 48 h. After, these biofilms were exposed to 13.5 or 54 μg SN ml(-1) for 24 h. Then, extracellular matrices were extracted from biofilms and analysed chemically in terms of proteins, carbohydrates and DNA. To investigate the biofilm structure, scanning electron microscopy (SEM) and epifluorescence microscopy were used. SN interfered with the matrix composition of Candida biofilms tested in terms of protein, carbohydrate and DNA, except for the protein content of C. albicans biofilm. By SEM, Candida biofilms treated with SN revealed structural differences, when compared with the control groups. Further, SN showed a trend of agglomeration within the biofilms. Epifluorescence microscopy images suggest that SN induced damage on cell walls of the Candida isolates tested. In general, irrespective of concentration, SN affected the matrix composition and structure of Candida biofilms and these findings may be related to the mechanisms of biocide action of SN. This study reveals new insights about the behaviour of SN when in contact with Candida biofilms. SN may contribute to the development of therapies to prevent or control Candida infections. © 2012 The Society for Applied Microbiology.

Ovary transcriptome profiling via artificial intelligence reveals a transcriptomic fingerprint predicting egg quality in striped bass, Morone saxatilis.

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Robert W Chapman

Full Text Available Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis, a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs and supervised machine learning, collective changes in the expression of a limited suite of genes (233 representing 90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold, with most individual transcripts making a small contribution (<1% to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic "fingerprint". Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness.

Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle

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Li Robert W

2011-11-01

Full Text Available Abstract The response of the abomasal transcriptome to gastrointestinal parasites was evaluated in parasite-susceptible and parasite-resistant Angus cattle using RNA-seq at a depth of 23.7 million sequences per sample. These cattle displayed distinctly separate resistance phenotypes as assessed by fecal egg counts. Approximately 65.3% of the 23 632 bovine genes were expressed in the fundic abomasum. Of these, 13 758 genes were expressed in all samples tested and likely represent core components of the bovine abomasal transcriptome. The gene (BT14427 with the most abundant transcript, accounting for 10.4% of sequences in the transcriptome, is located on chromosome 29 and has unknown functions. Additionally, PIGR (1.6%, Complement C3 (0.7%, and Immunoglobulin J chain (0.5% were among the most abundant transcripts in the transcriptome. Among the 203 genes impacted, 64 were significantly over-expressed in resistant animals at a stringent cutoff (FDR

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

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Legeai, Fabrice; Gimenez, Sylvie; Duvic, Bernard; Escoubas, Jean-Michel; Gosselin Grenet, Anne-Sophie; Blanc, Florence; Cousserans, François; Séninet, Imène; Bretaudeau, Anthony; Mutuel, Doriane; Girard, Pierre-Alain; Monsempes, Christelle; Magdelenat, Ghislaine; Hilliou, Frédérique; Feyereisen, René; Ogliastro, Mylène; Volkoff, Anne-Nathalie; Jacquin-Joly, Emmanuelle; d'Alençon, Emmanuelle; Nègre, Nicolas; Fournier, Philippe

2014-08-23

Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and grass. In addition, the Sf9 cell line, widely used in biochemistry for in vitro protein production, is derived from S. frugiperda tissues. Many research groups are using S. frugiperda as a model organism to investigate questions such as plant adaptation, pest behavior or resistance to pesticides. In this study, we constructed a reference transcriptome assembly (Sf_TR2012b) of RNA sequences obtained from more than 35 S. frugiperda developmental time-points and tissue samples. We assessed the quality of this reference transcriptome by annotating a ubiquitous gene family--ribosomal proteins--as well as gene families that have a more constrained spatio-temporal expression and are involved in development, immunity and olfaction. We also provide a time-course of expression that we used to characterize the transcriptional regulation of the gene families studied. We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome. While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts. That allowed us to explore the spatial and temporal expression of genes and to observe that some olfactory receptors are expressed in antennae and palps but also in other non related tissues such as fat bodies. Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

A comparative transcriptomic approach to understanding the formation of cork.

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Boher, Pau; Soler, Marçal; Sánchez, Anna; Hoede, Claire; Noirot, Céline; Paiva, Jorge Almiro Pinto; Serra, Olga; Figueras, Mercè

2018-01-01

The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development.

Detailed transcriptome description of the neglected cestode Taenia multiceps.

Science.gov (United States)

Wu, Xuhang; Fu, Yan; Yang, Deying; Zhang, Runhui; Zheng, Wanpeng; Nie, Huaming; Xie, Yue; Yan, Ning; Hao, Guiying; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

2012-01-01

The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS) of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. We obtained a total of 31,282 unigenes (mean length 920 bp) using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam). We identified 26,110 (83.47%) unigenes and inferred 20,896 (66.8%) coding sequences (CDS). Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis) and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum) showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of the biology of T. multiceps, and helps in the identification of drug targets and

Analysis of the salivary gland transcriptome of Frankliniella occidentalis.

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Candice A Stafford-Banks

Full Text Available Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande (the western flower thrips is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E-6 to known proteins, whereas a high percentage (61.24% of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the

Detailed transcriptome description of the neglected cestode Taenia multiceps.

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Xuhang Wu

Full Text Available BACKGROUND: The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. METHODOLOGY/PRINCIPAL FINDINGS: We obtained a total of 31,282 unigenes (mean length 920 bp using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam. We identified 26,110 (83.47% unigenes and inferred 20,896 (66.8% coding sequences (CDS. Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. CONCLUSIONS/SIGNIFICANCE: This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

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Timothy T Perkins

2009-07-01

Full Text Available High-density, strand-specific cDNA sequencing (ssRNA-seq was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi. By mapping sequence data to the entire S. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously un-annotated, and 3'- or 5'-untranslated regions (UTR. An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.

Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals.

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Jules Gagnon

2015-02-01

Full Text Available Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome, and encompass a wide variety of sequences, indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes, and their impact on RNA expression is linked to growth conditions. Together, the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals

Science.gov (United States)

Gagnon, Jules; Lavoie, Mathieu; Catala, Mathieu; Malenfant, Francis; Elela, Sherif Abou

2015-01-01

Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome, and encompass a wide variety of sequences, indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes, and their impact on RNA expression is linked to growth conditions. Together, the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. PMID:25680180

Chromosomal clustering of a human transcriptome reveals regulatory background

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Purmann Antje

2005-09-01

Full Text Available Abstract Background There has been much evidence recently for a link between transcriptional regulation and chromosomal gene order, but the relationship between genomic organization, regulation and gene function in higher eukaryotes remains to be precisely defined. Results Here, we present evidence for organization of a large proportion of a human transcriptome into gene clusters throughout the genome, which are partly regulated by the same transcription factors, share biological functions and are characterized by non-housekeeping genes. This analysis was based on the cardiac transcriptome identified by our genome-wide array analysis of 55 human heart samples. We found 37% of these genes to be arranged mainly in adjacent pairs or triplets. A significant number of pairs of adjacent genes are putatively regulated by common transcription factors (p = 0.02. Furthermore, these gene pairs share a significant number of GO functional classification terms. We show that the human cardiac transcriptome is organized into many small clusters across the whole genome, rather than being concentrated in a few larger clusters. Conclusion Our findings suggest that genes expressed in concert are organized in a linear arrangement for coordinated regulation. Determining the relationship between gene arrangement, regulation and nuclear organization as well as gene function will have broad biological implications.

Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation

Science.gov (United States)

Wang, Ying; Ding, Jia-tong; Yang, Hai-ming; Yan, Zheng-jie; Cao, Wei; Li, Yang-bai

2015-01-01

Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp) were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species. PMID:26599806

Analysis of Pigeon (Columba Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

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Ying Wang

Full Text Available Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

Estudo de uma cepa humana de Schistosoma mansoni resistente a agentes esquistossomicidas

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Naftale Katz

1973-12-01

Full Text Available Foi isolada uma cepa de Schistosoma mansoni proveniente de dois pacientes tratados com hycanthone, por duas vezes, na dose de 2,5mg/kg, i.m., em janeiro e em abril de 1970, e com niridazole (25mg/kg dia x 5 oral, em abril de 1971. O número de ovos por grama de fezes nestes pacientes antes do tratamento era de 2675 e 1025, respectivamente e, após o terceiro tratamento, em torno de 100 ovos/g. Miracídios obtidos das fezes destes pacientes, infectaram caramujos (Biomphalaria glabrata, que passaram a eliminar cercárias (cepa WW. Estas foram utilizadas para infecção experimental de camundongos albinos. Os animais infectados foram tratados com esquemas múltiplos de hycanthone, niridazole e oxamniquine. Estudos comparativos das cepas WW e LE (esta última mantida rotineiramente em nossos laboratórios mostraram diferenças acentuadas quando à sensibilidade aos esquistossomicidas usados. De fato, com hycanthone, na dose de 80mg/kg, i.m. houve 100% de alteração do oograma nos camundongos infectados com a cepa L.E. e de 0,0% nos infectados com a cepa WW. Com a oxamniquine e niridazole as diferenças foram menores, mas, ainda assim, suficientes para indicar maior resistência da cepa WW a estes esquistossomicidas. Esta é a primeira vez na literatura, que se demonstra resistência em cepas de S. mansoni provenientes de pacientes tratados.There has been isolated a Schistosoma mansoni strain from two patients submitted to two courses of treatment with hycanthone (2,5mg/kg, i.m., in January and April, 1970, and to one course with niridazole (25mg/kg/day x 5, per os, in April, 1971. Before treatment, the number of eggs in the faeces of those patients was, per gram, 2,675 and 1,025, respectively; after completion of treatment, such number had come down to around 100 eggs/gram. Miracidia hatched from the patients faeces could infect Biomphalaria glabrata snails, which elimmated cercariae (WW strain that were used for experimental infection of albino

Transcriptomic impacts of rumen epithelium induced by butyrate infusion in dairy cattle in dry period

Science.gov (United States)

Transcriptomics and bioinformatics are utilized to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion. Butyrate, as an essential element of nutrients, is an HDAC inhibitor that can alter histone acetylation and methyl...

De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology.

Science.gov (United States)

Canales, Javier; Bautista, Rocio; Label, Philippe; Gómez-Maldonado, Josefa; Lesur, Isabelle; Fernández-Pozo, Noe; Rueda-López, Marina; Guerrero-Fernández, Dario; Castro-Rodríguez, Vanessa; Benzekri, Hicham; Cañas, Rafael A; Guevara, María-Angeles; Rodrigues, Andreia; Seoane, Pedro; Teyssier, Caroline; Morel, Alexandre; Ehrenmann, François; Le Provost, Grégoire; Lalanne, Céline; Noirot, Céline; Klopp, Christophe; Reymond, Isabelle; García-Gutiérrez, Angel; Trontin, Jean-François; Lelu-Walter, Marie-Anne; Miguel, Celia; Cervera, María Teresa; Cantón, Francisco R; Plomion, Christophe; Harvengt, Luc; Avila, Concepción; Gonzalo Claros, M; Cánovas, Francisco M

2014-04-01

Maritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full-length cDNAs. Quality of the transcriptome assembly was validated by RT-PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme-encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple-sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

SNP discovery in the transcriptome of white Pacific shrimp Litopenaeus vannamei by next generation sequencing.

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Yang Yu

Full Text Available The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.

Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization.

Science.gov (United States)

Sager, Monica; Yeat, Nai Chien; Pajaro-Van der Stadt, Stefan; Lin, Charlotte; Ren, Qiuyin; Lin, Jimmy

2015-01-01

Transcriptomic technologies are evolving to diagnose cancer earlier and more accurately to provide greater predictive and prognostic utility to oncologists and patients. Digital techniques such as RNA sequencing are replacing still-imaging techniques to provide more detailed analysis of the transcriptome and aberrant expression that causes oncogenesis, while companion diagnostics are developing to determine the likely effectiveness of targeted treatments. This article examines recent advancements in molecular profiling research and technology as applied to cancer diagnosis, clinical applications and predictions for the future of personalized medicine in oncology.

The transcriptome of the Didelphis virginiana opossum kidney OK proximal tubule cell line.

Science.gov (United States)

Eshbach, Megan L; Sethi, Rahil; Avula, Raghunandan; Lamb, Janette; Hollingshead, Deborah J; Finegold, David N; Locker, Joseph D; Chandran, Uma R; Weisz, Ora A

2017-09-01

The OK cell line derived from the kidney of a female opossum Didelphis virginiana has proven to be a useful model in which to investigate the unique regulation of ion transport and membrane trafficking mechanisms in the proximal tubule (PT). Sequence data and comparison of the transcriptome of this cell line to eutherian mammal PTs would further broaden the utility of this culture model. However, the genomic sequence for D. virginiana is not available and although a draft genome sequence for the opossum Monodelphis domestica (sequenced in 2012 by the Broad Institute) exists, transcripts sequenced from both species show significant divergence. The M. domestica sequence is not highly annotated, and the majority of transcripts are predicted rather than experimentally validated. Using deep RNA sequencing of the D. virginiana OK cell line, we characterized its transcriptome via de novo transcriptome assembly and alignment to the M. domestica genome. The quality of the de novo assembled transcriptome was assessed by the extent of homology to sequences in nucleotide and protein databases. Gene expression levels in the OK cell line, from both the de novo transcriptome and genes aligned to the M. domestica genome, were compared with publicly available rat kidney nephron segment expression data. Our studies demonstrate the expression in OK cells of numerous PT-specific ion transporters and other key proteins relevant for rodent and human PT function. Additionally, the sequence and expression data reported here provide an important resource for genetic manipulation and other studies on PT cell function using these cells. Copyright © 2017 the American Physiological Society.

Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.

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Wu, Hong-xia; Jia, Hui-min; Ma, Xiao-wei; Wang, Song-biao; Yao, Quan-sheng; Xu, Wen-tian; Zhou, Yi-gang; Gao, Zhong-shan; Zhan, Ru-lin

2014-06-13

Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Transcriptome analysis of the response of Burmese python to digestion.

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Duan, Jinjie; Sanggaard, Kristian Wejse; Schauser, Leif; Lauridsen, Sanne Enok; Enghild, Jan J; Schierup, Mikkel Heide; Wang, Tobias

2017-08-01

Exceptional and extreme feeding behaviour makes the Burmese python (Python bivittatus) an interesting model to study physiological remodelling and metabolic adaptation in response to refeeding after prolonged starvation. In this study, we used transcriptome sequencing of 5 visceral organs during fasting as well as 24 hours and 48 hours after ingestion of a large meal to unravel the postprandial changes in Burmese pythons. We first used the pooled data to perform a de novo assembly of the transcriptome and supplemented this with a proteomic survey of enzymes in the plasma and gastric fluid. We constructed a high-quality transcriptome with 34 423 transcripts, of which 19 713 (57%) were annotated. Among highly expressed genes (fragments per kilo base per million sequenced reads > 100 in 1 tissue), we found that the transition from fasting to digestion was associated with differential expression of 43 genes in the heart, 206 genes in the liver, 114 genes in the stomach, 89 genes in the pancreas, and 158 genes in the intestine. We interrogated the function of these genes to test previous hypotheses on the response to feeding. We also used the transcriptome to identify 314 secreted proteins in the gastric fluid of the python. Digestion was associated with an upregulation of genes related to metabolic processes, and translational changes therefore appear to support the postprandial rise in metabolism. We identify stomach-related proteins from a digesting individual and demonstrate that the sensitivity of modern liquid chromatography/tandem mass spectrometry equipment allows the identification of gastric juice proteins that are present during digestion. © The Authors 2017. Published by Oxford University Press.

De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

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Yeonhwa Jo

2015-12-01

Full Text Available Sour cherry (Prunus cerasus in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170. De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.

Transcriptome analysis in cotton boll weevil (Anthonomus grandis and RNA interference in insect pests.

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Alexandre Augusto Pereira Firmino

Full Text Available Cotton plants are subjected to the attack of several insect pests. In Brazil, the cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The use of insecticidal proteins and gene silencing by interference RNA (RNAi as techniques for insect control are promising strategies, which has been applied in the last few years. For this insect, there are not much available molecular information on databases. Using 454-pyrosequencing methodology, the transcriptome of all developmental stages of the insect pest, A. grandis, was analyzed. The A. grandis transcriptome analysis resulted in more than 500.000 reads and a data set of high quality 20,841 contigs. After sequence assembly and annotation, around 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein database and 65.7% was similar to Tribolium castaneum sequences. A comparison of A. grandis, Drosophila melanogaster and Bombyx mori protein families' data showed higher similarity to dipteran than to lepidopteran sequences. Several contigs of genes encoding proteins involved in RNAi mechanism were found. PAZ Domains sequences extracted from the transcriptome showed high similarity and conservation for the most important functional and structural motifs when compared to PAZ Domains from 5 species. Two SID-like contigs were phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No RdRP gene was found. A contig matching chitin synthase 1 was mined from the transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis female adults resulted in normal oviposition of unviable eggs and malformed alive larvae that were unable to develop in artificial diet. This is the first study that characterizes the transcriptome of the coleopteran, A. grandis. A new and representative transcriptome database for this insect pest is now available. All data support the state of the art of RNAi mechanism in insects.

Transcriptome analysis in cotton boll weevil (Anthonomus grandis) and RNA interference in insect pests.

Science.gov (United States)

Firmino, Alexandre Augusto Pereira; Fonseca, Fernando Campos de Assis; de Macedo, Leonardo Lima Pepino; Coelho, Roberta Ramos; Antonino de Souza, José Dijair; Togawa, Roberto Coiti; Silva-Junior, Orzenil Bonfim; Pappas, Georgios Joannis; da Silva, Maria Cristina Mattar; Engler, Gilbert; Grossi-de-Sa, Maria Fatima

2013-01-01

Cotton plants are subjected to the attack of several insect pests. In Brazil, the cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The use of insecticidal proteins and gene silencing by interference RNA (RNAi) as techniques for insect control are promising strategies, which has been applied in the last few years. For this insect, there are not much available molecular information on databases. Using 454-pyrosequencing methodology, the transcriptome of all developmental stages of the insect pest, A. grandis, was analyzed. The A. grandis transcriptome analysis resulted in more than 500.000 reads and a data set of high quality 20,841 contigs. After sequence assembly and annotation, around 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein database and 65.7% was similar to Tribolium castaneum sequences. A comparison of A. grandis, Drosophila melanogaster and Bombyx mori protein families' data showed higher similarity to dipteran than to lepidopteran sequences. Several contigs of genes encoding proteins involved in RNAi mechanism were found. PAZ Domains sequences extracted from the transcriptome showed high similarity and conservation for the most important functional and structural motifs when compared to PAZ Domains from 5 species. Two SID-like contigs were phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No RdRP gene was found. A contig matching chitin synthase 1 was mined from the transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis female adults resulted in normal oviposition of unviable eggs and malformed alive larvae that were unable to develop in artificial diet. This is the first study that characterizes the transcriptome of the coleopteran, A. grandis. A new and representative transcriptome database for this insect pest is now available. All data support the state of the art of RNAi mechanism in insects.

Transcriptome differences between enrofloxacin-resistant and enrofloxacin-susceptible strains of Aeromonas hydrophila

OpenAIRE

Zhu, Fengjiao; Yang, Zongying; Zhang, Yiliu; Hu, Kun; Fang, Wenhong

2017-01-01

Enrofloxacin is the most commonly used antibiotic to control diseases in aquatic animals caused by A. hydrophila. This study conducted de novo transcriptome sequencing and compared the global transcriptomes of enrofloxacin-resistant and enrofloxacin-susceptible strains. We got a total of 4,714 unigenes were assembled. Of these, 4,122 were annotated. A total of 3,280 unigenes were assigned to GO, 3,388 unigenes were classified into Cluster of Orthologous Groups of proteins (COG) using BLAST an...

Transcriptome analysis of Anopheles stephensi embryo using ...

Indian Academy of Sciences (India)

Germ band retraction (GBR) stage is one of the important stages during insect development. It is associated with an extensive epithelial morphogenesis and may also be pivotal in generation of morphological diversity in insects. Despite its importance, only a handful of studies report the transcriptome repertoire of this stage ...

Global daily dynamics of the pineal transcriptome

DEFF Research Database (Denmark)

Bustos, Diego M; Bailey, Michael J; Sugden, David

2011-01-01

Transcriptome profiling of the pineal gland has revealed night/day differences in the expression of a major fraction of the genes active in this tissue, with two-thirds of these being nocturnal increases. A set of over 600 transcripts exhibit two-fold to >100-fold daily differences in abundance...

Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes.

Science.gov (United States)

Kumar, Vikas; Kutschera, Verena E; Nilsson, Maria A; Janke, Axel

2015-08-07

The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic

Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle

Science.gov (United States)

2011-01-01

The response of the abomasal transcriptome to gastrointestinal parasites was evaluated in parasite-susceptible and parasite-resistant Angus cattle using RNA-seq at a depth of 23.7 million sequences per sample. These cattle displayed distinctly separate resistance phenotypes as assessed by fecal egg counts. Approximately 65.3% of the 23 632 bovine genes were expressed in the fundic abomasum. Of these, 13 758 genes were expressed in all samples tested and likely represent core components of the bovine abomasal transcriptome. The gene (BT14427) with the most abundant transcript, accounting for 10.4% of sequences in the transcriptome, is located on chromosome 29 and has unknown functions. Additionally, PIGR (1.6%), Complement C3 (0.7%), and Immunoglobulin J chain (0.5%) were among the most abundant transcripts in the transcriptome. Among the 203 genes impacted, 64 were significantly over-expressed in resistant animals at a stringent cutoff (FDR parasite resistance in cattle. Our results provide insights into the development of host immunity to gastrointestinal nematode infection and will facilitate understanding of mechanism underlying host resistance. PMID:22129081

RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges

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Muhamad Afiq Akbar

2018-01-01

Full Text Available Dinoflagellates are the large group of marine phytoplankton with primary studies interest regarding their symbiosis with coral reef and the abilities to form harmful algae blooms (HABs. Toxin produced by dinoflagellates during events of HABs cause severe negative impact both in the economy and health sector. However, attempts to understand the dinoflagellates genomic features are hindered by their complex genome organization. Transcriptomics have been employed to understand dinoflagellates genome structure, profile genes and gene expression. RNA-seq is one of the latest methods for transcriptomics study. This method is capable of profiling the dinoflagellates transcriptomes and has several advantages, including highly sensitive, cost effective and deeper sequence coverage. Thus, in this review paper, the current workflow of dinoflagellates RNA-seq starts with the extraction of high quality RNA and is followed by cDNA sequencing using the next-generation sequencing platform, dinoflagellates transcriptome assembly and computational analysis will be discussed. Certain consideration needs will be highlighted such as difficulty in dinoflagellates sequence annotation, post-transcriptional activity and the effect of RNA pooling when using RNA-seq.

De Novo Assembly and Characterization of the Transcriptome of Grasshopper Shirakiacris shirakii

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Zhongying Qiu

2016-07-01

Full Text Available Background: The grasshopper Shirakiacris shirakii is an important agricultural pest and feeds mainly on gramineous plants, thereby causing economic damage to a wide range of crops. However, genomic information on this species is extremely limited thus far, and transcriptome data relevant to insecticide resistance and pest control are also not available. Methods: The transcriptome of S. shirakii was sequenced using the Illumina HiSeq platform, and we de novo assembled the transcriptome. Results: Its sequencing produced a total of 105,408,878 clean reads, and the de novo assembly revealed 74,657 unigenes with an average length of 680 bp and N50 of 1057 bp. A total of 28,173 unigenes were annotated for the NCBI non-redundant protein sequences (Nr, NCBI non-redundant nucleotide sequences (Nt, a manually-annotated and reviewed protein sequence database (Swiss-Prot, Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG databases. Based on the Nr annotation results, we manually identified 79 unigenes encoding cytochrome P450 monooxygenases (P450s, 36 unigenes encoding carboxylesterases (CarEs and 36 unigenes encoding glutathione S-transferases (GSTs in S. shirakii. Core RNAi components relevant to miroRNA, siRNA and piRNA pathways, including Pasha, Loquacious, Argonaute-1, Argonaute-2, Argonaute-3, Zucchini, Aubergine, enhanced RNAi-1 and Piwi, were expressed in S. shirakii. We also identified five unigenes that were homologous to the Sid-1 gene. In addition, the analysis of differential gene expressions revealed that a total of 19,764 unigenes were up-regulated and 4185 unigenes were down-regulated in larvae. In total, we predicted 7504 simple sequence repeats (SSRs from 74,657 unigenes. Conclusions: The comprehensive de novo transcriptomic data of S. shirakii will offer a series of valuable molecular resources for better studying insecticide resistance, RNAi and molecular marker discovery in the transcriptome.

Determining the optimal number of independent components for reproducible transcriptomic data analysis.

Science.gov (United States)

Kairov, Ulykbek; Cantini, Laura; Greco, Alessandro; Molkenov, Askhat; Czerwinska, Urszula; Barillot, Emmanuel; Zinovyev, Andrei

2017-09-11

Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data. Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets. We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

Comportamento reológico de méis de florada de silvestre Rheological behavior of honey from Serjania glabrata flowers

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Alexandre J. de M. Queiroz

2007-04-01

Full Text Available Estudou-se o comportamento reológico de méis de Apis mellifera produzidos no estado do Piauí, no semi-árido brasileiro, elaborados com florada predominante de silvestre (Serjania glabrata. As amostras foram coletadas ao longo do ano 2000, a partir de coletas realizadas por apicultores, associações e cooperativas de apicultura da região abrangida pelos municípios de Picos, Itainópolis, Vera Mendes e Isaías Coelho. Após as coletas as amostras passaram pelos processos de centrifugação, filtragem e decantação. As medidas reológicas foram feitas nas temperaturas de 20 a 40 ºC utilizando-se um viscosímetro Brookfield, modelo RVT. As leituras de velocidade de rotação e torque foram transformadas em valores de taxa de deformação e tensão de cisalhamento. Os dados de taxa de deformação e tensão de cisalhamento foram ajustados pelas equações da Lei-da-Potência e de Herschel-Bulkley. As amostras apresentaram comportamento pseudoplástico. As equações se ajustaram adequadamente aos resultados experimentais de tensão de cisalhamento em função da taxa de deformação. O aumento de temperatura reduziu a viscosidade aparente em níveis próximos de 80%. Os valores de viscosidade aparente foram bem ajustados por uma equação do tipo Arrhenius.The rheological behavior of Apis mellifera honey produced in the State of Piauí, in the Brazilian semi-arid, obtained with predominance of Serjania glabrata flowers was studied. The samples were collected in the year 2000 by beekeepers and associations and cooperatives of beekeepers in the area covered by the municipal districts of Picos, Itainópolis, Vera Mendes and Isaías Coelho. The samples were centrifuged, filtered, decanted and the rheological measures at temperatures of 20 to 40 ºC using a Brookfield Viscometer RVT model were made. The readings of rotation speed and torque were transformed in shear rate and shear stress values. The data of shear rate and shear stress were fitted

De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.

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Tian, Xin-Jie; Long, Yan; Wang, Jiao; Zhang, Jing-Wen; Wang, Yan-Yan; Li, Wei-Min; Peng, Yu-Fa; Yuan, Qian-Hua; Pei, Xin-Wu

2015-01-01

The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice. In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses. This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.

Developmental transcriptome of Aplysia californica'

KAUST Repository

Heyland, Andreas

2010-12-06

Genome-wide transcriptional changes in development provide important insight into mechanisms underlying growth, differentiation, and patterning. However, such large-scale developmental studies have been limited to a few representatives of Ecdysozoans and Chordates. Here, we characterize transcriptomes of embryonic, larval, and metamorphic development in the marine mollusc Aplysia californica and reveal novel molecular components associated with life history transitions. Specifically, we identify more than 20 signal peptides, putative hormones, and transcription factors in association with early development and metamorphic stages-many of which seem to be evolutionarily conserved elements of signal transduction pathways. We also characterize genes related to biomineralization-a critical process of molluscan development. In summary, our experiment provides the first large-scale survey of gene expression in mollusc development, and complements previous studies on the regulatory mechanisms underlying body plan patterning and the formation of larval and juvenile structures. This study serves as a resource for further functional annotation of transcripts and genes in Aplysia, specifically and molluscs in general. A comparison of the Aplysia developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms that are likely a consequence of the different developmental modes of these organisms. © 2010 Wiley-Liss, Inc., A Wiley Company.

Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific.

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Kenkel, Carly D; Bay, Line K

2017-09-01

Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata, and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperatures. Trinity was used to create de novo assemblies for each species from 92-102 million raw Illumina Hiseq 2 × 150 bp reads. Host-specific assemblies contained 65 460-72 405 contigs, representing 26 693-37 894 isogroups (∼genes) with an average N50 of 2254. Gene name and/or gene ontology annotations were possible for 58% of isogroups on average. Transcriptomes contained 93.1-94.3% of EuKaryotic Orthologous Groups comprising the core eukaryotic gene set, and 89.98-91.92% of the single-copy metazoan core gene set orthologs were complete, indicating fairly comprehensive assemblies. This work expands the complement of transcriptomic resources available for scleractinian coral species, including the first reference for a representative of Goniopora spp. as well as species with novel morphology. © The Authors 2017. Published by Oxford University Press.

Purification, Reconstitution, and Inhibition of Cytochrome P-450 Sterol Δ22-Desaturase from the Pathogenic Fungus Candida glabrata

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Lamb, David C.; Maspahy, Segula; Kelly, Diane E.; Manning, Nigel J.; Geber, Antonia; Bennett, John E.; Kelly, Steven L.

1999-01-01

Sterol Δ22-desaturase has been purified from a strain of Candida glabrata with a disruption in the gene encoding sterol 14α-demethylase (cytochrome P-45051; CYP51). The purified cytochrome P-450 exhibited sterol Δ22-desaturase activity in a reconstituted system with NADPH–cytochrome P-450 reductase in dilaurylphosphatidylcholine, with the enzyme kinetic studies revealing a Km for ergosta-5,7-dienol of 12.5 μM and a Vmax of 0.59 nmol of this substrate metabolized/min/nmol of P-450. This enzyme is encoded by CYP61 (ERG5) in Saccharomyces cerevisiae, and homologues have been shown in the Candida albicans and Schizosaccharomyces pombe genome projects. Ketoconazole, itraconazole, and fluconazole formed low-spin complexes with the ferric cytochrome and exhibited type II spectra, which are indicative of an interaction between the azole moiety and the cytochrome heme. The azole antifungal compounds inhibited reconstituted sterol Δ22-desaturase activity by binding to the cytochrome with a one-to-one stoichiometry, with total inhibition of enzyme activity occurring when equimolar amounts of azole and cytochrome P-450 were added. These results reveal the potential for sterol Δ22-desaturase to be an antifungal target and to contribute to the binding of drugs within the fungal cell. PMID:10390230

Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing

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Taketo Okada

2016-12-01

Full Text Available Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo assembly of short cDNA sequence reads generated 23,358, 13,373, and 28,579 contigs longer than 200 bases from aerial stems, roots, or both aerial stems and roots, respectively. The presumed functions encoded by these contig sequences were annotated by BLAST (blastx. Subsequently, these contigs were classified based on gene ontology slims, Enzyme Commission numbers, and the InterPro database. Furthermore, comparative gene expression analysis was performed between aerial stems and roots. These transcriptome analyses revealed differences and similarities between the transcriptomes of aerial stems and roots in E. sinica. Deep transcriptome sequencing of Ephedra should open the door to molecular biological studies based on the entire transcriptome, tissue- or organ-specific transcriptomes, or targeted genes of interest.

Transcriptome Analysis of Two Different Developmental Stages of Paeonia lactiflora Seeds

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Yonglei Ma

2017-01-01

Full Text Available Paeonia lactiflora is a herbaceous flower in the family Paeoniaceae with both hypocotyl and epicotyl dormant seeds. We used high-throughput transcriptome sequencing on two different developmental stages of P. lactiflora seeds to identify seed dormancy and germination-related genes. We performed de novo assembly and annotated a total of 123,577 unigenes, which encoded 24,688 putative proteins with 47 GO categories. A total of 10,714 unigenes were annotated in the KEGG database, and 258 pathways were involved in the annotations. A total of 1795 genes were differentially expressed in the functional enrichment analysis. The key genes for seed germination and dormancy, such as GAI1 and ARF, were confirmed by quantitative reverse transcription-polymerase chain reaction analysis. This is the first report of sequencing the P. lactiflora seed transcriptome. Our results provide fundamental frame work and technical support for further selective breeding and cultivation of Paeonia. Our transcriptomic data also serves as the basis for future genetics and genomics research on Paeonia and its closely related species.

Identification of strong promoters based on the transcriptome of Bacillus licheniformis.

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Liu, Xin; Yang, Haiyan; Zheng, Junwei; Ye, Yanrui; Pan, Li

2017-06-01

To expand the repertoire of strong promoters for high level expression of proteins based on the transcriptome of Bacillus licheniformis. The transcriptome of B. licheniformis ATCC14580 grown to the early stationary phase was analyzed and the top 10 highly expressed genes/operons out of the 3959 genes and 1249 operons identified were chosen for study promoter activity. Using beta-galactosidase gene as a reporter, the candidate promoter pBL9 exhibited the strongest activity which was comparable to that of the widely used strong promoter p43. Furthermore, the pro-transglutaminase from Streptomyces mobaraensis (pro-MTG) was expressed under the control of promoter pBL9 and the activity of pro-MTG reached 82 U/ml after 36 h, which is 23% higher than that of promoter p43 (66.8 U/ml). In our analyses of the transcriptome of B. licheniformis, we have identified a strong promoter pBL9, which could be adapted for high level expression of proteins in the host Bacillus subtilis.

The Transcriptomic Responses of Pinus massoniana to Drought Stress

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Mingfeng Du

2018-06-01

Full Text Available Masson pine (Pinus massoniana is a major fast-growing timber species planted in southern China, a region of seasonal drought. Using a drought-tolerance genotype of Masson pine, we conducted large-scale transcriptome sequencing using Illumina technology. This work aimed to evaluate the transcriptomic responses of Masson pine to different levels of drought stress. First, 3397, 1695 and 1550 unigenes with differential expression were identified by comparing plants subjected to light, moderate or severe drought with control plants. Second, several gene ontology (GO categories (oxidation-reduction and metabolism and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways (plant hormone signal transduction and metabolic pathways were enriched, indicating that the expression levels of some genes in these enriched GO terms and pathways were altered under drought stress. Third, several transcription factors (TFs associated with circadian rhythms (HY5 and LHY, signal transduction (ERF, and defense responses (WRKY were identified, and these TFs may play key roles in adapting to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to osmotic adjustment (P5CS, abscisic acid (ABA responses (NCED, PYL, PP2C and SnRK, and reactive oxygen species (ROS scavenging (GPX, GST and GSR. These transcriptomic results provide insight into the molecular mechanisms of drought stress adaptation in Masson pine.

Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

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Jennifer A Mitchell

Full Text Available In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.

De novo transcriptome assembly of two contrasting pumpkin cultivars

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Aliki Xanthopoulou

2016-03-01

Full Text Available Cucurbita pepo (squash, pumpkin, gourd, a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, ‘Big Moose’ with large round fruits and ‘Munchkin’ with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882 and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883 sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively, which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for ‘Big Moose’ and ‘Munchkin’ were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses. Keywords: RNA-Seq, Pumpkin, Contrasting cultivars, Cucurbita pepo

[SSR loci information analysis in transcriptome of Andrographis paniculata].

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Li, Jun-Ren; Chen, Xiu-Zhen; Tang, Xiao-Ting; He, Rui; Zhan, Ruo-Ting

2018-06-01

To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. Copyright© by the Chinese Pharmaceutical Association.

Construction of an EST-SSR-based interspecific transcriptome ...

Indian Academy of Sciences (India)

Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. CHUANXIANG LIU, DAOJUN YUAN and ZHONGXU LIN. ∗. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan),. Huazhong Agricultural University, Wuhan ...

The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.

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Michael K DeSalvo

2014-11-01

Full Text Available AbstractCentral nervous system (CNS function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with FACS and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ABC and SLC transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.

Science.gov (United States)

DeSalvo, Michael K; Hindle, Samantha J; Rusan, Zeid M; Orng, Souvinh; Eddison, Mark; Halliwill, Kyle; Bainton, Roland J

2014-01-01

Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

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Pernille Sarup

2011-01-01

Full Text Available Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

Transcriptomic dissection of tongue squamous cell carcinoma

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Schwartz Joel L

2008-02-01

Full Text Available Abstract Background The head and neck/oral squamous cell carcinoma (HNOSCC is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristics. The oral tongue squamous cell carcinoma (OTSCC is one of the most common types of HNOSCC. It is significantly more aggressive than other forms of HNOSCC, in terms of local invasion and spread. In this study, we aim to identify specific transcriptomic signatures that associated with OTSCC. Results Genome-wide transcriptomic profiles were obtained for 53 primary OTSCCs and 22 matching normal tissues. Genes that exhibit statistically significant differences in expression between OTSCCs and normal were identified. These include up-regulated genes (MMP1, MMP10, MMP3, MMP12, PTHLH, INHBA, LAMC2, IL8, KRT17, COL1A2, IFI6, ISG15, PLAU, GREM1, MMP9, IFI44, CXCL1, and down-regulated genes (KRT4, MAL, CRNN, SCEL, CRISP3, SPINK5, CLCA4, ADH1B, P11, TGM3, RHCG, PPP1R3C, CEACAM7, HPGD, CFD, ABCA8, CLU, CYP3A5. The expressional difference of IL8 and MMP9 were further validated by real-time quantitative RT-PCR and immunohistochemistry. The Gene Ontology analysis suggested a number of altered biological processes in OTSCCs, including enhancements in phosphate transport, collagen catabolism, I-kappaB kinase/NF-kappaB signaling cascade, extracellular matrix organization and biogenesis, chemotaxis, as well as suppressions of superoxide release, hydrogen peroxide metabolism, cellular response to hydrogen peroxide, keratinization, and keratinocyte differentiation in OTSCCs. Conclusion In summary, our study provided a transcriptomic signature for OTSCC that may lead to a diagnosis or screen tool and provide the foundation for further functional validation of these specific candidate genes for OTSCC.

The draft genome and transcriptome of Cannabis sativa.

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van Bakel, Harm; Stout, Jake M; Cote, Atina G; Tallon, Carling M; Sharpe, Andrew G; Hughes, Timothy R; Page, Jonathan E

2011-10-20

Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored. We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp. The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.

Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds.

Science.gov (United States)

Pradhan, Seema; Bandhiwal, Nitesh; Shah, Niraj; Kant, Chandra; Gaur, Rashmi; Bhatia, Sabhyata

2014-01-01

Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

Global transcriptome analysis of developing chickpea (Cicer arietinum L. seeds

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Seema ePradhan

2014-12-01

Full Text Available Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L. seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilised to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analysed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs, about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

Illumina–based de novo transcriptome sequencing and analysis of ...

Indian Academy of Sciences (India)

Administrator

2017-10-25

Oct 25, 2017 ... (Shanghai, China) following manufacturer's protocols (Illumina, San .... suggests that pathways involved in musk production are expressed at a ..... Strickler S. R., Aureliano B. and Mueller L. A. 2012 Designing a transcriptome.

De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome

Science.gov (United States)

Schulze, Thomas T.; Ali, Jonathan M.; Bartlett, Maggie L.; McFarland, Madalyn M.; Clement, Emalie J.; Won, Harim I.; Sanford, Austin G.; Monzingo, Elyssa B.; Martens, Matthew C.; Hemsley, Ryan M.; Kumar, Sidharta; Gouin, Nicolas; Kolok, Alan S.; Davis, Paul H.

2016-01-01

Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included. PMID:27672404

Transcriptome profiling of Finnsheep ovaries during out-of-season breeding period

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Kisun Pokharel

2015-03-01

Full Text Available   Finnsheep is one of the most prolific sheep breeds in the world. We sequenced RNA-Seq libraries from the ovaries of Finnsheep ewes collected during out of season breeding period at about 30X sequence coverage. A total of 86 966 348 and 105 587 994 reads from two samples were mapped against latest available ovine reference genome (Oarv3.1. The transcriptome assembly revealed 14 870 known ovine genes, including the 15 candidate genes for fertility and out-of-season breeding. In this study we successfully used our bioinformatics pipeline to assemble the first ovarian transcriptome of Finnsheep.

Integrative Transcriptomic and Metabonomic Molecular Profiling of Colonic Mucosal Biopsies Indicates a Unique Molecular Phenotype for Ulcerative Colitis

DEFF Research Database (Denmark)

Rantalainen, Mattias; Bjerrum, Jacob Tveiten; Olsen, Jørgen

2015-01-01

characterized the molecular phenotype of ulcerative colitis through transcriptomic and metabonomic profiling of colonic mucosal biopsies from patients and controls. We have characterized the extent to which metabonomic and transcriptomic molecular phenotypes are associated with ulcerative colitis versus...... transcriptomic and metabonomic data have previously been shown to predict the clinical course of ulcerative colitis and related clinical phenotypes, indicating that molecular phenotypes reveal molecular changes associated with the disease. Our analyses indicate that variables of both transcriptomics...... and metabonomics are associated with disease case and control status, that a large proportion of transcripts are associated with at least one metabolite in mucosal colonic biopsies, and that multiple pathways are connected to disease-related metabolites and transcripts....

Transcriptomes of Frankia sp. strain CcI3 in growth transitions

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Bickhart Derek M

2011-08-01

Full Text Available Abstract Background Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days and by culture conditions (NH4+ added vs. N2 fixing. Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions The overall pattern of

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

OpenAIRE

Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

2010-01-01

Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resoluti...

Spatial transcriptomics: paving the way for tissue-level systems biology.

Science.gov (United States)

Moor, Andreas E; Itzkovitz, Shalev

2017-08-01

The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates. In this review we describe how recent advances in spatial transcriptomics open the way for tissue-level systems biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

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Scoté-Blachon Céline

2008-09-01

Full Text Available Abstract Background "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression, LongSAGE and MPSS (Massively Parallel Signature Sequencing are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered. Results In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method. Conclusion We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.

Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

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Muhamad Afiq Akbar

2018-02-01

Full Text Available Dinoflagellates are essential components in marine ecosystems, and they possess two dissimilar flagella to facilitate movement. Dinoflagellates are major components of marine food webs and of extreme importance in balancing the ecosystem energy flux in oceans. They have been reported to be the primary cause of harmful algae bloom (HABs events around the world, causing seafood poisoning and therefore having a direct impact on human health. Interestingly, dinoflagellates in the genus Symbiodinium are major components of coral reef foundations. Knowledge regarding their genes and genome organization is currently limited due to their large genome size and other genetic and cytological characteristics that hinder whole genome sequencing of dinoflagellates. Transcriptomic approaches and genetic analyses have been employed to unravel the physiological and metabolic characteristics of dinoflagellates and their complexity. In this review, we summarize the current knowledge and findings from transcriptomic studies to understand the cell growth, effects on environmental stress, toxin biosynthesis, dynamic of HABs, phylogeny and endosymbiosis of dinoflagellates. With the advancement of high throughput sequencing technologies and lower cost of sequencing, transcriptomic approaches will likely deepen our understanding in other aspects of dinoflagellates’ molecular biology such as gene functional analysis, systems biology and development of model organisms.

Quantitative developmental transcriptomes of the Mediterranean sea urchin Paracentrotus lividus.

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Gildor, Tsvia; Malik, Assaf; Sher, Noa; Avraham, Linor; Ben-Tabou de-Leon, Smadar

2016-02-01

Embryonic development progresses through the timely activation of thousands of differentially activated genes. Quantitative developmental transcriptomes provide the means to relate global patterns of differentially expressed genes to the emerging body plans they generate. The sea urchin is one of the classic model systems for embryogenesis and the models of its developmental gene regulatory networks are of the most comprehensive of their kind. Thus, the sea urchin embryo is an excellent system for studies of its global developmental transcriptional profiles. Here we produced quantitative developmental transcriptomes of the sea urchin Paracentrotus lividus (P. lividus) at seven developmental stages from the fertilized egg to prism stage. We generated de-novo reference transcriptome and identified 29,817 genes that are expressed at this time period. We annotated and quantified gene expression at the different developmental stages and confirmed the reliability of the expression profiles by QPCR measurement of a subset of genes. The progression of embryo development is reflected in the observed global expression patterns and in our principle component analysis. Our study illuminates the rich patterns of gene expression that participate in sea urchin embryogenesis and provide an essential resource for further studies of the dynamic expression of P. lividus genes. Copyright © 2015 Elsevier B.V. All rights reserved.

Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior.

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Michael K Skinner

Full Text Available Embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes an epigenetic reprogramming of the male germ-line that is associated with transgenerational adult onset disease states. Further analysis of this transgenerational phenotype on the brain demonstrated reproducible changes in the brain transcriptome three generations (F3 removed from the exposure. The transgenerational alterations in the male and female brain transcriptomes were distinct. In the males, the expression of 92 genes in the hippocampus and 276 genes in the amygdala were transgenerationally altered. In the females, the expression of 1,301 genes in the hippocampus and 172 genes in the amygdala were transgenerationally altered. Analysis of specific gene sets demonstrated that several brain signaling pathways were influenced including those involved in axon guidance and long-term potentiation. An investigation of behavior demonstrated that the vinclozolin F3 generation males had a decrease in anxiety-like behavior, while the females had an increase in anxiety-like behavior. These observations demonstrate that an embryonic exposure to an environmental compound appears to promote a reprogramming of brain development that correlates with transgenerational sex-specific alterations in the brain transcriptomes and behavior. Observations are discussed in regards to environmental and transgenerational influences on the etiology of brain disease.

Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

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Rebecca M. Davidson

2011-11-01

Full Text Available Transcriptome sequencing is a powerful method for studying global expression patterns in large, complex genomes. Evaluation of sequence-based expression profiles during reproductive development would provide functional annotation to genes underlying agronomic traits. We generated transcriptome profiles for 12 diverse maize ( L. reproductive tissues representing male, female, developing seed, and leaf tissues using high throughput transcriptome sequencing. Overall, ∼80% of annotated genes were expressed. Comparative analysis between sequence and hybridization-based methods demonstrated the utility of ribonucleic acid sequencing (RNA-seq for expression determination and differentiation of paralagous genes (∼85% of maize genes. Analysis of 4975 gene families across reproductive tissues revealed expression divergence is proportional to family size. In all pairwise comparisons between tissues, 7 (pre- vs. postemergence cobs to 48% (pollen vs. ovule of genes were differentially expressed. Genes with expression restricted to a single tissue within this study were identified with the highest numbers observed in leaves, endosperm, and pollen. Coexpression network analysis identified 17 gene modules with complex and shared expression patterns containing many previously described maize genes. The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.

Impact of the age of Biomphalaria alexandrina snails on Schistosoma mansoni transmission: modulation of the genetic outcome and the internal defence system of the snail

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Iman Fathy Abou-El-Naga

2015-08-01

Full Text Available Of the approximately 34 identified Biomphalariaspecies,Biomphalaria alexandrinarepresents the intermediate host of Schistosoma mansoniin Egypt. Using parasitological and SOD1 enzyme assay, this study aimed to elucidate the impact of the age of B. alexandrinasnails on their genetic variability and internal defence against S. mansoniinfection. Susceptible and resistant snails were reared individually for self-reproduction; four subgroups of their progeny were used in experiment. The young susceptible subgroup showed the highest infection rate, the shortest pre-patent period, the highest total cercarial production, the highest mortality rate and the lowest SOD1 activity. Among the young and adult susceptible subgroups, 8% and 26% were found to be resistant, indicating the inheritance of resistance alleles from parents. The adult resistant subgroup, however, contained only resistant snails and showed the highest enzyme activity. The complex interaction between snail age, genetic background and internal defence resulted in great variability in compatibility patterns, with the highest significant difference between young susceptible and adult resistant snails. The results demonstrate that resistance alleles function to a greater degree in adults, with higher SOD1 activity and provide potential implications for Biomphalariacontrol. The identification of the most susceptible snail age enables determination of the best timing for applying molluscicides. Moreover, adult resistant snails could be beneficial in biological snail control.

Susceptibility of Biomphalaria straminea (Dunker, 1848 from Serra da Mesa Dam, Goiás, Brazil to infection with three strains of Schistosoma mansoni Sambon, 1907

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Monica Ammon Fernandez

2002-10-01

Full Text Available Ecological changes from water resources development projects often affect the epidemiology of water-associated diseases. In order to investigate the occurrence and distribution of freshwater snails of medical and veterinary importance in the area of influence of the Serra da Mesa Hydroelectric a survey has been performed since 1997 and revealed the occurrence of well-established populations of Biomphalaria straminea (Dunker, 1848 in the 8 municipalities surrounding the lake. Areas of epidemiologic risk for schistosomiasis were selected and studies of parasite-mollusc compatibility were undertaken using specimens from 19 populations of B. straminea and 3 strains (CM, EC and PB originally isolated from B. straminea. Among 1,135 specimens used 15 became infected (infection index of 1.3% and 8 populations were susceptible to the schistosome strains: B. straminea from Campinorte (Castelão, susceptible to CM and EC strains, and Planeta Água, EC strain, Colinas (Tocantinzinho river, CM and EC strains, Minaçu (Canabrava river, EC strain, Niquelândia (Codemin, CM and PB strains, and Almas river, CM strain, Uruaçu (touristic area, PB strain and Santa Rita do Novo Destino (Maranhão river, CM and EC strains. These results, associated with marked social and ecological changes occurred, strongly suggest the possibility of B. straminea coming to act as a vector of schistosomiasis in the studied area.

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

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Gruenheit Nicole

2012-03-01

Full Text Available Abstract Background Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for de novo assembly and also reference based assembly protocols that use short reads (35 - 100 bp. Results Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from Pachycladon fastigiatum and Pachycladon cheesemanii. Both are allopolyploid plant species (2n = 20 that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i none of the genes could be assembled across all of the parameter space ii assembly of each gene required an optimal set of parameter values and iii these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes. Conclusions To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.

A pathology atlas of the human cancer transcriptome

DEFF Research Database (Denmark)

Uhlén, Mathias; Zhang, Xi-Cheng; Lee, Sunjae

2017-01-01

Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes o...

Transcriptome profiling of Curcuma longa L. cv. Suvarna

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Ambika Sahoo

2016-12-01

Full Text Available Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10. Resequencing of Suvarna variety has generated 5 Gbases raw data with 75 bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with accession number SRR4042181. Reads were assembled using Cufflinks-2.2.1 tool which ended up with 42994 numbers of transcripts. The length of transcripts ranged from 83 to15565, with a N50 value 1216 and median transcript length 773. The transcripts were annotated through number of databases. For the first time transcriptome profiling of cultivar Suvarna has been done, which could help towards identification of single nucleotide polymorphisms (SNPs between Suvarna and other turmeric cultivars for its authentic identification.

An Atlas of annotations of Hydra vulgaris transcriptome.

Science.gov (United States)

Evangelista, Daniela; Tripathi, Kumar Parijat; Guarracino, Mario Rosario

2016-09-22

RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Starting from a previous work, Transcriptator, we present the Atlas of Hydra's vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra vulgaris exposed to the distinct experimental treatments. WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas .

Analysis of embryonic development in the unsequenced axolotl: waves of transcriptomic upheaval and stability

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Jiang, Peng; Nelson, Jeffrey D.; Leng, Ning; Collins, Michael; Swanson, Scott; Dewey, Colin N.; Thomson, James A.; Stewart, Ron

2016-01-01

The axolotl (Ambystoma mexicanum) has long been the subject of biological research, primarily owing to its outstanding regenerative capabilities. However, the gene expression programs governing its embryonic development are particularly underexplored, especially when compared to other amphibian model species. Therefore, we performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development. As the axolotl genome is unsequenced and its gene annotation is incomplete, we built de novo transcriptome assemblies for each stage and garnered functional annotation by comparing expressed contigs with known genes in other organisms. In evaluating the number of differentially expressed genes over time, we identify three waves of substantial transcriptome upheaval each followed by a period of relative transcriptome stability. The first wave of upheaval is between the one and two cell stage. We show that the number of differentially expressed genes per unit time is higher between the one and two cell stage than it is across the mid-blastula transition (MBT), the period of zygotic genome activation. We use total RNA sequencing to demonstrate that the vast majority of genes with increasing polyA+ signal between the one and two cell stage result from polyadenylation rather than de novo transcription. The first stable phase begins after the two cell stage and continues until the mid-blastula transition, corresponding with the pre-MBT phase of transcriptional quiescence in amphibian development. Following this is a peak of differential gene expression corresponding with the activation of the zygotic genome and a phase of transcriptomic stability from stages 9 to 11. We observe a third wave of transcriptomic change between stages 11 and 14, followed by a final stable period. The last two stable phases have not been documented in amphibians previously and correspond to times of major morphogenic change in the axolotl embryo: gastrulation and

Comparative transcriptomics in the Triticeae

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Waugh Robbie

2009-06-01

Full Text Available Abstract Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring. For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able

Transcriptomic responses to biotic stresses in Malus x domestica: a meta-analysis study

OpenAIRE

Balan, Bipin; Marra, Francesco Paolo; Caruso, Tiziano; Martinelli, Federico

2018-01-01

RNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an...

Major differences between human atopic dermatitis and murine models, as determined by using global transcriptomic profiling

DEFF Research Database (Denmark)

Ewald, David A.; Noda, Shinji; Oliva, Margeaux

2017-01-01

, and a comparison of these models with the human AD transcriptomic fingerprint is lacking. Objective We sought to evaluate the transcriptomic profiles of 6 common murine models and determine how they relate to human AD skin. Methods Transcriptomic profiling was performed by using microarrays and quantitative RT......-PCR on biopsy specimens from NC/Nga, flaky tail, Flg-mutated, ovalbumin-challenged, oxazolone-challenged, and IL-23–injected mice. Gene expression data of patients with AD, psoriasis, and contact dermatitis were obtained from previous patient cohorts. Criteria of a fold change of 2 or greater and a false...... discovery rate of 0.05 or less were used for gene arrays. Results IL-23–injected, NC/Nga, and oxazolone-challenged mice show the largest homology with our human meta-analysis–derived AD transcriptome (37%, 18%, 17%, respectively). Similar to human AD, robust TH1, TH2, and also TH17 activation are seen in IL...

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

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Donald M. Bryant

2017-01-01

Full Text Available Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource for future research in regenerative biology.

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

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Duan Jialei

2012-08-01

Full Text Available Abstract Background Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq. The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments. Results In this study, we used 212.6 million pair-end reads, which accounted for 16.2 Gb, to assemble the hexaploid wheat transcriptome. Two state-of-the-art assemblers, Trinity and Trans-ABySS, which use the single and multiple k-mer methods, respectively, were used, and the whole de novo assembly process was divided into the following four steps: pre-assembly, merging different samples, removal of redundancy and scaffolding. We documented every detail of these steps and how these steps influenced assembly performance to gain insight into transcriptome assembly from short reads. After optimization, the assembled transcripts were comparable to Sanger-derived ESTs in terms of both continuity and accuracy. We also provided considerable new wheat transcript data to the community. Conclusions It is feasible to assemble the hexaploid wheat transcriptome from short reads. Special attention should be paid to dealing with multiple samples to balance the spectrum of expression levels and redundancy. To obtain an accurate overview of RNA profiling, removal of redundancy may be crucial in de novo assembly.

Transcriptome analysis of Pinus halepensis under drought stress and during recovery.

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Fox, Hagar; Doron-Faigenboim, Adi; Kelly, Gilor; Bourstein, Ronny; Attia, Ziv; Zhou, Jing; Moshe, Yosef; Moshelion, Menachem; David-Schwartz, Rakefet

2018-03-01

Forest trees use various strategies to cope with drought stress and these strategies involve complex molecular mechanisms. Pinus halepensis Miller (Aleppo pine) is found throughout the Mediterranean basin and is one of the most drought-tolerant pine species. In order to decipher the molecular mechanisms that P. halepensis uses to withstand drought, we performed large-scale physiological and transcriptome analyses. We selected a mature tree from a semi-arid area with suboptimal growth conditions for clonal propagation through cuttings. We then used a high-throughput experimental system to continuously monitor whole-plant transpiration rates, stomatal conductance and the vapor pressure deficit. The transcriptomes of plants were examined at six physiological stages: pre-stomatal response, partial stomatal closure, minimum transpiration, post-irrigation, partial recovery and full recovery. At each stage, data from plants exposed to the drought treatment were compared with data collected from well-irrigated control plants. A drought-stressed P. halepensis transcriptome was created using paired-end RNA-seq. In total, ~6000 differentially expressed, non-redundant transcripts were identified between drought-treated and control trees. Cluster analysis has revealed stress-induced down-regulation of transcripts related to photosynthesis, reactive oxygen species (ROS)-scavenging through the ascorbic acid (AsA)-glutathione cycle, fatty acid and cell wall biosynthesis, stomatal activity, and the biosynthesis of flavonoids and terpenoids. Up-regulated processes included chlorophyll degradation, ROS-scavenging through AsA-independent thiol-mediated pathways, abscisic acid response and accumulation of heat shock proteins, thaumatin and exordium. Recovery from drought induced strong transcription of retrotransposons, especially the retrovirus-related transposon Tnt1-94. The drought-related transcriptome illustrates this species' dynamic response to drought and recovery and unravels

An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus

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Gross, Joshua B.; Furterer, Allison; Carlson, Brian M.; Stahl, Bethany A.

2013-01-01

Numerous organisms around the globe have successfully adapted to subterranean environments. A powerful system in which to study cave adaptation is the freshwater characin fish, Astyanax mexicanus. Prior studies in this system have established a genetic basis for the evolution of numerous regressive traits, most notably vision and pigmentation reduction. However, identification of the precise genetic alterations that underlie these morphological changes has been delayed by limited genetic and genomic resources. To address this, we performed a transcriptome analysis of cave and surface dwelling Astyanax morphs using Roche/454 pyrosequencing technology. Through this approach, we obtained 576,197 Pachón cavefish-specific reads and 438,978 surface fish-specific reads. Using this dataset, we assembled transcriptomes of cave and surface fish separately, as well as an integrated transcriptome that combined 1,499,568 reads from both morphotypes. The integrated assembly was the most successful approach, yielding 22,596 high quality contiguous sequences comprising a total transcriptome length of 21,363,556 bp. Sequence identities were obtained through exhaustive blast searches, revealing an adult transcriptome represented by highly diverse Gene Ontology (GO) terms. Our dataset facilitated rapid identification of sequence polymorphisms between morphotypes. These data, along with positional information collected from the Danio rerio genome, revealed several syntenic regions between Astyanax and Danio. We demonstrated the utility of this positional information through a QTL analysis of albinism in a surface x Pachón cave F2 pedigree, using 65 polymorphic markers identified from our integrated assembly. We also adapted our dataset for an RNA-seq study, revealing many genes responsible for visual system maintenance in surface fish, whose expression was not detected in adult Pachón cavefish. Conversely, several metabolism-related genes expressed in cavefish were not detected in

Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing

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Tiancheng Liu

2015-01-01

Full Text Available High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO studies. EVO-DEVO studies focus on the evolutionary pressure affecting the morphogenesis of development and previous works have been conducted to illustrate the most conserved stages during embryonic development. Old measurements of these studies are based on the morphological similarity from macro view and new technology enables the micro detection of similarity in molecular mechanism. Evolutionary model of embryo development, which includes the “funnel-like” model and the “hourglass” model, has been evaluated by combination of these new comparative transcriptomic methods with prior comparative genomic information. Although the technology has promoted the EVO-DEVO studies into a new era, technological and material limitation still exist and further investigations require more subtle study design and procedure.

De novo Transcriptome Assemblies of Rana (Lithobates catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes.

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Inanc Birol

Full Text Available In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates catesbeiana and the African clawed frog (Xenopus laevis. We used high throughput RNA sequencing (RNA-seq data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences.

Comparative Analysis of the Arabidopsis Pollen Transcriptome

Czech Academy of Sciences Publication Activity Database

Honys, David; Twell, D.

2003-01-01

Roč. 132, - (2003), s. 640ů652 ISSN 0032-0889 R&D Projects: GA AV ČR IAA5038207 Grant - others:Royal Society(GB) NATO Postdoctoral Fellowship (to D.H.) Institutional research plan: CEZ:AV0Z5038910; CEZ:MSM 113100003 Keywords : transcriptome profiling * Arabidopsis pollen * male gametophyte Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.634, year: 2003

Defining the maize transcriptome de novo using deep RNA-Seq

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

2011-06-01

De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

Defining the maize transcriptome de novo using deep RNA-Seq

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

2011-06-02

De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L. using sanger and next generation sequencing platforms: development and applications.

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Himabindu Kudapa

Full Text Available A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201, comprising 46,369 transcript assembly contigs (TACs has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8% of the TACs and gene ontology assignments were determined for 21,471 (46.3%. The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs and intron spanning regions (ISRs for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding

Acute schistosomiasis diagnosis: a new tool for the diagnosis of schistosomiasis in a group of travelers recently infected in a new focus of Schistosoma mansoni

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Rafaella Fortini Queiroz Grenfell

2013-04-01

Full Text Available Introduction The diagnosis of schistosomiasis mansoni on early stages of infection is important to prevent late morbidity. A simple, cheap, sensitive and specific assay for routine diagnosis of schistosome infection based on the detection of specific IgG for schistosomula tegument antigens (ELISA-SmTeg was developed by our group. Methods We describe here an acute outbreak involving a travel group of 80 individuals from a non-endemic area of the State of Minas Gerais, Brazil. These individuals were in contact with a freshwater pool where Biomphalaria glabrata was found. Results obtained from our new methodology were compared to IgG antibody titers against soluble worm antigenic preparation (SWAP by ELISA and, also to parasitological examination, nuclear magnetic resonance and clinical findings. Results ELISA-SmTeg was capable of detecting 64 positive cases among the 80 individuals participating at the survey with a positivity ratio of 80% and a higher sensitivity than ELISA-SWAP that was only sensitive for 56% of positive cases. Besides, a significant correlation was found for the severity of the infection and the specific IgG titers against SmTeg. Conclusions Our data showed that ELISA-SmTeg might serve as the initial diagnostic tool for acute stages of the infection in community-based helminth control programs or for the surveillance of individuals from non-endemic areas.

New insights into parental effects and toxicity: Mate availability and diet in the parental environment affect offspring responses to contaminants

International Nuclear Information System (INIS)

Plautz, Stephanie C.; Funkhouser, Meghan A.; Salice, Christopher J.

2013-01-01

Parental effects manifest as alterations in offspring phenotype resulting from the parental phenotype and/or parental environment. We evaluated the effects of parental diet quality and mating strategy on the toxicant tolerance of offspring in Biomphalaria glabrata snails. We raised snails either individually (self-fertilizing) or in groups of three (outcrossing) on a diet of uncooked lettuce, fish food, cooked lettuce, or cooked lettuce plus fish food. We then exposed their offspring to cadmium and malathion challenges. Cadmium tolerance varied with parental diet and was greater in the offspring of outcrossing snails than self-fertilizing snails. Malathion tolerance was not affected by parental diet but was greater in the offspring of outcrossing snails. These results indicate that offspring responses to stressors are heavily influenced by parental experience, but may depend on the specific stressor and the mechanism of action and/or detoxification. -- Highlights: •We reared parental snails either alone or in groups and fed them one of four diets. •We exposed their juvenile offspring to cadmium and malathion survival challenges. •Outcrossing increased toxicant tolerance of juveniles compared to self-fertilizing. •Parental diet affected juvenile offspring tolerance to cadmium but not malathion. •Toxicant characteristics likely influenced parental effects on toxicant tolerance. -- Both parental diet composition and mating strategy can significantly alter the toxicant tolerance of offspring, and toxicant characteristics likely influence the probability of parental effects

Proteolytic activity in the adult and larval stages of the human roundworm parasite Angiostrongylus costaricensis

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Karina Mastropasqua Rebello

2012-09-01

Full Text Available Angiostrongylus costaricensis is a nematode that causes abdominal angiostrongyliasis, a widespread human parasitism in Latin America. This study aimed to characterize the protease profiles of different developmental stages of this helminth. First-stage larvae (L1 were obtained from the faeces of infected Sigmodon hispidus rodents and third-stage larvae (L3 were collected from mollusks Biomphalaria glabrata previously infected with L1. Adult worms were recovered from rodent mesenteric arteries. Protein extraction was performed after repeated freeze-thaw cycles followed by maceration of the nematodes in 40 mM Tris base. Proteolysis of gelatin was observed by zymography and found only in the larval stages. In L3, the gelatinolytic activity was effectively inhibited by orthophenanthroline, indicating the involvement of metalloproteases. The mechanistic class of the gelatinases from L1 could not be precisely determined using traditional class-specific inhibitors. Adult worm extracts were able to hydrolyze haemoglobin in solution, although no activity was observed by zymography. This haemoglobinolytic activity was ascribed to aspartic proteases following its effective inhibition by pepstatin, which also inhibited the haemoglobinolytic activity of L1 and L3 extracts. The characterization of protease expression throughout the A. costaricensis life cycle may reveal key factors influencing the process of parasitic infection and thus foster our understanding of the disease pathogenesis.

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: Assembly of the duck (Anas platyrhynchos transcriptome.

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Joanna eMoreton

2014-06-01

Full Text Available For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1 assessing the performance of three different assembly tools (2 using both single and multiple k-mer approaches (3 examining the influence of the number of reads used in the assembly (4 merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck. We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT and CEGMA (Core Eukaryotic Genes Mapping Approach provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of multiple k-mers in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi.org/10.6084/m9.figshare.1032613.

Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica.

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Qiu, Zhongying; Liu, Fei; Lu, Huimeng; Huang, Yuan

2017-05-01

The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a de novo transcriptome study of adult and larval T. japonica to provide a better understanding of its gene expression and develop genomic resources for future work. We sequenced and explored the characteristics of the de novo transcriptome of T. japonica using Illumina HiSeq 2000 platform. A total of 107 608 206 paired-end clean reads were assembled into 61 141 unigenes using the trinity software; the mean unigene size was 771 bp, and the N50 length was 1238 bp. A total of 29 225 unigenes were functionally annotated to the NCBI nonredundant protein sequences (Nr), NCBI nonredundant nucleotide sequences (Nt), a manually annotated and reviewed protein sequence database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of putative genes that are potentially involved in pigment pathways, juvenile hormone (JH) metabolism and signalling pathways were identified in the T. japonica transcriptome. Additionally, 165 769 and 156 796 putative single nucleotide polymorphisms occurred in the adult and larvae transcriptomes, respectively, and a total of 3162 simple sequence repeats were detected in this assembly. This comprehensive transcriptomic data for T. japonica will provide a usable resource for gene predictions, signalling pathway investigations and molecular marker development for this species and other pygmy grasshoppers. © 2016 John Wiley & Sons Ltd.

Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum.

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Gao, Bei; Li, Xiaoshuang; Zhang, Daoyuan; Liang, Yuqing; Yang, Honglan; Chen, Moxian; Zhang, Yuanming; Zhang, Jianhua; Wood, Andrew J

2017-08-08

The desiccation tolerant bryophyte Bryum argenteum is an important component of desert biological soil crusts (BSCs) and is emerging as a model system for studying vegetative desiccation tolerance. Here we present and analyze the hydration-dehydration-rehydration transcriptomes in B. argenteum to establish a desiccation-tolerance transcriptomic atlas. B. argenteum gametophores representing five different hydration stages (hydrated (H0), dehydrated for 2 h (D2), 24 h (D24), then rehydrated for 2 h (R2) and 48 h (R48)), were sampled for transcriptome analyses. Illumina high throughput RNA-Seq technology was employed and generated more than 488.46 million reads. An in-house de novo transcriptome assembly optimization pipeline based on Trinity assembler was developed to obtain a reference Hydration-Dehydration-Rehydration (H-D-R) transcriptome comprising of 76,206 transcripts, with an N50 of 2,016 bp and average length of 1,222 bp. Comprehensive transcription factor (TF) annotation discovered 978 TFs in 62 families, among which 404 TFs within 40 families were differentially expressed upon dehydration-rehydration. Pfam term enrichment analysis revealed 172 protein families/domains were significantly associated with the H-D-R cycle and confirmed early rehydration (i.e. the R2 stage) as exhibiting the maximum stress-induced changes in gene expression.

Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa

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Dalia Ponce

2016-04-01

Full Text Available Jellyfish venoms are rich sources of toxins designed to capture prey or deter predators, but they can also elicit harmful effects in humans. In this study, an integrated transcriptomic and proteomic approach was used to identify putative toxins and their potential role in the venom of the scyphozoan jellyfish Chrysaora fuscescens. A de novo tentacle transcriptome, containing more than 23,000 contigs, was constructed and used in proteomic analysis of C. fuscescens venom to identify potential toxins. From a total of 163 proteins identified in the venom proteome, 27 were classified as putative toxins and grouped into six protein families: proteinases, venom allergens, C-type lectins, pore-forming toxins, glycoside hydrolases and enzyme inhibitors. Other putative toxins identified in the transcriptome, but not the proteome, included additional proteinases as well as lipases and deoxyribonucleases. Sequence analysis also revealed the presence of ShKT domains in two putative venom proteins from the proteome and an additional 15 from the transcriptome, suggesting potential ion channel blockade or modulatory activities. Comparison of these potential toxins to those from other cnidarians provided insight into their possible roles in C. fuscescens venom and an overview of the diversity of potential toxin families in cnidarian venoms.

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.

Science.gov (United States)

Gross, Stephen M; Martin, Jeffrey A; Simpson, June; Abraham-Juarez, María Jazmín; Wang, Zhong; Visel, Axel

2013-08-19

Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis. Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.

Analysis of the transcriptome of Isodon rubescens and key enzymes involved in terpenoid biosynthesis

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Xiuhong Su

2016-05-01

Full Text Available Isodon rubescens is an important medicinal plant in China that has been shown to reduce tumour growth due to the presence of the compound oridonin. In an effort to facilitate molecular research on oridonin biosynthesis, we reported the use of next generation massively parallel sequencing technologies and de novo transcriptome assembly to gain a comprehensive overview of I. rubescens transcriptome. In our study, a total of 50,934,276 clean reads, 101,640 transcripts and 44,626 unigenes were generated through de novo transcriptome assembly. A number of unigenes – 23,987, 10,263, 7359, 18,245, 17,683, 19,485, 9361 – were annotated in the National Center for Biotechnology Information (NCBI non-redundant protein (Nr, NCBI nucleotide sequences (Nt, Kyoto Encyclopedia of Genes and Genomes (KEGG Orthology (KO, Swiss-Prot, protein family (Pfam, gene ontology (GO, eukaryotic ortholog groups (KOG databases, respectively. Furthermore, the annotated unigenes were functionally classified according to the GO, KOG and KEGG. Based on these results, candidate genes encoding enzymes involved in terpenoids backbone biosynthesis were detected. Our data provided the most comprehensive sequence resource available for the study on I. rubescens, as well as demonstrated the effective use of Illumina sequencing and de novo transcriptome assembly on a species lacking genomic information.

Transcriptome changes favoring intramuscular fat deposition in the longissimus muscle following castration of bulls.

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Jeong, J; Bong, J; Kim, G D; Joo, S T; Lee, H-J; Baik, M

2013-10-01

Castration increases intramuscular fat (IMF) deposition, improving beef quality in cattle. The present study was performed to determine the global transcriptome changes following castration of bulls and to identify genes associated with IMF deposition in the longissimus dorsi (LM) of Korean cattle. A customized bovine CombiMatrix oligonucleotide microarray was constructed, and transcriptome changes following castration were determined by microarray hybridization. Transcriptome comparison between bulls and steers indicated that 428 of 8,407 genes were differentially expressed in the LM by greater than two fold (P castration. Castration upregulated transcription of adipogenic perilipin 2 (PLIN2) and visfatin, lipogenic fatty acid synthase, fatty acid esterification 1-acylglycerol-3-phosphate O-acyltransferase 5, and many fatty acid oxidation-related genes. Many TCA cycle and OP genes were also transcriptionally upregulated. Correlation analysis indicated that the IMF content in the LM was highly correlated with mRNA levels of PLIN2 (r = 0.70, P castration shifts transcription of lipid metabolism genes, favoring IMF deposition by increasing adipogenesis, lipogenesis, and triglyceride synthesis. This study also indicated that castration increases transcription of genes involved in fatty acid oxidation and subsequent energy production (TCA and OP genes). Our microarray analysis provided novel information that castration alters the transcriptome associated with lipid/energy metabolism, favoring IMF deposition in the LM.

Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa)

Science.gov (United States)

Ponce, Dalia; Brinkman, Diane L.; Potriquet, Jeremy; Mulvenna, Jason

2016-01-01

Jellyfish venoms are rich sources of toxins designed to capture prey or deter predators, but they can also elicit harmful effects in humans. In this study, an integrated transcriptomic and proteomic approach was used to identify putative toxins and their potential role in the venom of the scyphozoan jellyfish Chrysaora fuscescens. A de novo tentacle transcriptome, containing more than 23,000 contigs, was constructed and used in proteomic analysis of C. fuscescens venom to identify potential toxins. From a total of 163 proteins identified in the venom proteome, 27 were classified as putative toxins and grouped into six protein families: proteinases, venom allergens, C-type lectins, pore-forming toxins, glycoside hydrolases and enzyme inhibitors. Other putative toxins identified in the transcriptome, but not the proteome, included additional proteinases as well as lipases and deoxyribonucleases. Sequence analysis also revealed the presence of ShKT domains in two putative venom proteins from the proteome and an additional 15 from the transcriptome, suggesting potential ion channel blockade or modulatory activities. Comparison of these potential toxins to those from other cnidarians provided insight into their possible roles in C. fuscescens venom and an overview of the diversity of potential toxin families in cnidarian venoms. PMID:27058558

Analysis of a human brain transcriptome map

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Greene Jonathan R

2002-04-01

Full Text Available Abstract Background Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome. Expressed Sequence Tags (ESTs from the public dbEST and proprietary Incyte LifeSeq databases were used to derive a transcript map in conjunction with the working draft assembly of the human genome sequence. Results Examination of ESTs derived from brain tissues (excluding brain tumor tissues suggests that these genes are distributed on chromosomes in a non-random fashion. Some regions on the genome are dense with brain-enriched genes while some regions lack brain-enriched genes, suggesting a significant correlation between distribution of genes along the chromosome and tissue type. ESTs from brain tumor tissues have also been mapped to the human genome working draft. We reveal that some regions enriched in brain genes show a significant decrease in gene expression in brain tumors, and, conversely that some regions lacking in brain genes show an increased level of gene expression in brain tumors. Conclusions This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.