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Sample records for biomphalaria glabrata transcriptome

  1. Deep, multi-stage transcriptome of the schistosomiasis vector Biomphalaria glabrata provides platform for understanding molluscan disease-related pathways

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    Nathan J Kenny

    2016-10-01

    Full Text Available Abstract Background The gastropod mollusc Biomphalaria glabrata is well known as a vector for the tropical disease schistosomiasis, which affects nearly 200 million people worldwide. Despite intensive study, our understanding of the genetic basis of B. glabrata development, growth and disease resistance is constrained by limited genetic resources, constraints for which next-generation sequencing methods provide a ready solution. Methods Illumina sequencing and de novo assembly using the Trinity program was used to generate a high-quality transcriptomic dataset spanning the entirety of in ovo development in schistosomiasis-free B. glabrata. This was subjected to automated (KEGG, BLAST2GO and manual annotation efforts, allowing insight into the gene complements of this species in a number of contexts. Results Excellent dataset recovery was observed, with 133,084 contigs produced of mean size 2219.48 bp. 80,952 (60.8 % returned a BLASTx hit with an E value of less than 10-3, and 74,492 (55.97 % were either mapped or assigned a GO identity using the BLAST2GO program. The CEGMA set of core eukaryotic genes was found to be 99.6 % present, indicating exceptional transcriptome completeness. We were able to identify a wealth of disease-pathway related genes within our dataset, including the Wnt, apoptosis and Notch pathways. This provides an invaluable reference point for further work into molluscan development and evolution, for studying the impact of schistosomiasis in this species, and perhaps providing targets for the treatment of this widespread disease. Conclusions Here we present a deep transcriptome of an embryonic sample of schistosomiasis-free B. glabrata, presenting a comprehensive dataset for comparison to disease-affected specimens and from which conclusions can be drawn about the genetics of this widespread medical model. Furthermore, the dataset provided by this sequencing provides a useful reference point for comparison to other mollusc

  2. Development of Schistosoma mansoni in Biomphalaria tenagophila, Biomphalaria straminea and Biomphalaria glabrata Desenvolvimento do Schistosoma mansoni em Biomphalaria tenagophila, Biomphalaria straminea e Biomphalaria glabrata

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    Cecilia Pereira de Souza

    1995-06-01

    Full Text Available A comparative study of the development of Schistosoma mansoni during the intra-molluscan phase was made by means of histological sections of Biomphalaria tenagophila, B. straminea and B. glabrata from Brazil. Two hundred snails of each species were individually exposed to 50 miracidia of the S. mansoni, AL line. No larvae were observed in the snails fixed 72 h after exposure. In specimens shedding cercariae, 31 days after exposure tissue reactions encapsulating the larvae were seen in B. tenagophila and B. straminea, in the head-foot, mantle collar and renal ducts. No tissue reactions occurred in the digestive glands of these two species. In B. glabrata the presence of numerous sporocysts and cercariae without tissue reactions was observed in the digestive gland, and other organs. The levels of infection of the snails and the average numbers of cercariae shed per day were 32.6% and 79±90 respectively for B. tenagophila, 11.3% and 112±100 for B. straminea and 75.3% and 432±436 for B. glabrata. The lower levels of infection and average numbers of cercariae shed by B. tenagophila and B. straminea are thus related to their more potent internal defense systems.Foi feito estudo comparativo do desenvolvimento do Schistosoma mansoni na fase intra-molusco, através de cortes histológicos, em Biomphalaria tenagophila, B. straminea e B. glabrata. Duzentos moluscos de cada espécie foram expostos individualmente a 50 miracídios de S. mansoni da linhagem AL. Nenhuma larva foi observada nos exemplares fixados 72 horas após a exposição. Nos exemplares eliminando cercárías, 31 dias após a exposição, foram observadas reações teciduais de encapsulamento de larvas em B. tenagophila e B. straminea, na região cefalopodal, colar do manto e dutos renais. Nas glândulas digestivas das duas espécies não foram observadas reações. Em B. glabrata foi registrada a presença de numerosos esporocistos e cercárias sem reação tecidual na gl

  3. Ultrastructural studies of Biomphalaria glabrata (Say, 1818) embryo

    International Nuclear Information System (INIS)

    Kikuchi, O.K.; Okazaki, K.; Kawano, T.; Ribeiro, A.A.G.F.C.

    1988-09-01

    Ultrastructural studies of Biomphalaria glabrata embryos (MOllusca: Gastropoda), and important snail vector of schistosomiasis has not been explored. In the present work it was evaluated a suitable electron microscopical technique for embryos processing. Promising results was obtained with double fixation in 1% glutaraldehyde plus 1% osmium tetroxide in 0.05 M cacodylate buffer (pH 7.4), preliminary staining overnight in 1% uranyl acetate and embedding in EPON or Polylite under vacuum. It was used embryos at young trochophore stage wich is characterized by active organogenesis. Some ultrastructural aspects of B. glabrata embryos cells are presented. (author) [pt

  4. Gastrointestinal transit and digestive rhythm in Biomphalaria glabrata (Say)

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    Florschutz, A.; Becker, W.

    1999-01-01

    Transit of X-ray opaque Micropaque™ particles in the digestive tract of Biomphalaria glabrata was investigated by X-radiography. Passage through the whole animal lasted up to 200 min depending on the experimental conditions (starvation, fed ad libitum etc.). For the first time, cyclic activity of the digestive gland could be visualised: the gland is emptied every 60-110 min discharging undigested particles. In the afternoon transport of probably predigested material from more distally located parts of the digestive tract into the esophagus can be observed indicating resorption processes occurring in the esophagus

  5. Weight loss and survival of Biomphalaria Glabrata deprived of water

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    Marc Vianey-Liaud

    1986-06-01

    Full Text Available Immature and mature Biomphalaria glabrata are kept out of water at relative humidities varying from 0 to 100%. When snails are submitted to a saturated atmosphere, they show a slow weight loss and survival may be long. If relative humidity (RH decreases, weight loss becomes important and survival is short. A reduced RH (0 to 65% produces similar effects. During desiccation, fasting has no noticeable effect; survival depends essentially on weight loss.Biomphalaria glabrata maduros ou imaturos são mantidos fora da água, variando a umidade de 0 a 100%. Quando caramujos são submetidos a uma atmosfera saturada, sofrem uma lenta perda de peso e a sobrevivência pode ser longa. Se a umidade relativa decresce, a perda de peso será importante e a sobrevida será abreviada. Uma umidade relativa de 0 a 65% pode produzir efeitos similares. Durante a dessecação, a privação de alimento não tem efeito notável, a sobrevivência dependendo essencialmente da perda de peso.

  6. 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)

  7. 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)

  8. On the origin of the Biomphalaria glabrata hemocytes

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    Samaly dos Santos Souza

    2006-10-01

    Full Text Available A histologic, morphometric and ultrastructural study performed on Biomphalaria glabrata submitted to infection with Schistosoma mansoni miracidia failed to provide significant evidences that the so-called amebocyte-producing organ (APO is really the central organ for hemocyte production. In infected snails no general reactive changes appeared in the APO, the mitoses were seen only occasionally, and the possibility of cellular hyperplasia was ruled out by morphometric measurements. Under the electron microscope the APO cells presented an essentially epithelial structure, without features indicative of transition toward hemocytes. On the other hand, the present findings pointed to a multicentric origin for the mollusck hemocytes, as earlier studies had indicated. Dense foci of hemocyte collections appeared sometimes around disintegrating sporocysts and cercariae in several organs and tissues of the infected snails, including a curious accumulation of such cells inside the ventricular cavity of the heart. In the heart and other sites, features suggestive of transformation of vascular space endothelial lining cells into hemocytes were apparent. To some extent, the postulated multicentric origin for B. glabrata hemocytes recapitulates earlier embryologic findings in vertebrates, when mesenchymal vascular spaces generate the circulating and phagocytic blood cells.

  9. Contribution to the histology of Biomphalaria glabrata Contribuição à histologia da Biomphalaria glabrata

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    Queli Teixeira Lemos

    1999-08-01

    Full Text Available A combination of histological techniques applied to the study of Biomphalaria glabrata yielded some interesting new data about the histology of this snail, a major intermediate host of Schistosoma mansoni in Brazil. Three kinds of pigments were identified: a dark pigment which bleached following oxidation with potassium permanganate; a lipofuchsin-like, diastase-resistant PAS-positive pigment and an iron-containing pigment, probably related to hemosiderin. Calcium was detected in small deposits within the connective tissue and forming a dense core inside the chitinous radular teeth. The presence of fibrils, staining with sirius-red and birefringence under polarized light strongly suggest primitive collagen tissue. The radular apparatus appeared as a storing site for glycogen, while abundant Alcian-blue positive material (proteoglycans was extremely concentrated in the radular sac.Uma combinação de várias técnicas histológicas permitiu alguns achados de interesse para a histologia da Biomphalaria glabrata, principal hospedeiro intermediário do Schistosoma mansoni no Brasil. Três tipos de pigmentos foram identificados: um pigmento escuro, que se descora após oxidação pelo permanganato de potássio; outro que é semelhante à lipofuscina, que se cora pelo PAS e é diastase- resistente, e um pigmento que contém ferro, provalvelmente, relacionado com a hemossiderina. O cálcio foi identificado em pequenos depósitos no interior do tecido conjuntivo e formando pequenos núcleos no interior dos dentes quitinosos da rádula. A presença de fibrilas coradas pelo sírius-vermelho, exibindo birrefrigência sob luz polarizada, sugere fortemente a presença de um tecido colágeno primitivo. O aparelho radular foi visto como um local de armazenamento do glicogênio, enquanto a presença de abundante material amorfo positivo para o azul de alciano (proteoglicano apareceu em grande concentração no saco radular.

  10. 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)

  11. Influence of the nontarget mollusc Marisa cornuarietis on the hourly cercarial production of Schistosoma mansoni from Biomphalaria glabrata.

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    Ferrer, J R; Pointier, J P; Théron, A; Moné, H

    1991-10-01

    A comparative study of hourly cercarial productivities of Schistosoma mansoni from infected Biomphalaria glabrata was carried out in the presence of either healthy B. glabrata (control) or healthy Marisa cornuarietis (experimental). The results showed that, with M. cornuarietis, almost all the hourly cercarial productivities increased by a factor varying from 1.3 to 2.5 without modification of the shedding period.

  12. Effects of CO-60 gamma radiation on the embryonary development of Biomphalaria Glabrata (Say, 1818)

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    Okazaki, K.

    1988-01-01

    Some aspects of the effects of the ionizing radiation on the embryo and on the genetical material of Biomphalaria glabrata (Mollusca: Gastropoda) are presented. The embryos weresubmitted at various stages of development to doses of 5,10,15,20 and 25 Gy of Co-60 gamma radiation. As a criteia of evaluation of the embryos radiosensitivity, four biological parameters were used: mortality, malformation, hatching and chromossomal aberrations. (M.A.C.) [pt

  13. Human schistosomiasis in Puerto Rico: reduced prevalence rate and absence of Biomphalaria glabrata.

    Science.gov (United States)

    Giboda, M; Malek, E A; Correa, R

    1997-11-01

    A combined epidemiologic and malacologic survey of schistosomiasis in Puerto Rico was carried out in areas where previous surveys had reported the prevalence of the disease. This limited survey, with 495 persons examined, found a low prevalence (0.6%) of Schistosoma mansoni infections. The infections were restricted to three people more than 36 years of age. No infections were detected in children 16 years of age or less, and this cohort comprised 57.8% of the study group. Malacologic surveys of the four streams, 10 rivers, and eight lakes throughout the island revealed the absence of intermediate host Biomphalaria glabrata and the presence of Thiara granifera, a competitive species of B. glabrata and the predatory snail Marisa cornuarietis. We believe that the absence of B. glabrata is the primary reason for the sustained reduction in the prevalence of schistosomiasis in Puerto Rico.

  14. Use of Biomphalaria glabrata hemocytes as a biomarker of exposure to ionizing radiation

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    Silva, Hianna A.M.F.; Lima, Maira V.; Sa, Jose L.F.; Siqueira, Williams N.; Luna Filho, Ricardo L.C.; Melo, Larissa S.A.; Morais, Vinicius H.T.; Melo, Ana M.M.A., E-mail: hiannaamfs@gmail.com, E-mail: mairavasconceloslima@gmail.com, E-mail: luismuma6@gmail.com, E-mail: williams.wns@gmail.com, E-mail: ricardolclf@hotmail.com, E-mail: larissamelo.pe@gmail.com, E-mail: viniciushtmorais@hotmail.com, E-mail: amdemelo@hotmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Biofisica e Radiobiologia

    2017-11-01

    The increase of the applications of ionizing radiation in several areas and sectors of modern society has given rise to a greater probability of occurrence of accidents. These accidental occurrences have revealed the need for methods that provide quantitative data on the radiation doses absorbed by biological systems. The mollusk Biomphalaria glabrata presents as a good bioindicator in several works referenced in the literature. In this way, the objective of this work was to evaluate the morphological and quantitative alterations of hemocytes of the Biomphalaria glabrata exposed to ionizing radiation. For the experiments, adult mollusks of the species B. glabrata pigmented were used. The selected mollusks were divided into six groups: five submitted to doses of 10, 20, 30, 40, 50 Gy of {sup 60}Co gamma radiation and the control group. After 48 h, the slides were prepared and then read in a microscope. Quantitative analysis showed a decrease in the total number of hemocytes after irradiation. In the cell classification, a higher number of hyalinocytes were observed in relation to the number of granulocytes, except for the animals exposed to a dose of 30 Gy. The presence of micronuclei and binucleations were observed at all doses used. Apoptosis was observed at doses starting at 30 Gy. Therefore, it is possible to conclude that the morphological and quantitative analysis of B. glabrata hemocytes provided significant data for the identification of biological damage caused by ionizing radiation, allowing the beginning of standardization of the morphological alteration counting technique in B. glabrata hemocytes as An environmental biomarker for the action of physical agents. (author)

  15. Use of Biomphalaria glabrata hemocytes as a biomarker of exposure to ionizing radiation

    International Nuclear Information System (INIS)

    Silva, Hianna A.M.F.; Lima, Maira V.; Sa, Jose L.F.; Siqueira, Williams N.; Luna Filho, Ricardo L.C.; Melo, Larissa S.A.; Morais, Vinicius H.T.; Melo, Ana M.M.A.

    2017-01-01

    The increase of the applications of ionizing radiation in several areas and sectors of modern society has given rise to a greater probability of occurrence of accidents. These accidental occurrences have revealed the need for methods that provide quantitative data on the radiation doses absorbed by biological systems. The mollusk Biomphalaria glabrata presents as a good bioindicator in several works referenced in the literature. In this way, the objective of this work was to evaluate the morphological and quantitative alterations of hemocytes of the Biomphalaria glabrata exposed to ionizing radiation. For the experiments, adult mollusks of the species B. glabrata pigmented were used. The selected mollusks were divided into six groups: five submitted to doses of 10, 20, 30, 40, 50 Gy of "6"0Co gamma radiation and the control group. After 48 h, the slides were prepared and then read in a microscope. Quantitative analysis showed a decrease in the total number of hemocytes after irradiation. In the cell classification, a higher number of hyalinocytes were observed in relation to the number of granulocytes, except for the animals exposed to a dose of 30 Gy. The presence of micronuclei and binucleations were observed at all doses used. Apoptosis was observed at doses starting at 30 Gy. Therefore, it is possible to conclude that the morphological and quantitative analysis of B. glabrata hemocytes provided significant data for the identification of biological damage caused by ionizing radiation, allowing the beginning of standardization of the morphological alteration counting technique in B. glabrata hemocytes as An environmental biomarker for the action of physical agents. (author)

  16. Duration of pairing and use of allosperm in Biomphalaria glabrata (Gastropoda: Planorbidae Duração do acasalamento e uso do aloesperma em Biomphalaria glabrata (Gastropode: Planorbidae

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    Marc Vianey-Liaud

    1989-03-01

    Full Text Available Virgin homozygous black pigmented and albino Biomphalaria glabrata are paired during a period varying from 1 to 20 days. The rate of cross-fertilized parents is statistically similar for the various lengths of pairing. As a whole, nearly 80% of the albino snails produce a pigmented progeny. This production begins as soon as the snails are mated and continues after their separation. To measure the actual use of the allosperm, its use during the postmating period must be added to the length of mating. So, it appears that the real use of the allosperm is statistically constant (mean slightly inferior to 8 weeks and not related to the length of the previous pairing.Espécimes virgens de Biomphalaria glabrata (um melâncio e um albino são acasalados durante um período variável de 1 a 20 dias. A proporção de espécimes parentais albinos fecundados por cruzamento é semelhante estatisticamente para os diversos períodos de acasalamento. Em conjunto, cerca de 80% dos albinos produziram descendência pigmentada. Essa produção começa assim que os moluscos são acasalados e continua depois que são separados. Para medir a utilização real do aloesperma, sua utilização durante o período de pós-acasalamento. Parece, assim, que a utilização real do aloesperma é estatisticamente constante (média ligeiramente inferior a oito semanas e não relacionada a duração do acasalamento anterior.

  17. 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

  18. 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)

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

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    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)

  20. Evaluation of radiosensitivity hemocytes of Biomphalaria glabrata exposed to gamma radiation

    International Nuclear Information System (INIS)

    Silva, L.R.S.; Amaral, A.J.; Silva, E.B.; Amancio, F.F.; Melo, A.M.M.A.

    2013-01-01

    The mollusc Biomphalaria glabrata have characteristics that allow them to be identified as an animal model ideal for monitoring areas exposed to chemical agents and physical. This study evaluated the effect of ionizing radiation from Cobalt-60 in haemocytes present in the hemolymph of Biomphalaria glabrata, with the goal of using these cells as indicators of the presence of radiation in aquatic environments. The mollusks were divided into five groups: one control and four subjected doses of 25, 35, 45 and 55 Gy of gamma radiation. After 48 hours of irradiation, the clam hemolymph was collected and slides were prepared and stained with Giemsa for analyses under a light microscope. Statistical analysis was performed using ANOVA and Tukey's test, p <0.05. The results showed that the total number of cells after irradiation reduced compared to control except at a dose of 55 Gy. During data analysis, morphological changes were observed in haemocytes of mollusks subjected to doses of 35, 45 and 55 Gy. These modifications consisted of nucleus bilobulated and nucleo plasmatic bridges. Another change was exclusively observed in the cellular exposure of 55 Gy, where hemocytes showed misshapen nuclei and cytoplasm vacuolisation, suggestive of apoptosis. It is concluded that hemocytes are sensitive to radiation and can be used as indicators of the presence of high doses of ionizing radiation in aquatic environments. (author)

  1. Behavior of Schistosoma mansoni-induced histopathological lesions in Biomphalaria glabrata submitted to ionizing radiation

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    Azevedo Carine M.

    2004-01-01

    Full Text Available Present report demonstrates that repeated radiation of Schistosoma mansoni-infected Biomphalaria glabrata, totaling 15,000 rads, caused a sudden, albeit transient, suppression of cercarial shedding. Initially, sporocysts practically disappeared from the snail tissues. The more resistant developing cercariae presented nuclear clumping and vacuolation, before undergoing lysis. No host tissue reaction was evident at any time. Thirty-four days after the last irradiation, the snails resumed cercarial elimination. By that time numerous sporocysts and developing cercariae were detected, disseminated throughout snail tissues in a pattern similar to that of a highly malignant neoplasm, with no signs of host cellular reactions, which on the other hand were present in non-irradiated infected controls. The region of the ovo-testis was apparently destroyed after radiation, but returned to its normal appearance around 40 days after the last radiation. Ionizing radiation affected both host and parasite in S. mansoni-infected Biomphalaria glabrata, but the resulting impressive changes were soon reversed.

  2. 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

  3. Nonhemocyte sources of selected lysosomal enzymes in Biomphalaria glabrata, B. tenagophila and B. straminea (Mollusca: Pulmonata

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    Gary E. Rodrick

    1981-09-01

    Full Text Available The specific activities of acid phosphatase, alkaline phosphatase, β-glucuronidase, lysozymes, glutamate-oxalacetate transaminase and glutamate-pyruvate transaminate were determined in the head-foot and digestive gland of Brazilian Biomphalaria glabrata (Touros, B. tenagophila (Caçapava and B. straminea (Monsenhor Gil. All six enzymes were detected inthe 3000g supernatant. Both cytoplasmic enzymes, glutamate-oxalacetate and glutamate-pyruvate transaminase exhibited the highest specific activities. In the case of the four hydrolytic enzymes assayed, β-glucuronidase exhibited the highest specific activity while lysozyme showed the lowest activity. All six enzymes are thought to be produced by cells within the head-foot and digestive gland of B. glabrata, B. tenagophila and B. straminea.Foram determinadas, na massa cefalopedal e na glândula digestiva de Biomphalaria glabrata de Touros (Rio Grande do Norte B. tenagophila de Cacapava (Sao Paulo e B. straminea de Monsenhor Gil (Piauí, as atividades específicas das seguintes enzimas: fosfatase acida, fosfatase alcalina, beta-glucuronidase, lisozima, transaminase glutâmico-oxalacetica e transaminase glutâmico-piruvica. As seis enzimas referidas foram detectadas no sobrenadante a 3000g. Ambas as enzimas citoplasmaticas - transaminases glutamico-oxalacetica e glutamico-piruvica - mostraram as atividades específicas mais altas. No caso das quatro enzimas hidrolíticas, a beta-glucuronidase revelou a mais alta atividade específica, enquanto a lisozima revelou a mais baixa. E admitido que todas as seis enzimas sao produzidas por celulas presentes na massa cefalopedal e na glândula digestiva das tres especies de moluscos examinadas.

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

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    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.

  5. 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

  6. 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

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

    International Nuclear Information System (INIS)

    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

  8. Ionotropic Receptors Identified within the Tentacle of the Freshwater Snail Biomphalaria glabrata, an Intermediate Host of Schistosoma mansoni.

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    Di Liang

    Full Text Available Biomphalaria glabrata (B. glabrata is an air-breathing aquatic mollusc found in freshwater habitats across the Western Hemisphere. It is most well-known for its recognized capacity to act as a major intermediate host for Schistosoma mansoni, the human blood fluke parasite. Ionotropic receptors (IRs, a variant family of the ionotropic glutamate receptors (iGluR, have an evolutionary ancient function in detecting odors to initiate chemosensory signaling. In this study, we applied an array of methods towards the goal of identifying IR-like family members in B. glabrata, ultimately revealing two types, the iGluR and IR. Sequence alignment showed that three ligand-binding residues are conserved in most Biomphalaria iGluR sequences, while the IRs did exhibit a variable pattern, lacking some or all known glutamate-interactingresidues, supporting their distinct classification from the iGluRs. We show that B. glabrata contains 7 putative IRs, some of which are expressed within its chemosensory organs. To further investigate a role for the more ancient IR25a type in chemoreception, we tested its spatial distribution pattern within the snail cephalic tentacle by in situ hybridization. The presence of IR25a within presumptive sensory neurons supports a role for this receptor in olfactory processing, contributing to our understanding of the molecular pathways that are involved in Biomphalaria olfactory processing.

  9. 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.

  10. 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.

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

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    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.

  12. 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.

  13. 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.

  14. Influence of gamma radiation on the levels of polyphenols and lethality of ethanol extracts of Anacardium occidentale Linn., against Biomphalaria glabrata; Influencia da radiacao gama na acao moluscicida de extratos de cajueiro em Biomphalaria glabrata

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    Santos, G.H.F.; Silva, E.B., E-mail: santosghf@hotmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Energia Nuclear. Grupo de Radioprotecao e Radioecologia; Melo, A.M.M.A.; Lima, C.S.A [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Biofisica; Amorim, E.L.C.; Peixoto Sobrinho, T.J.S. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Farmacia

    2013-08-15

    Plant materials rich in phenolic compounds, such as Anacardium occidentale Linn., Have been used as alternatives to synthetic pesticides in Biomphalaria glabrata control programs, intermediate host of Schistosoma mansoni. Studies show that ionizing radiation can influence the content of phenolic compounds and thus their biological actions. The aim of this study was to evaluate the influence of gamma radiation of {sup 60}Co in polyphenol composition of hydroalcoholic extracts of bark and leaves of A. occidentale and evaluate the toxicity of these extracts to embryos and adults of B. glabrata. To achieve this goal this, the extracts were irradiated at 10 kGy, the controls being maintained from 0 kGy and positive (CaCO{sub 3}) and negative (H{sub 2}O). We quantified the total phenols by the Folin-Ciocalteau and tannins by precipitation of casein. Extracts were used at a concentration of 100 mg/L. The results showed that the radiation caused the changes to the leaves, the percentage of polyphenols and tannins, and the percentage of lethality in embryos and adults Biomphalaria glabrata, these percentages being: 13 ± 5 (0 kGy) and 27 ± 2.5 (10 kGy), and 36.67 ± 5.77 (0 kGy), and 56.67 ± 5.77 (10 kGy), respectively. Gamma radiation caused significant changes in the levels of polyphenols in the extracts of leaves of Anacardium ocidentale Linn., translated by the increased toxicity of this extract against embryos and adults of Biomphalaria glabrata. This indicates that gamma radiation can be used as an agent potentiating the toxicity of plant extracts on the alternate use of these materials as molluscicides. (author)

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Atividade moluscicida de princípios ativos de folhas de Lycopersicon esculentum (Solanales, Solanaceae em Biomphalaria glabrata (Gastropoda, Planorbidae Moluscicide activity of active principles in the leaves of Lycopersicon esculentum (Solanales, Solanaceae on Biomphalaria glabrata (Gastropoda, Planorbidae

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    Vilma Leyton

    Full Text Available Foram obtidos extratos aquosos e alcoólicos a partir de pó de folhas secas de tomateiro (Lycopersicon esculentum, Mill. c.v. Cereja. Por extração metanólica e precipitação alcalina, foi obtido um produto que denominamos "glicoalcalóide esteroidal bruto" (GEb, no qual foi caracterizada a presença de tomatina. Em ensaios laboratoriais, os extratos aquosos, alcoólicos e o GEb apresentaram atividade moluscicida em Biomphalaria glabrata (Say, 1818. O "glicoalcalóide esteroidal bruto" apresentou alta atividade moluscicida (CL50 = 8,01 ppm e CL90 = 13,17 ppm, comparável à atividade da tomatina. Desovas de B. glabrata mostraram-se resistentes aos extratos testados. Os níveis de atividade moluscicida apresentados pelos diversos extratos e o GEb, apontam apenas o GEb como candidato para a continuação dos estudos visando a sua possível utilização em campo.Aqueous and alcoholic extracts were obtained from crushed dried leaves of tomato plant (Lycopersicon esculentum, Mill. c.v. Cherry. By the use of a methanolic extraction and alkaline precipitation, a product named crude steroidal glycoalkaloid (GEb, was obtained. The presence of tomatidine was characterized in this product. In laboratory, the aqueous and alcoholic extracts and GEb have shown molluscicidal activity against Biomphalaria glabrata (Say, 1818. The crude steroidal glycoalkaloid presented a high molluscicidal activity (LC50 = 8.01 ppm and LC90 = 13.17 ppm, similar to that of tomatine. None of the compounds tested affected B. glabrata egg masses. The level of activity showed by the different extracts and by the GEb, pointed out the GEb as the only candidate able to be considered for further tests toward field trials as molluscicidal agent.

  1. 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.

  2. 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)

  3. 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)

  4. 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)

  5. 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)

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  8. 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.

  9. 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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Influence of gamma radiation on the levels of polyphenols and lethality of ethanol extracts of Anacardium occidentale Linn., against Biomphalaria glabrata

    International Nuclear Information System (INIS)

    Santos, G.H.F.; Silva, E.B.; Melo, A.M.M.A.; Lima, C.S.A; Amorim, E.L.C.; Peixoto Sobrinho, T.J.S.

    2013-01-01

    Plant materials rich in phenolic compounds, such as Anacardium occidentale Linn., Have been used as alternatives to synthetic pesticides in Biomphalaria glabrata control programs, intermediate host of Schistosoma mansoni. Studies show that ionizing radiation can influence the content of phenolic compounds and thus their biological actions. The aim of this study was to evaluate the influence of gamma radiation of 60 Co in polyphenol composition of hydroalcoholic extracts of bark and leaves of A. occidentale and evaluate the toxicity of these extracts to embryos and adults of B. glabrata. To achieve this goal this, the extracts were irradiated at 10 kGy, the controls being maintained from 0 kGy and positive (CaCO 3 ) and negative (H 2 O). We quantified the total phenols by the Folin-Ciocalteau and tannins by precipitation of casein. Extracts were used at a concentration of 100 mg/L. The results showed that the radiation caused the changes to the leaves, the percentage of polyphenols and tannins, and the percentage of lethality in embryos and adults Biomphalaria glabrata, these percentages being: 13 ± 5 (0 kGy) and 27 ± 2.5 (10 kGy), and 36.67 ± 5.77 (0 kGy), and 56.67 ± 5.77 (10 kGy), respectively. Gamma radiation caused significant changes in the levels of polyphenols in the extracts of leaves of Anacardium ocidentale Linn., translated by the increased toxicity of this extract against embryos and adults of Biomphalaria glabrata. This indicates that gamma radiation can be used as an agent potentiating the toxicity of plant extracts on the alternate use of these materials as molluscicides. (author)

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

    Science.gov (United States)

    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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

    Science.gov (United States)

    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.

  11. 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.

    Science.gov (United States)

    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.

  12. 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.

  13. 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.

  14. 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...

  15. 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%.

  16. 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

  17. 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.

  18. Proteomics of drug resistance in Candida glabrata biofilms.

    Science.gov (United States)

    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.

  19. Transcriptome

    Science.gov (United States)

    ... 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 ...

  20. 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.

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

    Science.gov (United States)

    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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Candida glabrata: an emerging oral opportunistic pathogen.

    Science.gov (United States)

    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.

  9. 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

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

    Science.gov (United States)

    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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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...

  17. Assimilation of NAD(+) precursors in Candida glabrata.

    Science.gov (United States)

    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.

  18. 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.

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

    Science.gov (United States)

    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.

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Epithelial GM-CSF induction by Candida glabrata.

    Science.gov (United States)

    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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. The mating type-like loci of Candida glabrata.

    Science.gov (United States)

    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.

  17. 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...

  18. 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 ...

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

    Science.gov (United States)

    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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

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

    NARCIS (Netherlands)

    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

  6. 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 ...

  7. 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.

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

    Science.gov (United States)

    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.

  9. Metabolic engineering of Candida glabrata for diacetyl production.

    Directory of Open Access Journals (Sweden)

    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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. [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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  19. 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

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

    Science.gov (United States)

    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.

  1. 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...

  2. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. 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...

  6. 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...

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  11. 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.

  12. Further studies on the molecular systematics of Biomphalaria snails from Brazil

    Directory of Open Access Journals (Sweden)

    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

  13. 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...

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

    Science.gov (United States)

    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

  15. 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

  16. 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.)

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  20. 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

  1. Isolamento genético de populações de caramujos do gênero Biomphalaria

    Directory of Open Access Journals (Sweden)

    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.

  2. 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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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.

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

    International Nuclear Information System (INIS)

    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

  5. Isolamento genético de populações de caramujos do gênero Biomphalaria

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  7. 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.

  8. 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.

  9. 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.

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

    Science.gov (United States)

    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.

  11. 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.

  12. 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.

  13. 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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  16. 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  4. 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...

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

    Directory of Open Access Journals (Sweden)

    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

  6. 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

  7. 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.

  8. 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.

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

    Science.gov (United States)

    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.

  10. 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

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

    Directory of Open Access Journals (Sweden)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  14. 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.

  15. 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.

  16. 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.

  17. Silver colloidal nanoparticles: effect on matrix composition and structure of Candida albicans and Candida glabrata biofilms.

    Science.gov (United States)

    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.

  18. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    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

  19. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

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

    Science.gov (United States)

    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

  4. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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.

  9. High Throughput Transcriptomics @ USEPA (Toxicology ...

    Science.gov (United States)

    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.

  10. 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)

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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.

  13. Biomphalaria alexandrina in Egypt

    Indian Academy of Sciences (India)

    2013-06-04

    Jun 4, 2013 ... species within Egypt. The National Schistosoma Control Program has made great strides with respect to the .... barley and flax (Caminos 1997). Egyptian ..... Duke L 2008 Schistosomiasis in Ancient Egypt: The 'AAA' De- bate.

  14. 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 ...

  15. 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

  16. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  18. 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.

  19. 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

    Directory of Open Access Journals (Sweden)

    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.

  20. Perennial peanut (Arachis glabrata Benth.) contains polyphenol oxidase (PPO) and PPO substrates that can reduce post-harvest proteolysis.

    Science.gov (United States)

    Sullivan, Michael L; Foster, Jamie L

    2013-08-15

    Studies of perennial peanut (Arachis glabrata Benth.) suggest its hay and haylage have greater levels of rumen undegraded protein (RUP) than other legume forages such as alfalfa (Medicago sativa L.). Greater RUP can result in more efficient nitrogen utilization by ruminant animals with positive economic and environmental effects. We sought to determine whether, like red clover (Trifolium pretense L.), perennial peanut contains polyphenol oxidase (PPO) and PPO substrates that might be responsible for increased RUP. Perennial peanut extracts contain immunologically detectible PPO protein and high levels of PPO activity (>100 nkatal mg(-1) protein). Addition of caffeic acid (PPO substrate) to perennial peanut extracts depleted of endogenous substrates reduced proteolysis by 90%. Addition of phenolics prepared from perennial peanut leaves to extracts of either transgenic PPO-expressing or control (non-expressing) alfalfa showed peanut phenolics could reduce proteolysis >70% in a PPO-dependent manner. Two abundant likely PPO substrates are present in perennial peanut leaves including caftaric acid. Perennial peanut contains PPO and PPO substrates that together are capable of inhibiting post-harvest proteolysis, suggesting a possible mechanism for increased RUP in this forage. Research related to optimizing the PPO system in other forage crops will likely be applicable to perennial peanut. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

  1. Purification, Reconstitution, and Inhibition of Cytochrome P-450 Sterol Δ22-Desaturase from the Pathogenic Fungus Candida glabrata

    Science.gov (United States)

    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

  2. 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

  3. 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

    Directory of Open Access Journals (Sweden)

    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.

  4. Susceptibility of Biomphalaria straminea (Dunker, 1848 from Serra da Mesa Dam, Goiás, Brazil to infection with three strains of Schistosoma mansoni Sambon, 1907

    Directory of Open Access Journals (Sweden)

    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.

  5. 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

  6. 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.

  7. 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)

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  10. Comparative transcriptomics in the Triticeae

    Directory of Open Access Journals (Sweden)

    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

  11. Alterations in the fatty acid profile, antioxidant enzymes and protein pattern of Biomphalaria alexandrina snails exposed to the pesticides diazinon and profenfos.

    Science.gov (United States)

    Bakry, Fayez A; El-Hommossany, Karem; Abd El-Atti, Mahmoud; Ismail, Somaya M

    2016-04-01

    The use of pesticides is widespread in agricultural activities. These pesticides may contaminate the irrigation and drainage systems during agriculture activities and pests' control and then negatively affect the biotic and a biotic component of the polluted water courses. The present study aimed to evaluate the effect of the pesticides diazinon and profenfos on some biological activities of Biomphalaria alexandrina snails such as fatty acid profile, some antioxidant enzymes (thioredoxin reductase (TrxR), sorbitol dehydrogenase (SDH), superoxide dismutase (SOD), catalase (CAT) as well as glutathione reductase (GR) and lipid peroxidation (LP)) and protein patterns in snails' tissues exposed for 4 weeks to LC10 of diazinon and profenfos. The results showed that the two pesticides caused considerable reduction in survival rates and egg production of treated snails. Identification of fatty acid composition in snail tissues treated with diazinon and profenfos pesticides was carried out using gas-liquid chromatography (GLC). The results declared alteration in fatty acid profile, fluctuation in percentage of long chain and short chain fatty acid contributions either saturated or unsaturated ones, and a decrease in total lipid content in tissues of snails treated with these pesticides. The data demonstrate that there was a significant inhibition in the activities of tissues SOD, CAT, glutathione reductase (GR), TrxR, and SDH in tissues of treated snails, while a significant elevation was detected in LP as compared to the normal control. On the other hand, the electrophoretic pattern of total protein showed differences in number and molecular weights of protein bands due to the treatment of snails. It was concluded that the residues of diazinon and profenfos pesticides in aquatic environments have toxic effects onB. alexandrina snails. © The Author(s) 2013.

  12. 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-.

  13. 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...

  14. 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...

  15. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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

  18. 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

  19. 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.

  20. Blood transcriptomics: applications in toxicology

    Science.gov (United States)

    Joseph, Pius; Umbright, Christina; Sellamuthu, Rajendran

    2015-01-01

    The number of new chemicals that are being synthesized each year has been steadily increasing. While chemicals are of immense benefit to mankind, many of them have a significant negative impact, primarily owing to their inherent chemistry and toxicity, on the environment as well as human health. In addition to chemical exposures, human exposures to numerous non-chemical toxic agents take place in the environment and workplace. Given that human exposure to toxic agents is often unavoidable and many of these agents are found to have detrimental human health effects, it is important to develop strategies to prevent the adverse health effects associated with toxic exposures. Early detection of adverse health effects as well as a clear understanding of the mechanisms, especially at the molecular level, underlying these effects are key elements in preventing the adverse health effects associated with human exposure to toxic agents. Recent developments in genomics, especially transcriptomics, have prompted investigations into this important area of toxicology. Previous studies conducted in our laboratory and elsewhere have demonstrated the potential application of blood gene expression profiling as a sensitive, mechanistically relevant and practical surrogate approach for the early detection of adverse health effects associated with exposure to toxic agents. The advantages of blood gene expression profiling as a surrogate approach to detect early target organ toxicity and the molecular mechanisms underlying the toxicity are illustrated and discussed using recent studies on hepatotoxicity and pulmonary toxicity. Furthermore, the important challenges this emerging field in toxicology faces are presented in this review article. PMID:23456664

  1. [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

  2. 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.

  3. 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...

  4. The effect of increasing water temperatures on Schistosoma mansoni transmission and Biomphalaria pfeifferi population dynamics: an agent-based modelling study.

    Directory of Open Access Journals (Sweden)

    Nicky McCreesh

    Full Text Available There is increasing interest in the control and elimination of schistosomiasis. Little is known, however, about the likely effects of increasing water-body temperatures on transmission.We have developed an agent-based model of the temperature-sensitive stages of the Schistosoma and intermediate host snail life-cycles, parameterised using data from S. mansoni and Biomphalaria pfeifferi laboratory and field-based observations. Infection risk is calculated as the number of cercariae in the model, adjusted for their probability of causing infection.The number of snails in the model is approximately constant between 15-31°C. Outside this range, snail numbers drop sharply, and the snail population cannot survive outside the range 14-32°C. Mean snail generation time decreases with increasing temperature from 176 days at 14°C to 46 days at 26°C. Human infection risk is highest between 16-18°C and 1pm and 6-10pm in calm water, and 20-25°C and 12-4pm in flowing water. Infection risk increases sharply when temperatures increase above the minimum necessary for sustained transmission.The model suggests that, in areas where S. mansoni is already endemic, warming of the water at transmission sites will have differential effects on both snails and parasites depending on abiotic properties of the water-body. Snail generation times will decrease in most areas, meaning that snail populations will recover faster from natural population reductions and from snail-control efforts. We suggest a link between the ecological properties of transmission sites and infection risk which could significantly affect the outcomes of interventions designed to alter water contact behaviour--proposing that such interventions are more likely to reduce infection levels at river locations than lakes, where infection risk remains high for longer. In cooler areas where snails are currently found, increasing temperatures may significantly increase infection risk, potentially leading

  5. 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

  6. 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

  7. 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

  8. Blood transcriptomics and metabolomics for personalized medicine.

    Science.gov (United States)

    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.

  9. 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.

  10. 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

    Directory of Open Access Journals (Sweden)

    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

  11. 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

  12. The transcriptome of Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Roos David S

    2005-12-01

    Full Text Available Abstract Background Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. Results We have used serial analysis of gene expression (SAGE to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. Conclusion This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and

  13. 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

  14. 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...

  15. The transcriptome landscape of early maize meiosis

    Science.gov (United States)

    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...

  16. 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

  17. 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 ...

  18. 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

  19. 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.

  20. 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

    Directory of Open Access Journals (Sweden)

    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

  1. Synergistic mutual potentiation of antifungal activity of Zuccagnia punctata Cav. and Larrea nitida Cav. extracts in clinical isolates of Candida albicans and Candida glabrata.

    Science.gov (United States)

    Butassi, Estefanía; Svetaz, Laura A; Ivancovich, Juan J; Feresin, Gabriela E; Tapia, Alejandro; Zacchino, Susana A

    2015-06-01

    Zuccagnia punctata Cav. (Fabaceae) and Larrea nitida Cav. (Zygophyllaceae) are indistinctly or jointly used in traditional medicine for the treatment of fungal-related infections. Although their dichloromethane (DCM) extract have demonstrated moderate antifungal activities when tested on their own, antifungal properties of combinations of both plants have not been assessed previously. The aim of this study was to establish with statistical rigor whether Z. punctata (ZpE) and L. nitida DCM extract (LnE) interact synergistically against the clinically important fungi Candida albicans and Candida glabrata and to characterize the most synergistic combinations. For synergism assessment, the statistical-based Boik's design was applied. Eight ZpE-LnE fixed-ratio mixtures were prepared from four different months of 1 year and tested against Candida strains. Lϕ (Loewe index) of each mixture at different fractions affected (ϕ) allowed for the finding of the most synergistic combinations, which were characterized by HPLC fingerprint and by the quantitation of the selected marker compounds. Lϕ and confidence intervals were determined in vitro with the MixLow method, once the estimated parameters from the dose-response curves of independent extracts and mixtures, were obtained. Markers (four flavonoids for ZpE and three lignans for LnE) were quantified in each extract and their combinations, with a valid HPLC-UV method. The 3D-HPLC profiles of the most synergistic mixtures were obtained by HPLC-DAD. Three over four IC50ZpE/IC50LnE fixed-ratio mixtures displayed synergistic interactions at effect levels ϕ > 0.5 against C. albicans. The dosis of the most synergistic (Lϕ = 0.62) mixture was 65.96 µg/ml (ZpE = 28%; LnE = 72%) containing 8 and 36% of flavonoids and lignans respectively. On the other hand, one over four IC50ZpE/IC50LnE mixtures displays synergistic interactions at ϕ > 0.5 against C. glabrata. The dosis of the most synergistic (Lϕ = 0.67) mixture was 168

  2. 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

  3. Global meta-analysis of transcriptomics studies.

    Directory of Open Access Journals (Sweden)

    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.

  4. Transcriptome architecture across tissues in the pig

    Directory of Open Access Journals (Sweden)

    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.

  5. 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

  6. Transcriptome Dynamics during Maize Endosperm Development.

    Directory of Open Access Journals (Sweden)

    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.

  7. 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.

  8. Green synthesis and characterization of gold and silver nanoparticles using Mussaenda glabrata leaf extract and their environmental applications to dye degradation.

    Science.gov (United States)

    Francis, Sijo; Joseph, Siby; Koshy, Ebey P; Mathew, Beena

    2017-07-01

    Plant-derived nanomaterials opened a green approach in solving the current environment issues. Present study focused on rapid microwave-assisted synthesis and applications of gold and silver nanoparticles mediated by aqueous leaf extract of Mussaenda glabrata. The synthesized nanoparticles were characterized by UV-vis, FT-IR, powder XRD, energy-dispersive X-ray spectroscopy (EDX), transmission electron (TEM), and atomic force microscopic techniques (AFM). FCC crystal structure of both nanoparticles was confirmed by peaks corresponding to (111), (200), (220), and (311) planes in XRD spectra and bright circular spots in SAED pattern. IC 50 values shown by gold and silver nanoparticles (44.1 ± 0.82 and 57.92 ± 1.33 μg/mL) reflected their high free radical scavenging potential. The synthesized gold and silver nanoparticles revealed their potency to inhibit pathogenic microorganisms Bacillus pumilus, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Aspergillus niger, and Penicillium chrysogenum. Anthropogenic pollutants rhodamine B and methyl orange were effectively degraded from aquatic environment and waste water sewages of dye industries using the prepared nanocatalysts. The catalytic capacities of the synthesized nanoparticles were also exploited in the reduction of 4-nitrophenol. Graphical abstract.

  9. 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...

  10. The Escherichia coli transcriptome linked to growth fitness

    Directory of Open Access Journals (Sweden)

    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

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

    Directory of Open Access Journals (Sweden)

    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

  12. Transcriptomic dissection of tongue squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    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.

  13. The Characterization of the Phlebotomus papatasi Transcriptome

    Science.gov (United States)

    2013-04-01

    Le. infantum (Li: CAM68214.1), Le. major (Lm: XP_001683430.1), Homo sapiens (Hs: AAD17527.1) and Bo. mori (Bm: NP_001108470.1). The WAG substitution...blood meals in Ph. langeroni (Dillon, El Kordy 1997). Here we have identified 23 unique Ph. papatasi sequences with high identity (BLASTP, əe-50) to...Perkin SAH, Caler E, Bonaldo MF, Soares MB, El -Sayeed N, Aksoy S. Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  16. The Human Blood Metabolome-Transcriptome Interface

    Science.gov (United States)

    Schramm, Katharina; Adamski, Jerzy; Gieger, Christian; Herder, Christian; Carstensen, Maren; Peters, Annette; Rathmann, Wolfgang; Roden, Michael; Strauch, Konstantin; Suhre, Karsten; Kastenmüller, Gabi; Prokisch, Holger; Theis, Fabian J.

    2015-01-01

    Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the ‘human blood metabolome-transcriptome interface’ (BMTI). Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease. PMID:26086077

  17. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

    Full Text Available Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the 'human blood metabolome-transcriptome interface' (BMTI. Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease.

  18. Comparative Transcriptomics Among Four White Pine Species

    Directory of Open Access Journals (Sweden)

    Ethan A. G. Baker

    2018-05-01

    Full Text Available Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola, limber pine (Pinus flexilis, whitebark pine (Pinus albicaulis, and sugar pine (Pinus lambertiana was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

  19. Analysis of a human brain transcriptome map

    Directory of Open Access Journals (Sweden)

    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.

  20. 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....

  1. Candida glabrata binds to glycosylated and lectinic receptors on the coronary endothelial luminal membrane and inhibits flow sense and cardiac responses to agonists.

    Science.gov (United States)

    Torres-Tirado, David; Knabb, Maureen; Castaño, Irene; Patrón-Soberano, Araceli; De Las Peñas, Alejandro; Rubio, Rafael

    2016-01-01

    Candida glabrata (CG) is an opportunistic fungal pathogen that initiates infection by binding to host cells via specific lectin-like adhesin proteins. We have previously shown the importance of lectin-oligosaccharide binding in cardiac responses to flow and agonists. Because of the lectinic-oligosaccharide nature of CG binding, we tested the ability of CG to alter the agonist- and flow-induced changes in cardiac function in isolated perfused guinea pig hearts. Both transmission and scanning electron microscopy showed strong attachment of CG to the coronary endothelium, even after extensive washing. CG shifted the coronary flow vs. auricular-ventricular (AV) delay relationship upward, indicating that greater flow was required to achieve the same AV delay. This effect was completely reversed with mannose, partially reversed with galactose and N-acetylgalactosamine, but hyaluronan had no effect. Western blot analysis was used to determine binding of CG to isolated coronary endothelial luminal membrane (CELM) receptors, and the results indicate that flow-sensitive CELM receptors, ANG II type I, α-adrenergic 1A receptor, endothelin-2, and VCAM-1 bind to CG. In addition, CG inhibited agonist-induced effects of bradykinin, angiotensin, and phenylephrine on AV delay, coronary perfusion pressure, and left ventricular pressure. Mannose reversed the inhibitory effects of CG on the agonist responses. These results suggest that CG directly binds to flow-sensitive CELM receptors via lectinic-oligosaccharide interactions with mannose and disrupts the lectin-oligosaccharide binding necessary for flow-induced cardiac responses. Copyright © 2016 the American Physiological Society.

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

    Directory of Open Access Journals (Sweden)

    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

  3. 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

  4. 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.

    Science.gov (United States)

    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.

  5. 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

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

    Directory of Open Access Journals (Sweden)

    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

  7. 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

    Directory of Open Access Journals (Sweden)

    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

  8. Peroxidase gene discovery from the horseradish transcriptome.

    Science.gov (United States)

    Näätsaari, Laura; Krainer, Florian W; Schubert, Michael; Glieder, Anton; Thallinger, Gerhard G

    2014-03-24

    Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes.

  9. The human airway epithelial basal cell transcriptome.

    Directory of Open Access Journals (Sweden)

    Neil R Hackett

    2011-05-01

    Full Text Available The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population.Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the "human airway basal cell signature" as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels.The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium.

  10. A transcriptome anatomy of human colorectal cancers

    International Nuclear Information System (INIS)

    Lü, Bingjian; Xu, Jing; Lai, Maode; Zhang, Hao; Chen, Jian

    2006-01-01

    Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of β-catenin and. 7 novel genes in colorectal cancers. The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers. Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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...

  16. 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...

  17. Biological control of schistosome transmission in flowing water habitats.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  19. Principle considerations for the use of transcriptomics in doping research.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  1. Biological and morphological characteristics of Schistosoma mansoni from Ribeira Valley, State of São Paulo, Brazil: I - susceptibility of Biomphalaria tenagophila snail to sympatric S. mansoni strain Características biológicas e morfológicas de cepa paulista de Schistosoma mansoni do Vale do Ribeira: I - suscetibilidade de Biomphalaria tenagophila do Vale do Ribeira, SP, a cepa simpátrica de Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Ana Cristina Figueiredo

    1992-06-01

    Full Text Available In the São Paulo State, Brazil, where the Biomphalaria tenagophila is the intermediate host, the Ribeira Valley is an important endemic schistosomiasis mansoni area. During last eleven years there has been intense control measures focusing on schistosomiasis. The efforts have been concentrated in the municipalities of Pedro de Toledo and Itariri. We determined the susceptibility of B. tenagophila to sympatric strain of S. mansoni, both recently isolated from Itariri field. In 1988, this strain was isolated and maintained in the experimental model: Swiss mice - sympatric B. tenagophila. The second generation of the worm was evaluated. The snail were divided in the three groups of 60 snails each. One group was exposed to 1 miracidium and other to 10. The third group was the control. The mortality and the shedding of cercariae were checked during 78 days. After that, the positive snails were observed until they ceased to shed cercariae. The exposed molluscs showed mortality rates of 23% and 31% and infection indexes were of 8% and 60% to 1 and 10 miracidia respectively. The mortality was of 22% in the control group. The periods of shedding cercariae in the two groups were 82 and 104 days. We can conclude that B. tenagophila is an effective intermediate host to the sympatric strain of S. mansoni sympatric strainDentre as regiões do Estado de São Paulo, onde Biomphalaria tenagophila é hospedeira intermediária, o vale do Ribeira é área endêmica da esquistossomose. Nos últimos onze anos a endemia vem sendo intensamente controlada no vale, principalmente, nos municípios de Pedro de Toledo e Itariri. Estudamos a suscetibilidade de B. tenagophila de Itariri à linhagem simpátrica de Schistosoma mansoni, isolada do campo em 1988 e mantida no laboratório em camundongos suiço e B. tenagophila. Estudou-se a 2ª geração do trematódeo. Constituiram-se 3 grupos de 60 moluscos cada, sendo um grupo exposto a um miracídio e outro a 10 e um grupo

  2. 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

  3. 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

  4. Network Analysis of Rodent Transcriptomes in Spaceflight

    Science.gov (United States)

    Ramachandran, Maya; Fogle, Homer; Costes, Sylvain

    2017-01-01

    Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

  5. Transcriptomic analysis of Salmonella desiccation resistance.

    Science.gov (United States)

    Li, Haiping; Bhaskara, Anuhya; Megalis, Christina; Tortorello, Mary Lou

    2012-12-01

    The survival of Salmonella in low moisture foods and processing environments remains a great challenge for the food industry and public health. To explore the mechanisms of Salmonella desiccation resistance, we studied the transcriptomic responses in Salmonella Tennessee (Tennessee), using Salmonella Typhimurium LT2 (LT2), a strain weakly resistant to desiccation, as a reference strain. In response to 2 h of air-drying at 11% equilibrated relative humidity, approximately one-fourth of the open reading frames (ORFs) in the Tennessee genome and one-fifth in LT2 were differentially expressed (>2-fold). Among all differentially expressed functional groups (>5-fold) in both strains, the expression fold change associated with fatty acid metabolism was the highest, and constituted 51% and 35% of the total expression fold change in Tennessee and LT2, respectively. Tennessee showed greater changes in expression of genes associated with stress response and envelope modification than LT2, while showing lesser changes in protein biosynthesis expression. Expression of flagella genes was significantly more inhibited in stationary phase cells of Tennessee than LT2 both before and after desiccation. The accumulation of the osmolyte trehalose was significantly induced by desiccation in Tennessee, but no increase was detectable in LT2, which is consistent with the expression patterns of the entire trehalose biosynthesis and degradation pathways in both strains. Results from this study present a global view of the dynamic desiccation responses in Salmonella, which will guide future research efforts to control Salmonella in low moisture environments.

  6. Transcriptome States Reflect Imaging of Aging States.

    Science.gov (United States)

    Eckley, D Mark; Coletta, Christopher E; Orlov, Nikita V; Wilson, Mark A; Iser, Wendy; Bastian, Paul; Lehrmann, Elin; Zhang, Yonqing; Becker, Kevin G; Goldberg, Ilya G

    2018-06-14

    In this study, we describe a morphological biomarker that detects multiple discrete subpopulations (or "age-states") at several chronological ages in a population of nematodes (Caenorhabditis elegans). We determined the frequencies of three healthy adult states and the timing of the transitions between them across the lifespan. We used short-lived and long-lived strains to confirm the general applicability of the state classifier and to monitor state progression. This exploration revealed healthy and unhealthy states, the former being favored in long-lived strains and the latter showing delayed onset. Short-lived strains rapidly transitioned through the putative healthy state. We previously found that age-matched animals in different age-states have distinct transcriptome profiles. We isolated animals at the beginning and end of each identified state and performed microarray analysis (principal component analysis, relative sample to sample distance measurements, and gene set enrichment analysis). In some comparisons, chronologically identical individuals were farther apart than morphologically identical individuals isolated on different days. The age-state biomarker allowed assessment of aging in a novel manner, complementary to chronological age progression. We found hsp70 and some small heat shock protein genes are expressed later in adulthood, consistent with the proteostasis collapse model.

  7. A transcriptome approach to ecdysozoan phylogeny.

    Science.gov (United States)

    Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

    2014-11-01

    The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Gingival tissue transcriptomes in experimental gingivitis

    Science.gov (United States)

    Jönsson, Daniel; Ramberg, Per; Demmer, Ryan T.; Kebschull, Moritz; Dahlén, Gunnar; Papapanou, Panos N.

    2012-01-01

    Aims We investigated the sequential gene expression in the gingiva during the induction and resolution of experimental gingivitis. Methods Twenty periodontally and systemically healthy non-smoking volunteers participated in a 3-week experimental gingivitis protocol, followed by debridement and 2-week regular plaque control. We recorded clinical indices and harvested gingival tissue samples from 4 interproximal palatal sites in half of the participants at baseline, Day 7, 14 and 21 (‘induction phase’), and at day 21, 25, 30 and 35 in the other half (‘resolution phase’). RNA was extracted, amplified, reversed transcribed, amplified, labeled and hybridized with Affymetrix Human Genome U133Plus2.0 microarrays. Paired t-tests compared gene expression changes between consecutive time points. Gene ontology analyses summarized the expression patterns into biologically relevant categories. Results The median gingival index was 0 at baseline, 2 at Day 21 and 1 at Day 35. Differential gene regulation peaked during the third week of induction and the first four days of resolution. Leukocyte transmigration, cell adhesion and antigen processing/presentation were the top differentially regulated pathways. Conclusions Transcriptomic studies enhance our understanding of the pathobiology of the reversible inflammatory gingival lesion and provide a detailed account of the dynamic tissue responses during induction and resolution of experimental gingivitis. PMID:21501207

  9. Transcriptome analysis of zebrafish embryogenesis using microarrays.

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    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  10. 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.

  11. 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.

  12. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis.

    Science.gov (United States)

    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.

  13. Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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...

  15. 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...

  16. 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)

  17. 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...

  18. De novo transcriptome assembly of shrimp Palaemon serratus

    Directory of Open Access Journals (Sweden)

    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.

  19. Transcriptomic signatures of ash (Fraxinus spp. phloem.

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    Xiaodong Bai

    2011-01-01

    Full Text Available Ash (Fraxinus spp. is a dominant tree species throughout urban and forested landscapes of North America (NA. The rapid invasion of NA by emerald ash borer (Agrilus planipennis, a wood-boring beetle endemic to Eastern Asia, has resulted in the death of millions of ash trees and threatens billions more. Larvae feed primarily on phloem tissue, which girdles and kills the tree. While NA ash species including black (F. nigra, green (F. pennsylvannica and white (F. americana are highly susceptible, the Asian species Manchurian ash (F. mandshurica is resistant to A. planipennis perhaps due to their co-evolutionary history. Little is known about the molecular genetics of ash. Hence, we undertook a functional genomics approach to identify the repertoire of genes expressed in ash phloem.Using 454 pyrosequencing we obtained 58,673 high quality ash sequences from pooled phloem samples of green, white, black, blue and Manchurian ash. Intriguingly, 45% of the deduced proteins were not significantly similar to any sequences in the GenBank non-redundant database. KEGG analysis of the ash sequences revealed a high occurrence of defense related genes. Expression analysis of early regulators potentially involved in plant defense (i.e. transcription factors, calcium dependent protein kinases and a lipoxygenase 3 revealed higher mRNA levels in resistant ash compared to susceptible ash species. Lastly, we predicted a total of 1,272 single nucleotide polymorphisms and 980 microsatellite loci, among which seven microsatellite loci showed polymorphism between different ash species.The current transcriptomic data provide an invaluable resource for understanding the genetic make-up of ash phloem, the target tissue of A. planipennis. These data along with future functional studies could lead to the identification/characterization of defense genes involved in resistance of ash to A. planipennis, and in future ash breeding programs for marker development.

  20. 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

    Directory of Open Access Journals (Sweden)

    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

  1. 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...

  2. Transcriptome analysis of adiposity in domestic ducks by transcriptomic comparison with their wild counterparts.

    Science.gov (United States)

    Chen, L; Luo, J; Li, J X; Li, J J; Wang, D Q; Tian, Y; Lu, L Z

    2015-06-01

    Excessive adiposity is a major problem in the duck industry, but its molecular mechanisms remain unknown. Genetic comparisons between domestic and wild animals have contributed to the exploration of genetic mechanisms responsible for many phenotypic traits. Significant differences in body fat mass have been detected between domestic and wild ducks. In this study, we used the Peking duck and Anas platyrhynchos as the domestic breed and wild counterpart respectively and performed a transcriptomic comparison of abdominal fat between the two breeds to comprehensively analyze the transcriptome basis of adiposity in ducks. We obtained approximately 350 million clean reads; assembled 61 250 transcripts, including 23 699 novel ones; and identified alternative 5' splice sites, alternative 3' splice sites, skipped exons and retained intron as the main alternative splicing events. A differential expression analysis between the two breeds showed that 753 genes exhibited differential expression. In Peking ducks, some lipid metabolism-related genes (IGF2, FABP5, BMP7, etc.) and oncogenes (RRM2, AURKA, CYR61, etc.) were upregulated, whereas genes related to tumor suppression and immunity (TNFRSF19, TNFAIP6, IGSF21, NCF1, etc.) were downregulated, suggesting adiposity might closely associate with tumorigenesis in ducks. Furthermore, 280 576 single-nucleotide variations were found differentiated between the two breeds, including 8641 non-synonymous ones, and some of the non-synonymous ones were found enriched in genes involved in lipid-associated and immune-associated pathways, suggesting abdominal fat of the duck undertakes both a metabolic function and immune-related function. These datasets enlarge our genetic information of ducks and provide valuable resources for analyzing mechanisms underlying adiposity in ducks. © 2015 Stichting International Foundation for Animal Genetics.

  3. 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.

  4. 20180311 - High Throughput Transcriptomics: From screening to pathways (SOT 2018)

    Science.gov (United States)

    The EPA ToxCast effort has screened thousands of chemicals across hundreds of high-throughput in vitro screening assays. The project is now leveraging high-throughput transcriptomic (HTTr) technologies to substantially expand its coverage of biological pathways. The first HTTr sc...

  5. Transcriptome Profiling in Human Diseases: New Advances and Perspectives

    Directory of Open Access Journals (Sweden)

    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.

  6. 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...

  7. Transcriptome and genome size analysis of the venus flytrap

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Vogt, Josef Korbinian; Bressendorff, Simon

    2015-01-01

    . muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified...

  8. Minor class splicing shapes the zebrafish transcriptome during development

    DEFF Research Database (Denmark)

    Markmiller, Sebastian; Cloonan, Nicole; Lardelli, Rea M

    2014-01-01

    known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we...

  9. Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum

    DEFF Research Database (Denmark)

    Rodriguez, M. C.; Edsgard, Stefan Daniel; Hussain, S. S.

    2010-01-01

    the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture...

  10. 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.

  11. Illumina-based de novo transcriptome sequencing and analysis

    Indian Academy of Sciences (India)

    In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant ...

  12. Transcriptome of the Antarctic brooding gastropod mollusc Margarella antarctica.

    Science.gov (United States)

    Clark, Melody S; Thorne, Michael A S

    2015-12-01

    454 RNA-Seq transcriptome data were generated from foot tissue of the Antarctic brooding gastropod mollusc Margarella antarctica. A total of 6195 contigs were assembled de novo, providing a useful resource for researchers with an interest in Antarctic marine species, phylogenetics and mollusc biology, especially shell production. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Transcriptome dynamics-based operon prediction in prokaryotes.

    Science.gov (United States)

    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.

  14. De novo transcriptome assembly of heavy metal tolerant Silene dioica

    Czech Academy of Sciences Publication Activity Database

    Čegan, R.; Hudzieczek, V.; Hobza, Roman

    2017-01-01

    Roč. 11, MAR (2017), s. 118-119 ISSN 2213-5960 Institutional support: RVO:61389030 Keywords : genome * Silene dioica * RNA-Seq * Transcriptome * Heavy metal tolerance * Sex chromosomes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany

  15. Transcriptome of barley under three different heavy metal stress reaction

    Czech Academy of Sciences Publication Activity Database

    Kintlová, Martina; Blavet, Nicolas; Cegan, R.; Hobza, Roman

    2017-01-01

    Roč. 13, SEP (2017), s. 15-17 ISSN 2213-5960 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : plants * Barley * RNA-Seq * Transcriptome * Heavy metal * Copper * Zinc * Cadmium Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany

  16. 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.

  17. 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.

  18. Transcriptome profiling reveals regulatory mechanisms underlying Corolla Senescence in Petunia

    Science.gov (United States)

    Genetic regulatory mechanisms that govern petal natural senescence in petunia is complicated and unclear. To identify key genes and pathways that regulate the process, we initiated a transcriptome analysis in petunia petals at four developmental time points, including petal opening without anthesis ...

  19. 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 ...

  20. 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

  1. Transcriptome signature of the adult mouse choroid plexus

    Directory of Open Access Journals (Sweden)

    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.

  2. Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

    Directory of Open Access Journals (Sweden)

    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

  3. 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.

  4. Transcriptome analysis of monocyte-HIV interactions

    Directory of Open Access Journals (Sweden)

    Tran Huyen

    2010-06-01

    macrophages can contribute to sustained chronic immune activation during HIV infection, e.g. through the perturbation of cytokine and chemokine networks 141516. With the acknowledged notion of chronic immune activation as a paradoxical driving force of immune suppression 17, this pro-inflammatory macrophage phenotype during HIV infection may be a crucial parameter in disease progression. Yet other macrophage dysfunctions are associated with more peripheral HIV- or ART-associated disorders such as atherosclerosis 18, lipodystrophy 19, and metabolic syndrome during HIV infection and/or combination ART 2021. Monocytes, for their part, are much less permissive to infection with HIV, both in vitro 22 and in vivo, where estimates of infected circulating monocytes are consistently low 2324. Circulating monocytes represent the most accessible primary model for macrophage dysfunction during HIV infection, however, and are furthermore of sufficient importance to study in their own right. Infectious virus can be recovered from circulating monocytes, both in untreated patients 24 and in patients undergoing long-term successful combination ART 25. Additionally, the circulating monocyte pool as a whole does seem to be affected during HIV infection, despite the low frequency of actually infected monocytes. Transcriptome studies, in particular, show a form of hybrid phenotype exhibiting both increased and decreased pro-inflammatory features 2627. This modulation of the non-infected monocyte population could be due to the virus itself through mechanisms which do not require direct infection 28, or to other factors contributing to (aberrant immune activation occurring during HIV infection, such as perturbed cytokine networks 29 or other inflammatory stimulants 30. Several key factors in the described dysregulated processes have been identified 1831, but many molecular components remain elusive. Furthermore, other aspects of HIV and combination ART pathogenesis in which monocyte

  5. 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.

  6. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

    Directory of Open Access Journals (Sweden)

    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.

  7. 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....

  8. Transcriptome profiling of Curcuma longa L. cv. Suvarna

    Directory of Open Access Journals (Sweden)

    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.

  9. Alterations in the developing testis transcriptome following embryonic vinclozolin exposure.

    Science.gov (United States)

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

    2010-11-01

    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 days 13, 14 and 16. A total of 576 differentially expressed genes were identified and the major cellular functions and pathways associated with these altered transcripts were examined. The sets of regulated genes at the different development periods were found to be transiently altered and distinct. Categorization by major known functions of altered genes was performed. Specific cellular process and pathway analyses suggest the involvement of Wnt and calcium signaling, vascular development and epigenetic mechanisms as potential mediators of the direct F1 generation actions of vinclozolin. Copyright © 2010 Elsevier Inc. All rights reserved.

  10. Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

    Directory of Open Access Journals (Sweden)

    Sarah Lück

    2014-10-01

    Full Text Available The rich mammalian cellular circadian output affects thousands of genes in many cell types and has been the subject of genome-wide transcriptome and proteome studies. The results have been enigmatic because transcript peak abundances do not always follow the peaks of gene-expression activity in time. We posited that circadian degradation of mRNAs and proteins plays a pivotal role in setting their peak times. To establish guiding principles, we derived a theoretical framework that fully describes the amplitudes and phases of biomolecules with circadian half-lives. We were able to explain the circadian transcriptome and proteome studies with the same unifying theory, including cases in which transcripts or proteins appeared before the onset of increased production rates. Furthermore, we estimate that 30% of the circadian transcripts in mouse liver and Drosophila heads are affected by rhythmic posttranscriptional regulation.

  11. 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 .

  12. 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.

  13. Analysis of the salivary gland transcriptome of Frankliniella occidentalis.

    Directory of Open Access Journals (Sweden)

    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

  14. Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome.

    Directory of Open Access Journals (Sweden)

    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.

  15. Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

    Science.gov (United States)

    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.

  16. Transcriptome Analysis of the Response of Burmese Python to Digestion

    OpenAIRE

    Duan, Jinjie; Sanggaard, Kristian Wejse; Schauser, Leif; Lauridsen, Sanne Enok; Enghild, Jan J.; Schierup, Mikkel Heide; Wang, Tobias

    2017-01-01

    Abstract 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...

  17. 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

  18. Transcriptome profiling of male gametophyte development in Nicotiana tabacum

    Czech Academy of Sciences Publication Activity Database

    Bokvaj, Pavel; Hafidh, Said; Honys, David

    2015-01-01

    Roč. 3, MAR (2015), s. 106-111 ISSN 2213-5960 R&D Projects: GA ČR(CZ) GAP501/11/1462; GA ČR(CZ) GAP305/12/2611; GA MŠk(CZ) LD14109; GA ČR(CZ) GA13-06943S; GA MŠk(CZ) LD13049 Institutional support: RVO:61389030 Keywords : Pollen development transcriptome * Tobacco * Reproduction Subject RIV: EB - Genetics ; Molecular Biology

  19. Detailed transcriptome description of the neglected cestode Taenia multiceps.

    Directory of Open Access Journals (Sweden)

    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

  20. 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.

  1. 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

  2. Comparing de novo assemblers for 454 transcriptome data

    Directory of Open Access Journals (Sweden)

    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

  3. Transcriptome analysis of the Asian honey bee Apis cerana cerana.

    Directory of Open Access Journals (Sweden)

    Zi Long Wang

    Full Text Available BACKGROUND: The Eastern hive honey bee, Apis cerana cerana is a native and widely bred honey bee species in China. Molecular biology research about this honey bee species is scarce, and genomic information for A. c. cerana is not currently available. Transcriptome and expression profiling data for this species are therefore important resources needed to better understand the biological mechanisms of A. c. cerana. In this study, we obtained the transcriptome information of A. c. cerana by RNA-sequencing and compared gene expression differences between queens and workers of A. c. cerana by digital gene expression (DGE analysis. RESULTS: Using high-throughput Illumina RNA sequencing we obtained 51,581,510 clean reads corresponding to 4.64 Gb total nucleotides from a single run. These reads were assembled into 46,999 unigenes with a mean length of 676 bp. Based on a sequence similarity search against the five public databases (NR, Swissport, GO, COG, KEGG with a cut-off E-value of 10(-5 using BLASTX, a total of 24,630 unigenes were annotated with gene descriptions, gene ontology terms, or metabolic pathways. Using these transcriptome data as references we analyzed the gene expression differences between the queens and workers of A. c. cerana using a tag-based digital gene expression method. We obtained 5.96 and 5.66 million clean tags from the queen and worker samples, respectively. A total of 414 genes were differentially expressed between them, with 189 up-regulated and 225 down-regulated in queens. CONCLUSIONS: Our transcriptome data provide a comprehensive sequence resource for future A. c. cerana study, establishing an important public information platform for functional genomic studies in A. c. cerana. Furthermore, the DGE data provide comprehensive gene expression information for the queens and workers, which will facilitate our understanding of the molecular mechanisms of the different physiological aspects of the two castes.

  4. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.

    Science.gov (United States)

    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.

  5. A comparative transcriptomic approach to understanding the formation of cork.

    Science.gov (United States)

    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.

  6. 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.

  7. Global transcriptome analysis of developing chickpea (Cicer arietinum L. seeds

    Directory of Open Access Journals (Sweden)

    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.

  8. Transcriptome analysis of the response of Burmese python to digestion.

    Science.gov (United States)

    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.

  9. Massively parallel sequencing and analysis of the Necator americanus transcriptome.

    Directory of Open Access Journals (Sweden)

    Cinzia Cantacessi

    2010-05-01

    Full Text Available The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses.A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%, proteinase inhibitors (7.8% or calcium-binding EF-hand proteins (6.7%. Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%, oxidative phosphorylation (63% and/or proteases (60%; most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins or amino acid metabolism (e.g., asparagine t-RNA synthetase.This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human

  10. Genetic Dissection of the Spaceflight Transcriptome Responses in Plants: are some responses unnecessary?

    Data.gov (United States)

    National Aeronautics and Space Administration — Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural...

  11. Comparison of the spaceflight transcriptome of four commonly used Arabidopsis thaliana ecotypes

    Data.gov (United States)

    National Aeronautics and Space Administration — This experiment compared the spaceflight transcriptomes of four commonly used natural variants (ecotypes) of Arabidopsis thaliana using RNAseq. In nature Arabidopsis...

  12. 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.

  13. Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Quantitative developmental transcriptomes of the Mediterranean sea urchin Paracentrotus lividus.

    Science.gov (United States)

    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.

  16. Histological and Transcriptomic Analysis during Bulbil Formation in Lilium lancifolium

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    Panpan Yang

    2017-08-01

    Full Text Available Aerial bulbils are an important propagative organ, playing an important role in population expansion. However, the detailed gene regulatory patterns and molecular mechanism underlying bulbil formation remain unclear. Triploid Lilium lancifolium, which develops many aerial bulbils on the leaf axils of middle-upper stem, is a useful species for investigating bulbil formation. To investigate the mechanism of bulbil formation in triploid L. lancifolium, we performed histological and transcriptomic analyses using samples of leaf axils located in the upper and lower stem of triploid L. lancifolium during bulbil formation. Histological results indicated that the bulbils of triploid L. lancifolium are derived from axillary meristems that initiate de novo from cells on the adaxial side of the petiole base. Transcriptomic analysis generated ~650 million high-quality reads and 11,871 differentially expressed genes (DEGs. Functional analysis showed that the DEGs were significantly enriched in starch and sucrose metabolism and plant hormone signal transduction. Starch synthesis and accumulation likely promoted the initiation of upper bulbils in triploid L. lancifolium. Hormone-associated pathways exhibited distinct patterns of change in each sample. Auxin likely promoted the initiation of bulbils and then inhibited further bulbil formation. High biosynthesis and low degradation of cytokinin might have led to bulbil formation in the upper leaf axil. The present study achieved a global transcriptomic analysis focused on gene expression changes and pathways' enrichment during upper bulbil formation in triploid L. lancifolium, laying a solid foundation for future molecular studies on bulbil formation.

  17. 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.

  18. De novo transcriptome assembly of two contrasting pumpkin cultivars

    Directory of Open Access Journals (Sweden)

    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

  19. Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

    Directory of Open Access Journals (Sweden)

    Gyoungju Nah

    Full Text Available Prairie cordgrass (Spartina pectinata, a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY. The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

  20. [SSR loci information analysis in transcriptome of Andrographis paniculata].

    Science.gov (United States)

    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.

  1. Annotation of nerve cord transcriptome in earthworm Eisenia fetida

    Directory of Open Access Journals (Sweden)

    Vasanthakumar Ponesakki

    2017-12-01

    Full Text Available In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.

  2. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

    Directory of Open Access Journals (Sweden)

    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.

  3. The Transcriptomic Responses of Pinus massoniana to Drought Stress

    Directory of Open Access Journals (Sweden)

    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.

  4. Transcriptome profiling of ontogeny in the acridid grasshopper Chorthippus biguttulus.

    Science.gov (United States)

    Berdan, Emma L; Finck, Jonas; Johnston, Paul R; Waurick, Isabelle; Mazzoni, Camila J; Mayer, Frieder

    2017-01-01

    Acridid grasshoppers (Orthoptera:Acrididae) are widely used model organisms for developmental, evolutionary, and neurobiological research. Although there has been recent influx of orthopteran transcriptomic resources, many use pooled ontogenetic stages obscuring information about changes in gene expression during development. Here we developed a de novo transcriptome spanning 7 stages in the life cycle of the acridid grasshopper Chorthippus biguttulus. Samples from different stages encompassing embryonic development through adults were used for transcriptomic profiling, revealing patterns of differential gene expression that highlight processes in the different life stages. These patterns were validated with semi-quantitative RT-PCR. Embryonic development showed a strongly differentiated expression pattern compared to all of the other stages and genes upregulated in this stage were involved in signaling, cellular differentiation, and organ development. Our study is one of the first to examine gene expression during post-embryonic development in a hemimetabolous insect and we found that only the fourth and fifth instars had clusters of genes upregulated during these stages. These genes are involved in various processes ranging from synthesis of biogenic amines to chitin binding. These observations indicate that post-embryonic ontogeny is not a continuous process and that some instars are differentiated. Finally, genes upregulated in the imago were generally involved in aging and immunity. Our study highlights the importance of looking at ontogeny as a whole and indicates promising directions for future research in orthopteran development.

  5. Chromosomal clustering of a human transcriptome reveals regulatory background

    Directory of Open Access Journals (Sweden)

    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.

  6. Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

    Directory of Open Access Journals (Sweden)

    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.

  7. Whole transcriptome organisation in the dehydrated supraoptic nucleus

    Directory of Open Access Journals (Sweden)

    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.

  8. Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior.

    Directory of Open Access Journals (Sweden)

    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.

  9. Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

    Directory of Open Access Journals (Sweden)

    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.

  10. 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.

  11. and Biomphalaria pfeifferi (Krauss) at constant temperatures

    African Journals Online (AJOL)

    1988-03-16

    Mar 16, 1988 ... lifespan and net reproduction rate of H. dury; were higher than those of B. pfeifferi over the whole range of temperatures ... not itself act as an intermediate host of economically impor- tant parasite .... age-specific birth rate.

  12. 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

  13. Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Arbeitman Michelle N

    2011-07-01

    Full Text Available Abstract Background Understanding animal development and physiology at a molecular-biological level has been advanced by the ability to determine at high resolution the repertoire of mRNA molecules by whole transcriptome resequencing. This includes the ability to detect and quantify rare abundance transcripts and isoform-specific mRNA variants produced from a gene. The sex hierarchy consists of a pre-mRNA splicing cascade that directs the production of sex-specific transcription factors that specify nearly all sexual dimorphism. We have used deep RNA sequencing to gain insight into how the Drosophila sex hierarchy generates somatic sex differences, by examining gene and transcript isoform expression differences between the sexes in adult head tissues. Results Here we find 1,381 genes that differ in overall expression levels and 1,370 isoform-specific transcripts that differ between males and females. Additionally, we find 512 genes not regulated downstream of transformer that are significantly more highly expressed in males than females. These 512 genes are enriched on the × chromosome and reside adjacent to dosage compensation complex entry sites, which taken together suggests that their residence on the × chromosome might be sufficient to confer male-biased expression. There are no transcription unit structural features, from a set of features, that are robustly significantly different in the genes with significant sex differences in the ratio of isoform-specific transcripts, as compared to random isoform-specific transcripts, suggesting that there is no single molecular mechanism that generates isoform-specific transcript differences between the sexes, even though the sex hierarchy is known to include three pre-mRNA splicing factors. Conclusions We identify thousands of genes that show sex-specific differences in overall gene expression levels, and identify hundreds of additional genes that have differences in the abundance of isoform

  14. 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

  15. 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...

  16. 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

  17. 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

  18. 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

  19. 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...

  20. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  2. 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.

  3. A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome.

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    Cristian O Rohr

    Full Text Available Fungi of the genus Pycnoporus are white-rot basidiomycetes widely studied because of their ability to synthesize high added-value compounds and enzymes of industrial interest. Here we report the sequencing, assembly and analysis of the transcriptome of Pycnoporus sanguineus BAFC 2126 grown at stationary phase, in media supplemented with copper sulfate. Using the 454 pyrosequencing platform we obtained a total of 226,336 reads (88,779,843 bases that were filtered and de novo assembled to generate a reference transcriptome of 7,303 transcripts. Putative functions were assigned for 4,732 transcripts by searching similarities of six-frame translated sequences against a customized protein database and by the presence of conserved protein domains. Through the analysis of translated sequences we identified transcripts encoding 178 putative carbohydrate active enzymes, including representatives of 15 families with roles in lignocellulose degradation. Furthermore, we found many transcripts encoding enzymes related to lignin hydrolysis and modification, including laccases and peroxidases, as well as GMC oxidoreductases, copper radical oxidases and other enzymes involved in the generation of extracellular hydrogen peroxide and iron homeostasis. Finally, we identified the transcripts encoding all of the enzymes involved in terpenoid backbone biosynthesis pathway, various terpene synthases related to the biosynthesis of sesquiterpenoids and triterpenoids precursors, and also cytochrome P450 monooxygenases, glutathione S-transferases and epoxide hydrolases with potential functions in the biodegradation of xenobiotics and the enantioselective biosynthesis of biologically active drugs. To our knowledge this is the first report of a transcriptome of genus Pycnoporus and a resource for future molecular studies in P. sanguineus.

  4. Transcriptomic Response of Chinese Yew (Taxus chinensis to Cold Stress

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    Xianghua Yu

    2017-04-01

    Full Text Available Taxus chinensis is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of T. chinensis responds to low temperature is still unknown. To investigate cold response of the genus Taxus, we obtained the transcriptome profiles of T. chinensis grown under normal and low temperature (cold stress, 0°C conditions using Illumina Miseq sequencing. A transcriptome including 83,963 transcripts and 62,654 genes were assembled from 4.16 Gb of reads data. Comparative transcriptomic analysis identified 2,025 differently expressed (DE isoforms at p < 0.05, of which 1,437 were up-regulated by cold stress and 588 were down-regulated. Annotation of DE isoforms indicated that transcription factors (TFs in the MAPK signaling pathway and TF families of NAC, WRKY, bZIP, MYB, and ERF were transcriptionally activated. This might have been caused by the accumulation of secondary messengers, such as reactive oxygen species (ROS and Ca2+. While accumulation of ROS will have caused damages to cells, our results indicated that to adapt to low temperatures T. chinensis employed a series of mechanisms to minimize these damages. The mechanisms included: (i cold-enhanced expression of ROS deoxidant systems, such as peroxidase and phospholipid hydroperoxide glutathione peroxidase, to remove ROS. This was further confirmed by analyses showing increased activity of POD, SOD, and CAT under cold stress. (ii Activation of starch and sucrose metabolism, thiamine metabolism, and purine metabolism by cold-stress to produce metabolites which either protect cell organelles or lower the ROS content in cells. These processes are regulated by ROS signaling, as the “feedback” toward ROS accumulation.

  5. Perspectives on the use of transcriptomics to advance biofuels

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    Siseon Lee

    2015-11-01

    Full Text Available As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.

  6. 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.

  7. Transcriptome and proteome analysis of Eucalyptus infected with Calonectria pseudoreteaudii.

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    Chen, Quanzhu; Guo, Wenshuo; Feng, Lizhen; Ye, Xiaozhen; Xie, Wanfeng; Huang, Xiuping; Liu, Jinyan

    2015-02-06

    Cylindrocladium leaf blight is one of the most severe diseases in Eucalyptus plantations and nurseries. There are Eucalyptus cultivars with resistance to the disease. However, little is known about the defense mechanism of resistant cultivars. Here, we investigated the transcriptome and proteome of Eucalyptus leaves (E. urophylla×E. tereticornis M1), infected or not with Calonectria pseudoreteaudii. A total of 8585 differentially expressed genes (|log2 ratio| ≥1, FDR ≤0.001) at 12 and 24hours post-inoculation were detected using RNA-seq. Transcriptional changes for five genes were further confirmed by qRT-PCR. A total of 3680 proteins at the two time points were identified using iTRAQ technique.The combined transcriptome and proteome analysis revealed that the shikimate/phenylpropanoid pathway, terpenoid biosynthesis, signalling pathway (jasmonic acid and sugar) were activated. The data also showed that some proteins (WRKY33 and PR proteins) which have been reported to involve in plant defense response were up-regulated. However, photosynthesis, nucleic acid metabolism and protein metabolism were impaired by the infection of C. pseudoreteaudii. This work will facilitate the identification of defense related genes and provide insights into Eucalyptus defense responses to Cylindrocladium leaf blight. In this study, a total of 130 proteins and genes involved in the shikimate/phenylpropanoid pathway, terpenoid biosynthesis, signalling pathway, cell transport, carbohydrate and energy metabolism, nucleic acid metabolism and protein metabolism in Eucalyptus leaves after infected with C. pseudoreteaudii were identified. This is the first report of a comprehensive transcriptomic and proteomic analysis of Eucalyptus in response to Calonectria sp. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Construction of coffee transcriptome networks based on gene annotation semantics

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    Castillo Luis F.

    2012-12-01

    Full Text Available Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  9. Transcriptomic analysis of flower development in wintersweet (Chimonanthus praecox).

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    Liu, Daofeng; Sui, Shunzhao; Ma, Jing; Li, Zhineng; Guo, Yulong; Luo, Dengpan; Yang, Jianfeng; Li, Mingyang

    2014-01-01

    Wintersweet (Chimonanthus praecox) is familiar as a garden plant and woody ornamental flower. On account of its unique flowering time and strong fragrance, it has a high ornamental and economic value. Despite a long history of human cultivation, our understanding of wintersweet genetics and molecular biology remains scant, reflecting a lack of basic genomic and transcriptomic data. In this study, we assembled three cDNA libraries, from three successive stages in flower development, designated as the flower bud with displayed petal, open flower and senescing flower stages. Using the Illumina RNA-Seq method, we obtained 21,412,928, 26,950,404, 24,912,954 qualified Illumina reads, respectively, for the three successive stages. The pooled reads from all three libraries were then assembled into 106,995 transcripts, 51,793 of which were annotated in the NCBI non-redundant protein database. Of these annotated sequences, 32,649 and 21,893 transcripts were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 15,587 transcripts onto 312 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at the open flower and senescing flower stages. An analysis of differentially expressed genes involved in plant hormone signal transduction pathways indicated that although flower opening and senescence may be independent of the ethylene signaling pathway in wintersweet, salicylic acid may be involved in the regulation of flower senescence. We also succeeded in isolating key genes of floral scent biosynthesis and proposed a biosynthetic pathway for monoterpenes and sesquiterpenes in wintersweet flowers, based on the annotated sequences. This comprehensive transcriptomic analysis presents fundamental information on the genes and pathways which are involved in flower development in wintersweet. And our data

  10. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L..

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    Chandra Kant

    Full Text Available A hallmark trait of chickpea (Cicer arietinum L., like other legumes, is the capability to convert atmospheric nitrogen (N2 into ammonia (NH3 in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO, Cluster of Orthologous Groups (COG and Kyoto Encyclopedia of Genes and Genomes (KEGG metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.

  11. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

    2016-01-01

    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.

  12. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

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    Cseke Leland J

    2011-05-01

    Full Text Available Abstract Background Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. Results We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. Conclusions The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

  13. The past, present, and future of Leishmania genomics and transcriptomics

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    Cantacessi, Cinzia; Dantas-Torres, Filipe; Nolan, Matthew J.; Otranto, Domenico

    2015-01-01

    It has been nearly 10 years since the completion of the first entire genome sequence of a Leishmania parasite. Genomic and transcriptomic analyses have advanced our understanding of the biology of Leishmania, and shed new light on the complex interactions occurring within the parasite–host–vector triangle. Here, we review these advances and examine potential avenues for translation of these discoveries into treatment and control programs. In addition, we argue for a strong need to explore how disease in dogs relates to that in humans, and how an improved understanding in line with the ‘One Health’ concept may open new avenues for the control of these devastating diseases. PMID:25638444

  14. Transcriptome profiling of tobacco under water deficit conditions

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    Roel C. Rabara

    2015-09-01

    Full Text Available Drought is one of the limiting environmental factors that affect crop production. Understanding the molecular basis of how plants respond to this water deficit stress is key to developing drought tolerant crops. In this study we generated time course-based transcriptome profiles of tobacco plants under water deficit conditions using microarray technology. In this paper, we describe in detail the experimental procedures and analyses performed in our study. The data set we generated (available in the NCBI/GEO database under GSE67434 has been analysed to identify genes that are involved in the regulation of tobacco's responses to drought.

  15. 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.

  16. Transcriptomics and comparative analysis of three antarctic notothenioid fishes.

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    Seung Chul Shin

    Full Text Available For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.

  17. Similarities between Reproductive and Immune Pistil Transcriptomes of Arabidopsis Species.

    Science.gov (United States)

    Mondragón-Palomino, Mariana; John-Arputharaj, Ajay; Pallmann, Maria; Dresselhaus, Thomas

    2017-07-01

    Independent lines of evidence suggest that members from ancient and polymorphic gene families such as defensins and receptor-like kinases mediate intercellular communication during both the immune response and reproduction. Here, we report a large-scale analysis to investigate the extent of overlap between these processes by comparing differentially expressed genes (DEGs) in the pistil transcriptomes of Arabidopsis thaliana and Arabidopsis halleri during self-pollination and interspecific pollination and during infection with Fusarium graminearum In both Arabidopsis species, the largest number of DEGs was identified in infected pistils, where genes encoding regulators of cell division and development were most frequently down-regulated. Comparison of DEGs between infection and various pollination conditions showed that up to 79% of down-regulated genes are shared between conditions and include especially defensin-like genes. Interspecific pollination of A. thaliana significantly up-regulated thionins and defensins. The significant overrepresentation of similar groups of DEGs in the transcriptomes of reproductive and immune responses of the pistil makes it a prime system in which to study the consequences of plant-pathogen interactions on fertility and the evolution of intercellular communication in pollination. © 2017 American Society of Plant Biologists. All Rights Reserved.

  18. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae

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    Samuel E. Fox

    2013-03-01

    Full Text Available Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis, 104,950 (Spain, and 177,682 (Greece transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs and >20,000 simple sequence repeat (SSR DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.

  19. Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface.

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    Bolhuis, Henk; Martín-Cuadrado, Ana Belén; Rosselli, Riccardo; Pašić, Lejla; Rodriguez-Valera, Francisco

    2017-07-03

    Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic square-flattened cells, only 7 isolates are currently known with 2 genomes fully sequenced and annotated due to difficulties to grow them under laboratory conditions. We have performed a transcriptomic analysis of one of these isolates, the Spanish strain HBSQ001 in order to investigate gene transcription under light and dark conditions. Despite a potential advantage for light as additional source of energy, no significant differences were found between light and dark expressed genes. Constitutive high gene expression was observed in genes encoding surface glycoproteins, light mediated proton pumping by bacteriorhodopsin, several nutrient uptake systems, buoyancy and storage of excess carbon. Two low expressed regions of the genome were characterized by a lower codon adaptation index, low GC content and high incidence of hypothetical genes. Under the extant cultivation conditions, the square hyperhalophile devoted most of its transcriptome towards processes maintaining cell integrity and exploiting solar energy. Surface glycoproteins are essential for maintaining the large surface to volume ratio that facilitates light and organic nutrient harvesting whereas constitutive expression of bacteriorhodopsin warrants an immediate source of energy when light becomes available.

  20. Spatial transcriptomes within the Pseudomonas aeruginosa biofilm architecture.

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    Heacock-Kang, Yun; Sun, Zhenxin; Zarzycki-Siek, Jan; McMillan, Ian A; Norris, Michael H; Bluhm, Andrew P; Cabanas, Darlene; Fogen, Dawson; Vo, Hung; Donachie, Stuart P; Borlee, Bradley R; Sibley, Christopher D; Lewenza, Shawn; Schurr, Michael J; Schweizer, Herbert P; Hoang, Tung T

    2017-12-01

    Bacterial cooperative associations and dynamics in biofilm microenvironments are of special interest in recent years. Knowledge of localized gene-expression and corresponding bacterial behaviors within the biofilm architecture at a global scale has been limited, due to a lack of robust technology to study limited number of cells in stratified layers of biofilms. With our recent pioneering developments in single bacterial cell transcriptomic analysis technology, we generated herein an unprecedented spatial transcriptome map of the mature in vitro Pseudomonas aeruginosa biofilm model, revealing contemporaneous yet altered bacterial behaviors at different layers within the biofilm architecture (i.e., surface, middle and interior of the biofilm). Many genes encoding unknown functions were highly expressed at the biofilm-solid interphase, exposing a critical gap in the knowledge of their activities that may be unique to this interior niche. Several genes of unknown functions are critical for biofilm formation. The in vivo importance of these unknown proteins was validated in invertebrate (fruit fly) and vertebrate (mouse) models. We envisage the future value of this report to the community, in aiding the further pathophysiological understanding of P. aeruginosa biofilms. Our approach will open doors to the study of bacterial functional genomics of different species in numerous settings. © 2017 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

  1. Leading edge analysis of transcriptomic changes during pseudorabies virus infection

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    Damarius S. Fleming

    2016-12-01

    Full Text Available Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO (GSE74473 database.

  2. Characterization of gonadal transcriptomes from the turbot (Scophthalmus maximus).

    Science.gov (United States)

    Hu, Yulong; Huang, Meng; Wang, Weiji; Guan, Jiantao; Kong, Jie

    2016-01-01

    The mechanisms underlying sexual reproduction and sex ratio determination remains unclear in turbot, a flatfish of great commercial value. And there is limited information in the turbot database regarding genes related to the reproductive system. Here, we conducted high-throughput transcriptome profiling of turbot gonad tissues to better understand their reproductive functions and to supply essential gene sequence information for marker-assisted selection programs in the turbot industry. In this study, two gonad libraries representing sex differences in Scophthalmus maximus yielded 453 818 high-quality reads that were assembled into 24 611 contigs and 33 713 singletons by using 454 pyrosequencing, 13 936 contigs and singletons (CS) of which were annotated using BLASTx. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that various biological functions and processes were associated with many of the annotated CS. Expression analyses showed that 510 genes were differentially expressed in males versus females; 80% of these genes were annotated. In addition, 6484 and 6036 single nucleotide polymorphisms (SNPs) were identified in male and female libraries, respectively. This transcriptome resource will serve as the foundation for cDNA or SNP microarray construction, gene expression characterization, and sex-specific linkage mapping in turbot.

  3. High-throughput sequencing of black pepper root transcriptome

    Science.gov (United States)

    2012-01-01

    Background Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms. PMID:22984782

  4. Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid

    Directory of Open Access Journals (Sweden)

    Xiaoshen Zhang

    2014-03-01

    Full Text Available Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx. About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.

  5. Transcriptomic Analysis of Young and Old Erythrocytes of Fish

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    Miriam Götting

    2017-12-01

    Full Text Available Understanding gene expression changes over the lifespan of cells is of fundamental interest and gives important insights into processes related to maturation and aging. This study was undertaken to understand the global transcriptome changes associated with aging in fish erythrocytes. Fish erythrocytes retain their nuclei throughout their lifetime and they are transcriptionally and translationally active. However, they lose important functions during their lifespan in the circulation. We separated rainbow trout (Oncorhynchus mykiss erythrocytes into young and old fractions using fixed angle-centrifugation and analyzed transcriptome changes using RNA sequencing (RNA-seq technology and quantitative real-time PCR. We found 930 differentially expressed between young and old erythrocyte fractions; 889 of these showed higher transcript levels in young, while only 34 protein-coding genes had higher transcript levels in old erythrocytes. In particular genes involved in ion binding, signal transduction, membrane transport, and those encoding various enzyme classes are affected in old erythrocytes. The transcripts with higher levels in old erythrocytes were associated with seven different GO terms within biological processes and nine within molecular functions and cellular components, respectively. Our study furthermore found several highly abundant transcripts as well as a number of differentially expressed genes (DEGs for which the protein products are currently not known revealing the gaps of knowledge in most non-mammalian vertebrates. Our data provide the first insight into changes involved in aging on the transcriptional level and thus opens new perspectives for the study of maturation processes in fish erythrocytes.

  6. Functional organization of the transcriptome in human brain

    Science.gov (United States)

    Oldham, Michael C; Konopka, Genevieve; Iwamoto, Kazuya; Langfelder, Peter; Kato, Tadafumi; Horvath, Steve; Geschwind, Daniel H

    2009-01-01

    The enormous complexity of the human brain ultimately derives from a finite set of molecular instructions encoded in the human genome. These instructions can be directly studied by exploring the organization of the brain’s transcriptome through systematic analysis of gene coexpression relationships. We analyzed gene coexpression relationships in microarray data generated from specific human brain regions and identified modules of coexpressed genes that correspond to neurons, oligodendrocytes, astrocytes and microglia. These modules provide an initial description of the transcriptional programs that distinguish the major cell classes of the human brain and indicate that cell type–specific information can be obtained from whole brain tissue without isolating homogeneous populations of cells. Other modules corresponded to additional cell types, organelles, synaptic function, gender differences and the subventricular neurogenic niche. We found that subventricular zone astrocytes, which are thought to function as neural stem cells in adults, have a distinct gene expression pattern relative to protoplasmic astrocytes. Our findings provide a new foundation for neurogenetic inquiries by revealing a robust and previously unrecognized organization to the human brain transcriptome. PMID:18849986

  7. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

    2014-03-14

    Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

  8. De novo transcriptome assembly of Sorghum bicolor variety Taejin

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    Yeonhwa Jo

    2016-06-01

    Full Text Available Sorghum (Sorghum bicolor, also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

  9. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

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    Nagesh A. Kuravadi

    2015-08-01

    Full Text Available Neem (Azadirachta indica A. Juss is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC. Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.

  10. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

    Science.gov (United States)

    Rangiah, Kannan; Mahesh, HB; Rajamani, Anantharamanan; Shirke, Meghana D.; Russiachand, Heikham; Loganathan, Ramya Malarini; Shankara Lingu, Chandana; Siddappa, Shilpa; Ramamurthy, Aishwarya; Sathyanarayana, BN

    2015-01-01

    Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways. PMID:26290780

  11. Application of transcriptomics in Chinese herbal medicine studies

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    Hsin-Yi Lo

    2012-04-01

    Full Text Available Transcriptomics using DNA microarray has become a practical and popular tool for herbal medicine study because of high throughput, sensitivity, accuracy, specificity, and reproducibility. Therefore, this article focuses on the overview of DNA microarray technology and the application of DNA microarray in Chinese herbal medicine study. To understand the number and the objectives of articles utilizing DNA microarray for herbal medicine study, we surveyed 297 frequently used Chinese medicinal herbs listed in Pharmacopoeia Commission of People’s Republic of China. We classified these medicinal herbs into 109 families and then applied PudMed search using “microarray” and individual herbal family as keywords. Although thousands of papers applying DNA microarray in Chinese herbal studies have been published since 1998, most of the articles focus on the elucidation of mechanisms of certain biological effects of herbs. Construction of the bioactivity database containing large-scaled gene expression profiles of quality control herbs can be applied in the future to analyze the biological events induced by herbs, predict the therapeutic potential of herbs, evaluate the safety of herbs, and identify the drug candidate of herbs. Moreover, the linkage of systems biology tools, such as functional genomics, transcriptomics, proteomics, metabolomics, pharmacogenomics and toxicogenomics, will become a new translational platform between Western medicine and Chinese herbal medicine.

  12. High-throughput sequencing of black pepper root transcriptome

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    Gordo Sheila MC

    2012-09-01

    Full Text Available Abstract Background Black pepper (Piper nigrum L. is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

  13. De novo transcriptome assembly of Setatria italica variety Taejin

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    Yeonhwa Jo

    2016-06-01

    Full Text Available Foxtail millet (Setaria italica belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.

  14. De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys

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    Alexey V. Beletsky

    2017-03-01

    Full Text Available Monotropa hypopitys (pinesap is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform. The raw data obtained in this study can be available in NCBI SRA database with accession number of SRP069226. A total of 10.3 GB raw sequence data were obtained, corresponding to 103,357,809 raw reads. A total of 103,025,683 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 98,349 unigens with an N50 of 1342 bp. Using the TransDecoder program, we predicted 43,505 putative proteins. 38,416 unigenes were annotated in the Swiss-Prot protein sequence database using BLASTX. The obtained transcriptomic data will be useful for further studies of the evolution of plant genomes upon transition to a non-photosynthetic lifestyle and the loss of photosynthesis-related functions.

  15. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  16. Influence of Organic Farming on the Potato Transcriptome

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    Daniela Pacifico

    2017-05-01

    Full Text Available Organic agriculture sparks a lively debate on its potential health and environmental benefits. Comparative studies often investigate the response of crops to organic farming through targeted approaches and within a limited experimental work. To clarify this issue, the transcriptomic profile of a cultivar of the potato grown for two years under organic and conventional farming was compared with the profile of an experimental clone grown in the same location of Southern Italy for one year. Transcriptomic raw data were obtained through Potato Oligo Chip Initiative (POCI microarrays and were processed using unsupervised coupling multivariate statistical analysis and bioinformatics (MapMan software. One-hundred-forty-four genes showed the same expression in both years, and 113 showed the same expression in both genotypes. Their functional characterization revealed the strong involvement of the farming system in metabolism associated with the nutritional aspects of organic tubers (e.g., phenylpropanoid, flavonoid, glycoalcaloid, asparagine, ascorbic acid. Moreover, further investigation showed that eight of 42,034 features exhibited the same trend of expression irrespective of the year and genotype, making them possible candidates as markers of traceability. This paper raises the issue regarding the choice of genotype in organic management and the relevance of assessing seasonal conditions effects when studying the effects of organic cultivation on tuber metabolism.

  17. The head-regeneration transcriptome of the planarian Schmidtea mediterranea

    Science.gov (United States)

    2011-01-01

    Background Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. Results To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. Conclusions Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians. PMID:21846378

  18. Transcriptomics and the Mediterranean Diet: A Systematic Review

    Science.gov (United States)

    Herrera-Marcos, Luis V.; Lou-Bonafonte, José M.; Arnal, Carmen; Navarro, María A.; Osada, Jesús

    2017-01-01

    The Mediterranean diet has been proven to be highly effective in the prevention of cardiovascular diseases and cancer and in decreasing overall mortality. Nowadays, transcriptomics is gaining particular relevance due to the existence of non-coding RNAs capable of regulating many biological processes. The present work describes a systematic review of current evidence supporting the influence of the Mediterranean diet on transcriptomes of different tissues in various experimental models. While information on regulatory RNA is very limited, they seem to contribute to the effect. Special attention has been given to the oily matrix of virgin olive oil. In this regard, monounsaturated fatty acid-rich diets prevented the expression of inflammatory genes in different tissues, an action also observed after the administration of olive oil phenolic compounds. Among these, tyrosol, hydroxytyrosol, and secoiridoids have been found to be particularly effective in cell cycle expression. Less explored terpenes, such as oleanolic acid, are important modulators of circadian clock genes. The wide range of studied tissues and organisms indicate that response to these compounds is universal and poses an important level of complexity considering the different genes expressed in each tissue and the number of different tissues in an organism. PMID:28486416

  19. The Transcriptomics of Secondary Growth and Wood Formation in Conifers

    Science.gov (United States)

    Carvalho, Ana; Paiva, Jorge; Louzada, José; Lima-Brito, José

    2013-01-01

    In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality. PMID:24288610

  20. Leading edge analysis of transcriptomic changes during pseudorabies virus infection.

    Science.gov (United States)

    Fleming, Damarius S; Miller, Laura C

    2016-12-01

    Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.

  1. Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers.

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    Yuichi Shiraishi

    Full Text Available Recent studies applying high-throughput sequencing technologies have identified several recurrently mutated genes and pathways in multiple cancer genomes. However, transcriptional consequences from these genomic alterations in cancer genome remain unclear. In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis B virus (HBV-related hepatocellular carcinomas (HCCs and their matched controls. Comparison of whole genome sequence (WGS and RNA-Seq revealed much evidence that various types of genomic mutations triggered diverse transcriptional changes. Not only splice-site mutations, but also silent mutations in coding regions, deep intronic mutations and structural changes caused splicing aberrations. HBV integrations generated diverse patterns of virus-human fusion transcripts depending on affected gene, such as TERT, CDK15, FN1 and MLL4. Structural variations could drive over-expression of genes such as WNT ligands, with/without creating gene fusions. Furthermore, by taking account of genomic mutations causing transcriptional aberrations, we could improve the sensitivity of deleterious mutation detection in known cancer driver genes (TP53, AXIN1, ARID2, RPS6KA3, and identified recurrent disruptions in putative cancer driver genes such as HNF4A, CPS1, TSC1 and THRAP3 in HCCs. These findings indicate genomic alterations in cancer genome have diverse transcriptomic effects, and integrated analysis of WGS and RNA-Seq can facilitate the interpretation of a large number of genomic alterations detected in cancer genome.

  2. 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.

  3. Transcriptome Profiling of Pediatric Core Binding Factor AML.

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    Chih-Hao Hsu

    Full Text Available The t(8;21 and Inv(16 translocations disrupt the normal function of core binding factors alpha (CBFA and beta (CBFB, respectively. These translocations represent two of the most common genomic abnormalities in acute myeloid leukemia (AML patients, occurring in approximately 25% pediatric and 15% of adult with this malignancy. Both translocations are associated with favorable clinical outcomes after intensive chemotherapy, and given the perceived mechanistic similarities, patients with these translocations are frequently referred to as having CBF-AML. It remains uncertain as to whether, collectively, these translocations are mechanistically the same or impact different pathways in subtle ways that have both biological and clinical significance. Therefore, we used transcriptome sequencing (RNA-seq to investigate the similarities and differences in genes and pathways between these subtypes of pediatric AMLs. Diagnostic RNA from patients with t(8;21 (N = 17, Inv(16 (N = 14, and normal karyotype (NK, N = 33 were subjected to RNA-seq. Analyses compared the transcriptomes across these three cytogenetic subtypes, using the NK cohort as the control. A total of 1291 genes in t(8;21 and 474 genes in Inv(16 were differentially expressed relative to the NK controls, with 198 genes differentially expressed in both subtypes. The majority of these genes (175/198; binomial test p-value < 10(-30 are consistent in expression changes among the two subtypes suggesting the expression profiles are more similar between the CBF cohorts than in the NK cohort. Our analysis also revealed alternative splicing events (ASEs differentially expressed across subtypes, with 337 t(8;21-specific and 407 Inv(16-specific ASEs detected, the majority of which were acetylated proteins (p = 1.5 x 10(-51 and p = 1.8 x 10(-54 for the two subsets. In addition to known fusions, we identified and verified 16 de novo fusions in 43 patients, including three fusions involving NUP98 in six

  4. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    Soltis Douglas E

    2009-08-01

    Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

  5. Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

    Directory of Open Access Journals (Sweden)

    Man-Li He

    2016-11-01

    Full Text Available Abstract Background Psoroptic mange is a chronic, refractory, contagious and infectious disease mainly caused by the mange mite Psoroptes ovis, which can infect horses, sheep, buffaloes, rabbits, other domestic animals, deer, wild camels, foxes, minks, lemurs, alpacas, elks and other wild animals. Features of the disease include intense pruritus and dermatitis, depilation and hyperkeratosis, which ultimately result in emaciation or death caused by secondary bacterial infections. The infestation is usually transmitted by close contact between animals. Psoroptic mange is widespread in the world. In this paper, the transcriptome of P. ovis is described following sequencing and analysis of transcripts from samples of larvae (i.e. the Pso_L group and nymphs and adults (i.e. the Pso_N_A group. The study describes differentially expressed genes (DEGs and genes encoding allergens, which help understanding the biology of P. ovis and lay foundations for the development of vaccine antigens and drug target screening. Methods The transcriptome of P. ovis was assembled and analyzed using bioinformatic tools. The unigenes of P. ovis from each developmental stage and the unigenes differentially between developmental stages were compared with allergen protein sequences contained in the allergen database website to predict potential allergens. Results We identified 38,836 unigenes, whose mean length was 825 bp. On the basis of sequence similarity with seven databases, a total of 17,366 unigenes were annotated. A total of 1,316 DEGs were identified, including 496 upregulated and 820 downregulated in the Pso_L group compared with the Pso_N_A group. We predicted 205 allergens genes in the two developmental stages similar to genes from other mites and ticks, of these, 14 were among the upregulated DEGs and 26 among the downregulated DEGs. Conclusion This study provides a reference transcriptome of P. ovis in absence of a reference genome. The analysis of DEGs and

  6. Characterization of the cork oak transcriptome dynamics during acorn development.

    Science.gov (United States)

    Miguel, Andreia; de Vega-Bartol, José; Marum, Liliana; Chaves, Inês; Santo, Tatiana; Leitão, José; Varela, Maria Carolina; Miguel, Célia M

    2015-06-25

    Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. A total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability. To our knowledge this work

  7. Expression of interest: transcriptomics and the designation of conservation units.

    Science.gov (United States)

    Hansen, Michael M

    2010-05-01

    An important task within conservation genetics consists in defining intraspecific conservation units. Most conceptual frameworks involve two steps: (i) identifying demographically independent units, and (ii) evaluating their degree of adaptive divergence. Whereas a plethora of methods are available for delineating genetic population structure, assessment of functional genetic divergence remains a challenge. In this issue, Tymchuk et al. (2010) study Atlantic salmon (Salmo salar) populations using both microsatellite markers and analysis of global gene expression. They show that important gene expression differences exist that can be interpreted in the context of different ecological conditions experienced by the populations, along with the populations' histories. This demonstrates an important potential role of transcriptomics for designating conservation units.

  8. Transcriptome sequencing in prostate cancer identifies inter-tumor heterogeneity

    Directory of Open Access Journals (Sweden)

    Janet Mendonca

    2015-06-01

    Full Text Available Given the dearth of gene mutations in prostate cancer, [1] ,[2] it is likely that genomic rearrangements play a significant role in the evolution of prostate cancer. However, in the search for recurrent genomic alterations, "private alterations" have received less attention. Such alterations may provide insights into the evolution, behavior, and clinical outcome of an individual tumor. In a recent report in "Genome Biology" Wyatt et al. [3] defines unique alterations in a cohort of high-risk prostate cancer patient with a lethal phenotype. Utilizing a transcriptome sequencing approach they observe high inter-tumor heterogeneity; however, the genes altered distill into three distinct cancer-relevant pathways. Their analysis reveals the presence of several non-ETS fusions, which may contribute to the phenotype of individual tumors, and have significance for disease progression.

  9. Transcriptome profiling of mice testes following low dose irradiation

    DEFF Research Database (Denmark)

    Belling, Kirstine C.; Tanaka, Masami; Dalgaard, Marlene Danner

    2013-01-01

    ABSTRACT: BACKGROUND: Radiotherapy is used routinely to treat testicular cancer. Testicular cells vary in radio-sensitivity and the aim of this study was to investigate cellular and molecular changes caused by low dose irradiation of mice testis and to identify transcripts from different cell types...... in the adult testis. METHODS: Transcriptome profiling was performed on total RNA from testes sampled at various time points (n = 17) after 1 Gy of irradiation. Transcripts displaying large overall expression changes during the time series, but small expression changes between neighbouring time points were...... selected for further analysis. These transcripts were separated into clusters and their cellular origin was determined. Immunohistochemistry and in silico quantification was further used to study cellular changes post-irradiation (pi). RESULTS: We identified a subset of transcripts (n = 988) where changes...

  10. Transcriptome Dynamics of Pseudomonas putida KT2440 under Water Stress

    DEFF Research Database (Denmark)

    Gülez, Gamze; Dechesne, Arnaud; Workman, Christopher

    2012-01-01

    Water deprivation can be a major stressor to microbial life in surface and subsurface soil. In unsaturated soils, the matric potential (Ψm) is often the main component of the water potential, which measures the thermodynamic availability of water. A low matric potential usually translates...... into water forming thin liquid films in the soil pores. Little is known of how bacteria respond to such conditions, where, in addition to facing water deprivation that might impair their metabolism, they have to adapt their dispersal strategy as swimming motility may be compromised. Using the pressurized...... porous surface model (PPSM), which allows creation of thin liquid films by controlling Ψm, we examined the transcriptome dynamics of Pseudomonas putida KT2440. We identified the differentially expressed genes in cells exposed to a mild matric stress (–0.4 MPa) for 4, 24, or 72 h. The major response...

  11. Characterisation of the horse transcriptome from immunologically active tissues

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    Joanna Moreton

    2014-05-01

    Full Text Available The immune system of the horse has not been well studied, despite the fact that the horse displays several features such as sensitivity to bacterial lipopolysaccharide that make them in many ways a more suitable model of some human disorders than the current rodent models. The difficulty of working with large animal models has however limited characterisation of gene expression in the horse immune system with current annotations for the equine genome restricted to predictions from other mammals and the few described horse proteins. This paper outlines sequencing of 184 million transcriptome short reads from immunologically active tissues of three horses including the genome reference “Twilight”. In a comparison with the Ensembl horse genome annotation, we found 8,763 potentially novel isoforms.

  12. The transcriptomics of glucocorticoid receptor signaling in developing zebrafish.

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    Dinushan Nesan

    Full Text Available Cortisol is the primary corticosteroid in teleosts that is released in response to stressor activation of the hypothalamus-pituitary-interrenal axis. The target tissue action of this hormone is primarily mediated by the intracellular glucocorticoid receptor (GR, a ligand-bound transcription factor. In developing zebrafish (Danio rerio embryos, GR transcripts and cortisol are maternally deposited into the oocyte prior to fertilization and influence early embryogenesis. To better understand of the molecular mechanisms involved, we investigated changes in the developmental transcriptome prior to hatch, in response to morpholino oligonucleotide knockdown of GR using the Agilent zebrafish microarray platform. A total of 1313 and 836 mRNA transcripts were significantly changed at 24 and 36 hours post fertilization (hpf, respectively. Functional analysis revealed numerous developmental processes under GR regulation, including neurogenesis, eye development, skeletal and cardiac muscle formation. Together, this study underscores a critical role for glucocorticoid signaling in programming molecular events essential for zebrafish development.

  13. [Stimulation of proliferation by carnosine: cellular and transcriptome approaches].

    Science.gov (United States)

    Vishniakova, Kh S; Babizhaev, M A; Aliper, A M; Buzdin, A A; Kudriavtseva, A V; Egorov, E E

    2014-01-01

    Concentration of endogenous dipeptide carnosine in human muscle tissue reaches tens of millimoles. For more than 100 years of research, a lot of data concerning carnosine functions were accumulated, among which anti-aging effects are regarded most important. Heire, effect of carnosine in cell cultures was studied. It has been found that apart from the known action--an increase of the Hayflick limit and morphological rejuvenation--carnosine stimulates cell division in colony-forming assays and in the course of transition of cells to the quiescent state. The analysis of the transcriptome showed that carnosine-induced changes are mainly related to positive regulation of the cell cycle at all levels, from the onset of the DNA synthesis to chromosome condensation. One can suppose that the revealed stimulation of the cell cycle account for the carnosine-induced rejuvenation processes and a high concentration ofcarnosine in muscle tissue is required for the muscle recovery (regeneration) after excess loads.

  14. Geographical, environmental and pathophysiological influences on the human blood transcriptome.

    Science.gov (United States)

    Tabassum, Rubina; Nath, Artika; Preininger, Marcela; Gibson, Greg

    2013-12-01

    Gene expression variation provides a read-out of both genetic and environmental influences on gene activity. Geographical, genomic and sociogenomic studies have highlighted how life circumstances of an individual modify the expression of hundreds and in some cases thousands of genes in a co-ordinated manner. This review places such results in the context of a conserved set of 90 transcripts known as Blood Informative Transcripts (BIT) that capture the major conserved components of variation in the peripheral blood transcriptome. Pathophysiological states are also shown to associate with the perturbation of transcript abundance along the major axes. Discussion of false negative rates leads us to argue that simple significance thresholds provide a biased perspective on assessment of differential expression that may cloud the interpretation of studies with small sample sizes.

  15. Genome interplay in the grain transcriptome of hexaploid bread wheat.

    Science.gov (United States)

    Pfeifer, Matthias; Kugler, Karl G; Sandve, Simen R; Zhan, Bujie; Rudi, Heidi; Hvidsten, Torgeir R; Mayer, Klaus F X; Olsen, Odd-Arne

    2014-07-18

    Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome. Copyright © 2014, American Association for the Advancement of Science.

  16. Transcriptomic landscape of lncRNAs in inflammatory bowel disease

    DEFF Research Database (Denmark)

    Mirza, Aashiq Hussain; Bang-Berthelsen, Claus Heiner; Seemann, Ernst Stefan

    2015-01-01

    -coding genes and microRNAs in modulating the immune responses in IBD. METHODS: In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in 96 colon pinch biopsies (inflamed and non-inflamed) extracted from multiple colonic locations from 45 patients (CD = 13...... differentially expressed lncRNAs, respectively, while in cases of the non-inflamed CD and UC, we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (P-value ... their involvement in the immune response, pro-inflammatory cytokine activity and MHC protein complex. CONCLUSIONS: The lncRNA expression profiling in both inflamed and non-inflamed CD and UC successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional...

  17. Transcriptome datasets of oil palm pathogen Ganoderma boninense

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    Irene Liza Isaac

    2018-04-01

    Full Text Available Ganoderma boninense is known to be the causal agent for basal stem rot (BSR affecting the oil palm industry worldwide thus cumulating to high economic losses every year. Several reports have shown that a compatible monokaryon pair needs to mate; producing dikaryotic mycelia to initiate the infection towards the oil palm. However, the molecular events occurs during mating process are not well understood. We performed transcriptome sequencing using Illumina RNA-seq technology and de novo assembly of the transcripts from monokaryon, mating junction and dikaryon mycelia of G. boninense. Raw reads from these three libraries were deposited in the NCBI database with accession number SRR1745787, SRR1745773 and SRR1745777, respectively.

  18. A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species

    DEFF Research Database (Denmark)

    Andersen, Mikael Rørdam; Vongsangnak, Wanwipa; Panagiotou, Gianni

    2008-01-01

    The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available an Affymetrix GeneChip developed...... data identified 23 genes to be a conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. A promoter analysis of the up-regulated genes in all three species indicates the conserved XInR-binding site to be 5'-GGNTAAA-3'. The composition of the conserved gene......-set suggests that xylose acts as a molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross...

  19. Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana.

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    Yanan Liu

    Full Text Available The Eastern woodchuck (Marmota monax is a classical animal model for studying hepatitis B virus (HBV infection and hepatocellular carcinoma (HCC in humans. Recently, we found that Marmota himalayana, an Asian animal species closely related to Marmota monax, is susceptible to woodchuck hepatitis virus (WHV infection and can be used as a new mammalian model for HBV infection. However, the lack of genomic sequence information of both Marmota models strongly limited their application breadth and depth. To address this major obstacle of the Marmota models, we utilized Illumina RNA-Seq technology to sequence the cDNA libraries of liver and spleen samples of two Marmota monax and four Marmota himalayana. In total, over 13 billion nucleotide bases were sequenced and approximately 1.5 billion clean reads were obtained. Following assembly, 106,496 consensus sequences of Marmota monax and 78,483 consensus sequences of Marmota himalayana were detected. For functional annotation, in total 73,603 Unigenes of Marmota monax and 78,483 Unigenes of Marmota himalayana were identified using different databases (NR, NT, Swiss-Prot, KEGG, COG, GO. The Unigenes were aligned by blastx to protein databases to decide the coding DNA sequences (CDS and in total 41,247 CDS of Marmota monax and 34,033 CDS of Marmota himalayana were predicted. The single nucleotide polymorphisms (SNPs and the simple sequence repeats (SSRs were also analyzed for all Unigenes obtained. Moreover, a large-scale transcriptome comparison was performed and revealed a high similarity in transcriptome sequences between the two marmota species. Our study provides an extensive amount of novel sequence information for Marmota monax and Marmota himalayana. This information may serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the identification and characterization of functional genes that are involved in WHV infection and HCC

  20. Maternal bisphenol a exposure impacts the fetal heart transcriptome.

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    Kalyan C Chapalamadugu

    Full Text Available Conditions during fetal development influence health and disease in adulthood, especially during critical windows of organogenesis. Fetal exposure to the endocrine disrupting chemical, bisphenol A (BPA affects the development of multiple organ systems in rodents and monkeys. However, effects of BPA exposure on cardiac development have not been assessed. With evidence that maternal BPA is transplacentally delivered to the developing fetus, it becomes imperative to examine the physiological consequences of gestational exposure during primate development. Herein, we evaluate the effects of daily, oral BPA exposure of pregnant rhesus monkeys (Macaca mulatta on the fetal heart transcriptome. Pregnant monkeys were given daily oral doses (400 µg/kg body weight of BPA during early (50-100 ± 2 days post conception, dpc or late (100 ± 2 dpc--term, gestation. At the end of treatment, fetal heart tissues were collected and chamber specific transcriptome expression was assessed using genome-wide microarray. Quantitative real-time PCR was conducted on select genes and ventricular tissue glycogen content was quantified. Our results show that BPA exposure alters transcription of genes that are recognized for their role in cardiac pathophysiologies. Importantly, myosin heavy chain, cardiac isoform alpha (Myh6 was down-regulated in the left ventricle, and 'A Disintegrin and Metalloprotease 12', long isoform (Adam12-l was up-regulated in both ventricles, and the right atrium of the heart in BPA exposed fetuses. BPA induced alteration of these genes supports the hypothesis that exposure to BPA during fetal development may impact cardiovascular fitness. Our results intensify concerns about the role of BPA in the genesis of human metabolic and cardiovascular diseases.

  1. Transcriptome and microRNome of Theileria annulata Host Cells

    KAUST Repository

    Rchiad, Zineb

    2016-06-01

    Tropical Theileriosis is a parasitic disease of calves with a profound economic impact caused by Theileria annulata, an apicomplexan parasite of the genus Theileria. Transmitted by Hyalomma ticks, T. annulata infects and transforms bovine lymphocytes and macrophages into a cancer-like phenotype characterized by all six hallmarks of cancer. In the current study we investigate the transcriptional landscape of T. annulata-infected lymphocytes to define genes and miRNAs regulated by host cell transformation using next generation sequencing. We also define genes and miRNAs differentially expressed as a result of the attenuation of a T.annulata-infected macrophage cell line used as a vaccine. By comparing the transcriptional landscape of one attenuated and two transformed cell lines we identify four genes that we propose as key factors in transformation and virulence of the T. annulata host cells. We also identify miR- 126-5p as a key regulator of infected cells proliferation, adhesion, survival and invasiveness. In addition to the host cell trascriptome we studied T. annulata transcriptome and identified the role of ROS and TGF-β2 in controlling parasite gene expression. Moreover, we have used the deep parasite ssRNA-seq data to refine the available T. annulata annotation. Taken together, this study provides the full list of host cell’s genes and miRNAs transcriptionally perturbed after infection with T. annulata and after attenuation and describes genes and miRNAs never identified before as players in this type of host cell transformation. Moreover, this study provides the first database for the transcriptome of T. annulata and its host cells using next generation sequencing.

  2. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

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    Alicia R Martin

    2014-08-01

    Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

  3. Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome.

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    Melody S Clark

    Full Text Available BACKGROUND: The Antarctic krill Euphausia superba is a keystone species in the Antarctic food chain. Not only is it a significant grazer of phytoplankton, but it is also a major food item for charismatic megafauna such as whales and seals and an important Southern Ocean fisheries crop. Ecological data suggest that this species is being affected by climate change and this will have considerable consequences for the balance of the Southern Ocean ecosystem. Hence, understanding how this organism functions is a priority area and will provide fundamental data for life history studies, energy budget calculations and food web models. METHODOLOGY/PRINCIPAL FINDINGS: The assembly of the 454 transcriptome of E. superba resulted in 22,177 contigs with an average size of 492bp (ranging between 137 and 8515bp. In depth analysis of the data revealed an extensive catalogue of the cellular chaperone systems and the major antioxidant proteins. Full length sequences were characterised for the chaperones HSP70, HSP90 and the super-oxide dismutase antioxidants, with the discovery of potentially novel duplications of these genes. The sequence data contained 41,470 microsatellites and 17,776 Single Nucleotide Polymorphisms (SNPs/INDELS, providing a resource for population and also gene function studies. CONCLUSIONS: This paper details the first 454 generated data for a pelagic Antarctic species or any pelagic crustacean globally. The classical "stress proteins", such as HSP70, HSP90, ferritin and GST were all highly expressed. These genes were shown to be over expressed in the transcriptomes of Antarctic notothenioid fish and hypothesized as adaptations to living in the cold, with the associated problems of decreased protein folding efficiency and increased vulnerability to damage by reactive oxygen species. Hence, these data will provide a major resource for future physiological work on krill, but in particular a suite of "stress" genes for studies understanding

  4. Stress-dependent coordination of transcriptome and translatome in yeast.

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    Regula E Halbeisen

    2009-05-01

    Full Text Available Cells rapidly alter gene expression in response to environmental stimuli such as nutrients, hormones, and drugs. During the imposed "remodeling" of gene expression, changes in the levels of particular mRNAs do not necessarily correlate with those of the encoded proteins, which could in part rely on the differential recruitment of mRNAs to translating ribosomes. To systematically address this issue, we have established an approach to rapidly access the translational status of each mRNA in the yeast Saccharomyces cerevisiae by affinity purification of endogenously formed ribosomes and the analysis of associated mRNAs with DNA microarrays. Using this method, we compared changes in total mRNA levels (transcriptome with ribosome associations (translatome after the application of different conditions of cellular stress. Severe stresses, induced by amino acid depletion or osmotic shock, stimulated highly correlated responses affecting about 15% of both total RNA levels and translatome. Many of the regulated messages code for functionally related proteins, thus reflecting logical responses to the particular stress. In contrast, mild stress provoked by addition of Calcofluor-white and menadione altered the translatome of approximately 1% of messages with only marginal effects on total mRNA, suggesting largely uncorrelated responses of transcriptome and translatome. Among these putative translationally regulated messages were most components of the mitochondrial ATPase. Increased polysome associations of corresponding messages and higher mitochondrial ATPase activities upon treatment confirmed the relevance for regulation of this macromolecular complex. Our results suggest the presence of highly sensitive translational regulatory networks that coordinate functionally related messages. These networks are preferentially activated for rapid adaptation of cells to minor environmental perturbations.

  5. Legionella pneumophila transcriptome during intracellular multiplication in human macrophages

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    Sebastien P Faucher

    2011-04-01

    Full Text Available Legionella pneumophila is the causative agent of Legionnaires’ disease, an acute pulmonary infection. L. pneumophila is able to infect and multiply in both phagocytic protozoa, such as Acanthamoeba castellanii, and mammalian professional phagocytes. The best-known L. pneumophila virulence determinant is the Icm/Dot Type IVB secretion system (TFBSS, which is used to translocate more than 150 effector proteins to host cells. While the transcriptional response of Legionella to the intracellular environment of A. castellanii has been investigated, much less is known about the Legionella transcriptional response inside human macrophages. In this study, the transcriptome of L. pneumophila was monitored during exponential and post-exponential phase in rich AYE broth as well as during infection of human cultured macrophages. This was accomplished with microarrays and an RNA amplification procedure called SCOTS to detect small amounts of mRNA from low numbers of intracellular bacteria. Among the genes induced intracellularly are those involved in amino acid biosynthetic pathways leading to L-arginine, L-histidine and L-proline as well as many transport systems involved in amino acid and iron uptake. Gene involved in catabolism of glycerol is also induced during intracellular growth and could be used as a carbon source. The genes encoding the Icm/Dot system are not differentially expressed inside cells compared to control bacteria grown in rich broth, but the genes encoding several translocated effectors are strongly induced. Moreover, we used the transcriptome data to predict previously unrecognized Icm/Dot effector genes based on their expression pattern and confirmed translocation for three candidates. This study provides a comprehensive view of how L. pneumophila responds to the human macrophage intracellular environment.

  6. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum.

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    Zbynek Bozdech

    2003-10-01

    Full Text Available Plasmodium falciparum is the causative agent of the most burdensome form of human malaria, affecting 200-300 million individuals per year worldwide. The recently sequenced genome of P. falciparum revealed over 5,400 genes, of which 60% encode proteins of unknown function. Insights into the biochemical function and regulation of these genes will provide the foundation for future drug and vaccine development efforts toward eradication of this disease. By analyzing the complete asexual intraerythrocytic developmental cycle (IDC transcriptome of the HB3 strain of P. falciparum, we demonstrate that at least 60% of the genome is transcriptionally active during this stage. Our data demonstrate that this parasite has evolved an extremely specialized mode of transcriptional regulation that produces a continuous cascade of gene expression, beginning with genes corresponding to general cellular processes, such as protein synthesis, and ending with Plasmodium-specific functionalities, such as genes involved in erythrocyte invasion. The data reveal that genes contiguous along the chromosomes are rarely coregulated, while transcription from the plastid genome is highly coregulated and likely polycistronic. Comparative genomic hybridization between HB3 and the reference genome strain (3D7 was used to distinguish between genes not expressed during the IDC and genes not detected because of possible sequence variations. Genomic differences between these strains were found almost exclusively in the highly antigenic subtelomeric regions of chromosomes. The simple cascade of gene regulation that directs the asexual development of P. falciparum is unprecedented in eukaryotic biology. The transcriptome of the IDC resembles a "just-in-time" manufacturing process whereby induction of any given gene occurs once per cycle and only at a time when it is required. These data provide to our knowledge the first comprehensive view of the timing of transcription throughout the

  7. Transcriptome of the freshwater amphipod Gammarus pulex hepatopancreas

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    E. Gismondi

    2016-06-01

    Full Text Available So far, ecotoxicological studies used biomarkers of exposure or of effects in order to investigate the impacts of contaminated areas on biota (Peakall, 1994 [6]. However, although these results are important in the ecotoxicological risk assessment, biomarkers are very specific and only provide information on the biological processes or physiological pathways targeted by the biomarkers experimenters choose to test (Monsinjon and Knigge, 2007 [5]. In recent years, proteomics have become a major tool in ecotoxicology, as they provide a global insight into the mechanism of action of pollutants without the need of hypothesis testing or any preconception on the biological processes likely impacted (Gismondi et al., 2015; Trapp et al., 2015 [7]; Truebano, 2016 [8]. However, the analysis of proteomic results is often limited due to the lack of database, especially for non-model organisms, such as Gammarus sp, commonly used as biological model in ecotoxicology (Sornom et al., 2012 [11]; Vellinger et al., 2013 [9]; Gismondi and Thomé, 2014 [1]; Lebrun et al., 2014 [3]. Here, we performed Illumina HiSeq sequencing to total RNA isolated from the hepatopancreas (i.e. detoxification tissue of Gammarus pulex males and females coming from uncontaminated river and contaminated river (e.g. PCB, benzo(apyrene. Approximately 290 M paired-end reads were assembled, filtered and sorted into 39,801 contigs whose 10.878 were similar of proteins available in databases. The assembled contigs could represent a reference hepatopancreas transcriptome for G. pulex, and constitute an important resource for future investigations on the impacts of pollutants on invertebrate biota, since it would improve the understanding of the mechanisms of action involved in toxicity. In addition, the hepatopancreas transcriptome will also allow the identification of new potential biomarkers for the ecotoxicological risk assessments. Assembled contigs were deposited in the European

  8. Comparative genomics and transcriptomics of trait-gene association

    Directory of Open Access Journals (Sweden)

    Pierlé Sebastián

    2012-11-01

    Full Text Available Abstract Background The Order Rickettsiales includes important tick-borne pathogens, from Rickettsia rickettsii, which causes Rocky Mountain spotted fever, to Anaplasma marginale, the most prevalent vector-borne pathogen of cattle. Although most pathogens in this Order are transmitted by arthropod vectors, little is known about the microbial determinants of transmission. A. marginale provides unique tools for studying the determinants of transmission, with multiple strain sequences available that display distinct and reproducible transmission phenotypes. The closed core A. marginale genome suggests that any phenotypic differences are due to single nucleotide polymorphisms (SNPs. We combined DNA/RNA comparative genomic approaches using strains with different tick transmission phenotypes and identified genes that segregate with transmissibility. Results Comparison of seven strains with different transmission phenotypes generated a list of SNPs affecting 18 genes and nine promoters. Transcriptional analysis found two candidate genes downstream from promoter SNPs that were differentially transcribed. To corroborate the comparative genomics approach we used three RNA-seq platforms to analyze the transcriptomes from two A. marginale strains with different transmission phenotypes. RNA-seq analysis confirmed the comparative genomics data and found 10 additional genes whose transcription between strains with distinct transmission efficiencies was significantly different. Six regions of the genome that contained no annotation were found to be transcriptionally active, and two of these newly identified transcripts were differentially transcribed. Conclusions This approach identified 30 genes and two novel transcripts potentially involved in tick transmission. We describe the transcriptome of an obligate intracellular bacterium in depth, while employing massive parallel sequencing to dissect an important trait in bacterial pathogenesis.

  9. Transcriptomic insights into the genetic basis of mammalian limb diversity.

    Science.gov (United States)

    Maier, Jennifer A; Rivas-Astroza, Marcelo; Deng, Jenny; Dowling, Anna; Oboikovitz, Paige; Cao, Xiaoyi; Behringer, Richard R; Cretekos, Chris J; Rasweiler, John J; Zhong, Sheng; Sears, Karen E

    2017-03-23

    From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species. We assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species. Taken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.

  10. Transcriptome analyses of Anguillicola crassus from native and novel hosts

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    Emanuel Heitlinger

    2014-11-01

    Full Text Available Anguillicola crassus is a swim bladder nematode of eels. The parasite is native to the Asian eel Anguilla japonica, but was introduced to Europe and the European eel Anguilla anguilla in the early 1980s. A Taiwanese source has been proposed for this introduction. In the new host in the recipient area, the parasite appears to be more pathogenic. As a reason for these differences, genetically fixed differences in infectivity and development between Taiwanese and European A.crassus have been described and disentangled from plasticity induced by different host environments. To explore whether transcriptional regulation is involved in these lifecycle differences, we have analysed a “common garden”, cross infection experiment, using deep-sequencing transcriptomics. Surprisingly, in the face of clear phenotypic differences in life history traits, we identified no significant differences in gene expression between parasite populations or between experimental host species. From 120,000 SNPs identified in the transcriptome data we found that European A. crassus were not a genetic subset of the Taiwanese nematodes sampled. The loci that have the major contribution to the European-Taiwanese population differentiation show an enrichment of synonymous and non-coding polymorphism. This argues against positive selection in population differentiation. However, genes involved in protein processing in the endoplasmatic reticulum membrane and genes bearing secretion signal sequences were enriched in the set of genes most differentiated between European and Taiwanese A. crassus. These genes could be a source for the phenotypically visible genetically fixed differences between European and Taiwanese A. crassus.

  11. Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses.

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    Jennifer M Fitzpatrick

    2009-11-01

    Full Text Available Novel methods to identify anthelmintic drug and vaccine targets are urgently needed, especially for those parasite species currently being controlled by singular, often limited strategies. A clearer understanding of the transcriptional components underpinning helminth development will enable identification of exploitable molecules essential for successful parasite/host interactions. Towards this end, we present a combinatorial, bioinformatics-led approach, employing both statistical and network analyses of transcriptomic data, for identifying new immunoprophylactic and therapeutic lead targets to combat schistosomiasis.Utilisation of a Schistosoma mansoni oligonucleotide DNA microarray consisting of 37,632 elements enabled gene expression profiling from 15 distinct parasite lifecycle stages, spanning three unique ecological niches. Statistical approaches of data analysis revealed differential expression of 973 gene products that minimally describe the three major characteristics of schistosome development: asexual processes within intermediate snail hosts, sexual maturation within definitive vertebrate hosts and sexual dimorphism amongst adult male and female worms. Furthermore, we identified a group of 338 constitutively expressed schistosome gene products (including 41 transcripts sharing no sequence similarity outside the Platyhelminthes, which are likely to be essential for schistosome lifecycle progression. While highly informative, statistics-led bioinformatics mining of the transcriptional dataset has limitations, including the inability to identify higher order relationships between differentially expressed transcripts and lifecycle stages. Network analysis, coupled to Gene Ontology enrichment investigations, facilitated a re-examination of the dataset and identified 387 clusters (containing 12,132 gene products displaying novel examples of developmentally regulated classes (including 294 schistosomula and/or adult transcripts with no

  12. Sensitive detection of viral transcripts in human tumor transcriptomes.

    Directory of Open Access Journals (Sweden)

    Sven-Eric Schelhorn

    Full Text Available In excess of 12% of human cancer incidents have a viral cofactor. Epidemiological studies of idiopathic human cancers indicate that additional tumor viruses remain to be discovered. Recent advances in sequencing technology have enabled systematic screenings of human tumor transcriptomes for viral transcripts. However, technical problems such as low abundances of viral transcripts in large volumes of sequencing data, viral sequence divergence, and homology between viral and human factors significantly confound identification of tumor viruses. We have developed a novel computational approach for detecting viral transcripts in human cancers that takes the aforementioned confounding factors into account and is applicable to a wide variety of viruses and tumors. We apply the approach to conducting the first systematic search for viruses in neuroblastoma, the most common cancer in infancy. The diverse clinical progression of this disease as well as related epidemiological and virological findings are highly suggestive of a pathogenic cofactor. However, a viral etiology of neuroblastoma is currently contested. We mapped 14 transcriptomes of neuroblastoma as well as positive and negative controls to the human and all known viral genomes in order to detect both known and unknown viruses. Analysis of controls, comparisons with related methods, and statistical estimates demonstrate the high sensitivity of our approach. Detailed investigation of putative viral transcripts within neuroblastoma samples did not provide evidence for the existence of any known human viruses. Likewise, de-novo assembly and analysis of chimeric transcripts did not result in expression signatures associated with novel human pathogens. While confounding factors such as sample dilution or viral clearance in progressed tumors may mask viral cofactors in the data, in principle, this is rendered less likely by the high sensitivity of our approach and the number of biological replicates

  13. Comorbidities, confounders, and the white matter transcriptome in chronic alcoholism.

    Science.gov (United States)

    Sutherland, Greg T; Sheedy, Donna; Sheahan, Pam J; Kaplan, Warren; Kril, Jillian J

    2014-04-01

    Alcohol abuse is the world's third leading cause of disease and disability, and one potential sequel of chronic abuse is alcohol-related brain damage (ARBD). This clinically manifests as cognitive dysfunction and pathologically as atrophy of white matter (WM) in particular. The mechanism linking chronic alcohol intoxication with ARBD remains largely unknown but it is also complicated by common comorbidities such as liver damage and nutritional deficiencies. Liver cirrhosis, in particular, often leads to hepatic encephalopathy (HE), a primary glial disease. In a novel transcriptomic study, we targeted the WM only of chronic alcoholics in an attempt to tease apart the pathogenesis of ARBD. Specifically, in alcoholics with and without HE, we explored both the prefrontal and primary motor cortices, 2 regions that experience differential levels of neuronal loss. Our results suggest that HE, along with 2 confounders, gray matter contamination, and low RNA quality are major drivers of gene expression in ARBD. All 3 exceeded the effects of alcohol itself. In particular, low-quality RNA samples were characterized by an up-regulation of translation machinery, while HE was associated with a down-regulation of mitochondrial energy metabolism pathways. The findings in HE alcoholics are consistent with the metabolic acidosis seen in this condition. In contrast non-HE alcoholics had widespread but only subtle changes in gene expression in their WM. Notwithstanding the latter result, this study demonstrates that significant confounders in transcriptomic studies of human postmortem brain tissue can be identified, quantified, and "removed" to reveal disease-specific signals. Copyright © 2014 by the Research Society on Alcoholism.

  14. Systems toxicology: applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology

    NARCIS (Netherlands)

    Heijne, W.H.M.; Kienhuis, A.S.; Ommen, van B.; Stierum, R.; Groten, J.P.

    2005-01-01

    Toxicogenomics can facilitate the identification and characterization of toxicity, as illustrated in this review