Design, construction and evaluation of a row singulator for saffron flowers

Directory of Open Access Journals (Sweden)

hamed bakhshi

2017-12-01

Full Text Available Separation of stigma from petals is one of the required tasks in saffron production. The mechanical separation of saffron flowers may be performed through the following steps: I singulation of the flowers ii aligning the flowers iii cutting the style (Konje and iv separating the stigma from the petals. Because of the importance of saffron flower separation, a prototype device was constructed in this project for singulating and aligning of saffron flowers, prior to the cutting operation. This device can also be installed to work with other cutting and separating equipment and produce on an industrial scale. A pickup vacuum cylinder was used for singulating the flowers and an inclined V-shaped surface was employed for aligning of saffron flowers. The constructed apparatus was evaluated from the standpoint of singling efficiency and losses. For this purpose, three types of saffron flowers (buds, open short tail and long tail, three rotational speeds of pickup cylinder (6, 12 and 21.5 rpm, three levels of suction (30, 70 and 100 mm Hg, and four different inner diameters of finger’s nozzle (2, 3, 4 and 5 mm were used with three replications. The results of analysis on the constructed device showed that the highest efficiency (75% is observed for short tailopen saffron flowers with 5 mm inner diameter of sucking nozzles, suction of 100 mm Hg and the rotational speed of 6 rpm. To evaluate the performance of flower aligning, 100 saffron flowers with an average length of 5 cm were selected and tested with 5 replications. The average aligning with the correct direction obtained was equal to 84%.

Antiviral Effects of Saffron and its Major Ingredients.

Science.gov (United States)

Soleymani, Sepehr; Zabihollahi, Rezvan; Shahbazi, Sepideh; Bolhassani, Azam

2018-01-01

The lack of an effective vaccine against viral infections, toxicity of the synthetic anti-viral drugs and the generation of resistant viral strains led to discover novel inhibitors. Recently, saffron and its compounds were used to treat different pathological conditions. In this study, we tested the anti-HSV-1 and anti-HIV-1 activities of Iranian saffron extract and its major ingredients including crocin and picrocrocin as well as cytotoxicity in vitro. The data showed that the aqueous saffron extract was not active against HIV-1 and HSV-1 virions at certain doses (i.e., a mild activity), but crocin and picrocrocin indicated significant anti-HSV-1 and also anti-HIV-1 activities. Crocin inhibited the HSV replication at before and after entry of virions into Vero cells. Indeed, crocin carotenoid suppressed HSV penetration in the target cells as well as disturbed virus replication after entry into the cells. Picrocrocin was also effective for inhibiting virus entry and also its replication. This monoterpen aldehyde showed higher anti-HSV effects after virus penetrating in the cells. Generally, these sugar-containing compounds extracted from saffron showed to be effective antiherpetic drug candidates. The recent study is the first report suggesting antiviral activities for saffron extract and its major ingredients. Crocin and picrocrocin could be a promising anti-HSV and anti-HIV agent for herbal therapy against viral infections. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Evaluation of quantitative relationships between saffron yield and nutrition (on farm trial

Directory of Open Access Journals (Sweden)

mohamad ali behdani

2009-06-01

Full Text Available In order to relate production of saffron and utilization of nutrients, a study was conducted in 2001 and 2002. Four selected locations for this study were Birjand, Gonabad, Qaen and Torbat-Haydariah, which are the main saffron production centers in Iran. This study was performed in 160 saffron farms, aged between 1 and 5 years. Manure, nitrogen and phosphorous fertilizers showed a positive linear relation with yield and length of flowering, while nitrogen and phosphorous showed a negative linear relation with start of flowering period. Yield of saffron showed a significant and positive correlation with the amount of applied manure and the saffron farms with age 4-5 year had highest yield. Our results showed that manure was the most effective factor in production of saffron. The beneficial effects of manure could be due to slow release of nutrients and enhancing soil physical properties. Stepwise regression analysis of yield and fertilizer application showed that 67 percent of yield variations was attributed to manure and phosphorous application.

Razi’s Al-Hawi and saffron (Crocus sativus: a review

Directory of Open Access Journals (Sweden)

Hamid Mollazadeh

2015-12-01

Full Text Available Traditional knowledge can be used as a source for development of new medicines. In the present study, we compare the data on saffron in Razi's Al-Hawi book with modern scientific studies. A computerized search of published articles was performed using MEDLINE, Scopus as well as native references. The search terms used were saffron, Crocus sativus, crocetin, crocin, safranal, Razi, and Al-Hawi. A variety of properties of saffron including diuretic, analgesic, anti-inflammatory, hepatoprotective, appetite suppressant, hypnotic, antidepressant, and bronchodilator effects were mentioned in Al-Hawi. Modern studies also confirmed most of these characteristics. This review indicates that the pharmacological data on saffron and its constituents are similar to those found in Razi’s Al-Hawi monograph and it can be concluded that ethnobotanical information and ancient sources have precious data about medicinal plants that lead to finding new compounds for treatment of several diseases.

Some reasons for saffron yield loss over the last 30 years period (Review Article

Directory of Open Access Journals (Sweden)

Alireza Koocheki

2017-06-01

Full Text Available Saffron (Crocus sativus L. is a perennial plant which grows basically in arid and semi-arid regions of Iran. Despite saffron’s adaptation to these regions, the assessment of changes in cultivation area over the last 30 years reveals that cultivation of this crop has sharply increased. According to the available statistics, there are 21 provinces where saffron is cultivated on about 84,000 hectares of land. Nonetheless, saffron yield per unit area has aggressively fallen from 5.1 kg ha-1 in 1982 to 3.2 kg ha-1 in 2015. Saffron yield loss can be caused by several factors, such as mismanagement in agriculture section, economics and post-harvest processing as well as the recent droughts. Lack of attention to these factors could lead to further decline in saffron yield in the future. The saffron yield loss over the last 30 years is an alert for saffron-related institutions such as the universities, research centers and Agricultural Research, Education and Extension Organization (AREEO to pay more attention to this crop and prepare more comprehensive programs. In developing these programs, the importance of government policies for planning and approving enough budget is to be highlighted. In this review, first we focus on the reasons for saffron yield loss during the last 30 years and then we try to provide some solutions in relation to these reasons.

Determining the Most Important Soil Properties Affecting the Yield of Saffron in the Ghayenat Area

Directory of Open Access Journals (Sweden)

amir ranjbar

2016-02-01

Full Text Available Introduction: Saffron is one of the most important economic plants in the Khorasan province. Awareness of soil quality in agricultural lands is essential for the best management of lands and for obtaining maximum economic benefit. In general, plant growth is a function of environmental factors especially chemical and physical properties of soil (20. It has been demonstrated that there was a positive and high correlation between soil organic matter and saffron yield. Increasing the yield of saffron due to organic matter is probably due to soil nutrient, especially phosphorous and nitrogen and also improvement of soil physical quality (6, 28, 29. The yield of saffron in soils with high nitrogen as a result of vegetative growth is high (8. Shahandeh (6 found that most of the variation of saffron yield depends on soil properties. Due to the economic importance of saffron and the role of soil properties on saffron yield, this research was conducted to find the relationship between saffron yield and some soil physical and chemical properties, and to determine the contribution of soil properties that have the greatest impact on saffron yield in the Ghayenat area. Materials and Methods: This research was performed in 30 saffron fields (30 soil samples of the Ghayenat area (longitude 59° 10΄ 10.37˝ - 59° 11΄ 38.41˝ and latitude 33° 43΄ 35.08˝ - 33΄ 44΄ 02.78˝, which is located in the Khrasan province of Iran. In this research, 21 soil properties were regarded as the total data set (TDS. Then the principal component analysis (PCA was used to determine the most important soil properties affecting saffron yield as a minimum data set (MDS and the stepwise regression to estimate saffron yield. To estimate the yield of saffron in stepwise regression method, saffron yield was considered as a dependent variable and soil physical and chemical properties were considered to be independent variables. Results and Discussion: According to the PCA method

Comparison of chemical inputs consumption in saffron and wheat fields in Qaenat region

Directory of Open Access Journals (Sweden)

Fatemeh Yaghoubi

2014-09-01

Full Text Available Commercialization of agricultural operations and use of pesticides and chemical fertilizers in agricultural production has been created serious environmental impacts. Due to this issue and in order to assess the amount of chemical fertilizer and pesticide inputs in saffron and wheat production systems, a study was conducted in Qaenat region (South Khorasan province, 50 wheat fields and 48 saffron fields were investigated during 2011-12. The results showed that average nitrogen fertilizer consumption was 222.38 and 57.83 kg.ha-1 in wheat and saffron production systems, respectively, which from sstatistically point of view the difference was significant. In addition, unlike wheat, the use of pesticides very low in saffron cultivation and in many saffron farms it was zero. Therefore, the results can be considered saffron is an healthier product and have greater potential to organic product. Also, the amounts of nitrogen, phosphorus and potassium fertilizers which were using in wheat in the study area were significantly different with recommended values. While in saffron production there was no significant difference between the values of consumed and recommended. Therefore, it seems, performing soil testing in each region and providing appropriate fertilizer formulas and required promotional-educational services in this regard, and raising public awareness is a good strategy for reducing the use of chemical inputs.

Determination of antioxidant activity of saffron taken from the flower ...

African Journals Online (AJOL)

In this study, we determined the total polyphenols content in the Lebanese saffron and the antioxidant effects of different extracts from this saffron in vitro using electrolysis of physiological solution for generation of free radicals (FR) in the presence of colorimetric indicator N,N-di-ethyl-P-phenylenedialanine; the absorbance ...

Saffron (Crocus sativus L., a monomorphic or polymorphic species?

Directory of Open Access Journals (Sweden)

Zahra Nemati

2014-07-01

Full Text Available Saffron (Crocus sativus L. which contains exceptional anti-cancer properties is presently the world's most expensive spice. Iran is known as the original habitat of Crocus L. and a significant source of high-quality cultivated saffron production and export. Considering the importance of this species, we used 27 microsatellite markers to assess molecular variability and discriminating capacity of markers regarding their effectiveness in establishing genetic relationships in Iranian Crocus ecotypes. Thirty eight Iranian cultivated saffron ecotypes and 29 wild allies were evaluated in this research. The results from molecular analyses, including a molecular phylogenetic network and RB analysis, revealed two major groups and five subgroups, regardless of their geographical origins. Also, the results showed a clear distinction between C. sativus and other species of Crocus genus, taking into account their close relationship with C. speciosus and C. hausknechtii, which are assumed to be the two closest relatives of Iranian cultivated saffron among species studied. In this paper, we observed for the first time extensive genetic diversity among Iranian C. sativus despite their asexual reproduction. Considering suitable climatic conditions in Iran for cultivating saffron and the country’s leading high-quality production of Crocus sativus worldwide, studies on great genetic variability among Iranian C. sativus ecotypes as well as wild relatives native to Iran will further highlight the value of this crop. In addition, our results provide valuable information for genetic improvement, reduction of strong genetic erosion, and conservation of costly heritable resources of C. sativus in future breeding programs.

Genetic and Epigenetic Approaches for the Possible Detection of Adulteration and Auto-Adulteration in Saffron (Crocus sativus L. Spice

Directory of Open Access Journals (Sweden)

Giovanna Soffritti

2016-03-01

Full Text Available Saffron (Crocus sativus L. is very expensive and, because of this, often subject to adulteration. Modern genetic fingerprinting techniques are an alternative low cost technology to the existing chemical techniques, which are used to control the purity of food products. Buddleja officinalis Maxim, Gardenia jasminoides Ellis, Curcuma longa L., Carthamus tinctorius L. and Calendula officinalis L. are among the most frequently-used adulterants in saffron spice. Three commercial kits were compared concerning the ability to recover PCR-grade DNA from saffron, truly adulterated samples and possible adulterants, with a clear difference among them, mainly with the processed samples. Only one of the three kits was able to obtain amplifiable DNA from almost all of the samples, with the exception of extracts. On the recovered DNA, new markers were developed based on the sequence of the plastid genes matK and rbcL. These primers, mainly those developed on matK, were able to recognize saffron and the adulterant species and also in mixtures with very low percentages of adulterant. Finally, considering that the addition of different parts of saffron flowers is one of the most widespread adulterations, by analyzing the DNA of the different parts of the flower (styles, stamens and tepals at the genetic and epigenetic level, we succeeded in finding differences between the three tissues that can be further evaluated for a possible detection of the kind of fraud.

Effect of saffron (Crocus sativus L.) enrichment on antioxidant and sensorial properties of wheat flour pasta.

Science.gov (United States)

Armellini, R; Peinado, I; Pittia, P; Scampicchio, M; Heredia, A; Andres, A

2018-07-15

Saffron, used in cookery as a flavouring and colouring agent, is well-known for its antioxidant and beneficial health properties. In the present work, the effect of saffron addition (0-control, 0.1, 0.2 and 0.4%, w/w) in the formulation of fresh pasta was evaluated on textural, physical-chemical, and sensory properties of the cooked product. Content and retention of the bioactive molecules of saffron (crocins) were evaluated by HPLC along with the corresponding antioxidant activity of enriched pasta. The presence of saffron significantly influenced textural and physical-chemical properties of pasta. Higher saffron concentrations enhanced the antioxidant activity of pasta with the higher values of crocins in samples enriched with 0.4% saffron extract even after 3 min of cooking (4.23-5.06 mg/g db). Sensory analysis showed an increased acceptability of the saffron enriched pasta for all descriptors selected (visual aspect, colour, aroma, taste, chewiness, hardness, gumminess and overall acceptability). Copyright © 2018 Elsevier Ltd. All rights reserved.

A Comprehensive Look at Nitrogen and Phosphorus Use Efficiency in Saffron (Crocus Sativus L.

Directory of Open Access Journals (Sweden)

Alireza Koocheki

2016-08-01

Full Text Available Saffron (Crocus sativus L. is an annual plant from a biological aspect, but it has a perennial cycle in the field conditions. Cytological impairments such as triploid and self-incompatibility mechanisms are considered as the most important reasons for male-sterility in saffron. Therefore, saffron reproduction is made by meristems tissues and establishment of new daughter corms which are produced by the mother corms. During the growing season, mother corms deteriorate gradually with increasing daughter corms growth. Each daughter corm is considered as a mother corm for replanting in the next growing season. Duo to the life cycle of saffron as a perennial plant in the field conditions, the gradual deterioration of mother corms during the growing season and also the remobilization of nitrogen and phosphorus from aerial part to daughter corms at the end of each growing season, the study of acquisition and use efficiency of nitrogen and phosphorus in saffron is more complicated than other annual or biannual plants. Firstly, the objective of this review article is to describe the nitrogen and phosphorus concentration in aerial parts and daughter corms in saffron. In addition, relevant literature related to the most important strategies for improving nitrogen and phosphorus use efficiency is reviewed. Secondly, the relationship between nitrogen and phosphorus use efficiency in saffron is discussed.

Therapeutic effects of saffron (Crocus sativus L. in digestive disorders: a review

Directory of Open Access Journals (Sweden)

Alireza Rezaee Khorasany

2016-05-01

Full Text Available Saffron, the dried red-orange stigmas of Crocus sativus L, has been known as a flavoring agent, food coloring and traditional herbal medicine. Pharmacological effects of saffron are mainly attributed to crocin, crocetin, picrocrocin and safranal. These components especially crocin, have significant effects including antidepressant and anticonvulsant, analgesic, anti-cancer and other therapeutic effects on different parts of our body namely cardiovascular, immune, respiratory, genital-urinary and central nervous system. According to the reports and findings, saffron plays a key role to cure different digestive system disorders via chemopreventive, inhibition of cell proliferation, induction of apoptosis, antioxidant effects and radical scavenging, genoprotective property, prevention of lipid peroxidation and anti-inflammatory processes. The outcome of the above mentioned mechanisms shows potential therapeutic properties of saffron against liver cancer, hepatotoxicity, fatty liver, hyperlipidemia, stomach cancer, peptic ulcer, colon cancer, ulcerative colitis, diabetes and pancreas cancer and ileum contractions. According to global statistics, the susceptibility to intestinal diseases is considered as a significant matter and can be important in health planning in any community. Several strategies for treatment and prevention of the digestive system diseases have provided that the use of herbal remedies seems effective and useful. Considering the available findings, the present study aims to introduce saffron as a prophylactic and therapeutic agent against gastrointestinal tract disorders. However, further clinical studies seem necessary in various aspects of saffron effects in different parts of body to verify these findings.

Crocus sativus L. (saffron for cancer chemoprevention: A mini review

Directory of Open Access Journals (Sweden)

Prasan R. Bhandari

2015-04-01

Full Text Available Cancer is one of the most feared diseases globally and there has been a sustained rise in its incidence in both developing and developed countries. Despite the growing therapeutic options for patients with cancer, their efficacy is time-limited and non-curative. Hence to overcome these drawbacks, an incessant screening for superior and safer drugs has been ongoing for numerous decades, resulting in the detection of anti-cancer properties of several phytochemicals. Chemoprevention using readily available natural substances from vegetables, fruits, herbs and spices is one of the significantly important approaches for cancer prevention in the present era. Among the spices, Crocus sativus L. (saffron; 番紅花 fān hóng huā has generated interest because pharmacological experiments have established numerous beneficial properties including radical scavenging, anti-mutagenic and immuno-modulating effects. The more powerful components of saffron are crocin, crocetin and safranal. Studies in animal models and with cultured human malignant cell lines have demonstrated antitumor and cancer preventive activities of saffron and its main ingredients. This review provides a brief insight into the anticancer properties of saffron and its components.

Evaluation of saffron (Crocus sativus L.) adulteration with plant adulterants by (1)H NMR metabolite fingerprinting.

Science.gov (United States)

Petrakis, Eleftherios A; Cagliani, Laura R; Polissiou, Moschos G; Consonni, Roberto

2015-04-15

In the present work, a preliminary study for the detection of adulterated saffron and the identification of the adulterant used by means of (1)H NMR and chemometrics is reported. Authentic Greek saffron and four typical plant-derived materials utilised as bulking agents in saffron, i.e., Crocus sativus stamens, safflower, turmeric, and gardenia were investigated. A two-step approach, relied on the application of both OPLS-DA and O2PLS-DA models to the (1)H NMR data, was adopted to perform authentication and prediction of authentic and adulterated saffron. Taking into account the deficiency of established methodologies to detect saffron adulteration with plant adulterants, the method developed resulted reliable in assessing the type of adulteration and could be viable for dealing with extensive saffron frauds at a minimum level of 20% (w/w). Copyright © 2014 Elsevier Ltd. All rights reserved.

Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments.

Science.gov (United States)

Fancello, Francesco; Petretto, Giacomo; Sanna, Maria Lina; Pintore, Giorgio; Lage, Mounira; Zara, Severino

2018-05-20

Saffron may be spoiled by a variety of microorganisms during cultivation, harvesting, and post harvesting. As saffron can be dried and stored in different ways, this preliminary study explored the natural microbiota present in Moroccan saffron when subjected to different drying techniques. An analysis of the carotenoid-derived volatiles present in the saffron was also carried out. The culturable microbiota of the saffron samples dried using different methods, namely in the shade (also called natural), in the sun, or in the oven, were studied using classical and molecular approaches. The effect of the drying methods on head-space chemical volatiles was also determined. Eighty-two isolates grown in the different culture media were chosen from the colonies, and genotype analysis grouped the microorganisms into 58 clusters, revealing a wide diversity. Out of the 82 isolates, 75 belonged to the Bacillaceae family. The other isolates were distributed within the Dietziaceae, Paenibacillaceae and Carnobacteriaceae families. The dominant species was Bacillus simplex, which was detected in all samples, regardless of the drying method used. Lysinibacillus macroides was dominant in the sun-dried saffron. No pathogens were isolated, but an isolate belonging to Dietzia maris, a potential human pathogenic species, was detected. The biodiversity indexes were linked to the drying method and generally decreased as the intensity of the treatment increased. The results of this preliminary work show that the different drying methods strongly influenced the microbiota and affect the saffron volatile profile. Further analysis will be needed to determine possible effects of selected microbiota on saffron volatiles. Copyright © 2018 Elsevier B.V. All rights reserved.

Ranking factors affecting the packing of saffron from the perspective of consumers

Directory of Open Access Journals (Sweden)

Arash Dorandish

2017-06-01

Full Text Available Packaging is a tool for recognition and differentiation of product and it plays a crucial role in consumers' purchasing decisions, and it can be used to create competitive advantages. Saffron is one of the most important agricultural crops in Iran and its packaging in accordance with consumer demand increases sales and satisfaction of the consumers. Therefore, the main objective of this study is to rank the factors affecting the packaging from the perspective of consumers of saffron in Mashhad. Data was collected in the form of 99 questionnaires that have been answered by the consumers of saffron in Mashhad in 2015. Analytic hierarchy process (AHP was used to rank these factors. The results showed that labeling information about internal and international standards and saffron nutrients on the package have the greatest impact on consumer preferences. Also, the results of the ranking alternatives indicated that attention to the brand labelled on the packing is the most important issue from the perspective of the consumers. Hence, labelling information elements on the package can be a good way for brand differentiation and increasing its value. According to the results, it is recommended that producers and suppliers of saffron pay more attention to features and information elements in package design.

Hormone and Microorganism Treatments in the Cultivation of Saffron (Crocus Sativus L. Plants

Directory of Open Access Journals (Sweden)

Aynur Ozkul Acikgoz

2008-05-01

Full Text Available The difficult cultivation of the saffron plant (Crocus Sativus L. make the spice of the same name made from its dried stigmas very valuable. It is estimated that some 75,000 blossoms or 225,000 hand-picked stigmas are required to make a single pound of saffron, which explains why it is the world’s most expensive spice. The aim of this study was to identify ways of increasing the fertility and production of saffron. For this purpose, the treatment of saffron bulbs with a synthetic growth hormone – a mixture of Polystimulins A6 and K – and two different microorganism based materials – biohumus or vermicompost and Effective Microorganisms™ (EM – in four different ways (hormone alone, biohumus alone, EM alone and EM+biohumus was investigated to determine whether these treatments have any statistically meaningful effects on corms and stigmas. It has been shown that EM + biohumus was the most effective choice for improved saffron cultivation.

Determining Suitable Places for Saffron Planting Using Fuzzy Hierarchical Analysis Process in the City of Torbat Heydarieh

Directory of Open Access Journals (Sweden)

Mahdieh Rashid Sorkhabadi

2016-01-01

Full Text Available The city of Torbat Heydarieh located in the central Khorasan is the largest producer of saffron in the world. According to the influence of various environmental factors on the growth and yield of saffron, the process of assessing land ratio for its cultivation requires the use of various detailed spatial and descriptive pieces of information. In this study, first the conditions of cultivating saffron have been studied in detail and suitable regions for planting saffron have been identified using maps of elevation, slope, soil characteristics, water and some climatic factors influencing the cultivation of saffron including effective threshold temperature, rainfall and sunshine hours. For this purpose, Fuzzy Analytical Hierarchy Process (FAHP method was applied and modeling and spatial analysis were carried out using Arc GIS software environment based on the lands of the city of Torbat Heydarieh which were evaluated for their suitability for cultivation of saffron. It is worth noting that the final map showed that 43 percent of the central parts of Torbat Heydarieh have the highest potential for saffron cultivation. To evaluate the results and ensure the accuracy of the final map data, plant functions and crop qualities were compared with obtained data from final maps and the accuracy of the results was confirmed that shows the effectiveness of Fuzzy Analytical Hierarchy Process (FAHP method  in assessing the potential of lands for saffron cultivation.

On the Traceability of Commercial Saffron Samples Using 1H-NMR and FT-IR Metabolomics

Directory of Open Access Journals (Sweden)

Roberto Consonni

2016-02-01

Full Text Available In previous works on authentic samples of saffron of known history (harvest and processing year, storage conditions, and length of time some biomarkers were proposed using both FT-IR and NMR metabolomics regarding the shelf life of the product. This work addresses the difficulties to trace back the “age” of commercial saffron samples of unknown history, sets a limit value above which these products can be considered substandard, and offers a useful tool to combat saffron mislabeling and fraud with low-quality saffron material. Investigations of authentic and commercial saffron samples of different origin and harvest year, which had been stored under controlled conditions for different lengths of time, allowed a clear-cut clustering of samples in two groups according to the storage period irrespectively of the provenience. In this respect, the four-year cut off point proposed in our previous work assisted to trace back the “age” of unknown samples and to check for possible mislabeling practices.

Saffron: a promising natural medicine in the treatment of metabolic syndrome.

Science.gov (United States)

Razavi, Bibi Marjan; Hosseinzadeh, Hossein

2017-04-01

Metabolic syndrome is a disorder which encompasses obesity, high blood glucose, high cholesterol levels and high blood pressure. Moreover, metabolic syndrome is considered as the most important risk factor for cardiovascular disease (CVD). CVD is the leading cause of mortality in the world for both men and women. Several chemical drugs are available to treat metabolic risk factors, but because of the safety, efficacy, cultural acceptability and lesser side effects, nowadays herbal therapy has a critical role in the treatment of these CVD risk factors. Crocus sativus L. (saffron) is a perennial herb that belongs to the Iridaceae family. Saffron is an extensively used food additive for its colour and taste and has been widely used in traditional as well as modern medicine to treat several illnesses including cardiovascular diseases. Most of the unique properties of this plant are attributed to the presence of three major components, including crocin, safranal and crocetin. It has been proved that saffron has an important role in the management of metabolic syndrome because of its marvelous activities including anti-diabetic, anti-obesity, hypotensive and hypolipidaemic properties. In this review article, we discuss the beneficial properties of saffron and its active components to treat different components of metabolic syndrome and most relevant animal and human studies regarding the use of this plant in cardiovascular disease, with focus on the metabolic risk factors. This review also suggests that after randomised clinical trials, saffron may be implicated as a preventive or therapeutic agent against metabolic syndrome. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Extraction and Determination of Crocin in Saffron Samples by Dispersive Liquid-Liquid Microextraction

Directory of Open Access Journals (Sweden)

Somayeh Heydari

2016-11-01

Full Text Available The main component responsible for color in saffron is crocin with the chemical formula of C44H64O24. Crocin is one of several carotenoids in nature that is soluble in water. This solubility is one of the reasons for its widespread usage as a colorant in food and medicine compared to other carotenoids. The coloring strength of saffron is one of the major factors that determine the quality of the saffron stigma. It will be evaluated with measuring of crocin. Microextraction is the newest and easiest method that can be successfully applied for the preconcentration and separation of crocin in saffron samples. The advantages of this method are faster, cheaper and easier analysis by UV-Vis spectrophotometry in measurement of crocin compared to the chromatographic analysis methods. The studies showed that the type and volume of disperser and extractant solvent have a significant effect on the efficiency of crocin extraction. In this work, acetone as the disperser solvent and dichlorometane as the extractant solvent were found to be suitable combinations. Under the optimal conditions, the calibration curve was linear in the range of 0.15-0.00001 μg mL-1 and the limit of detection (LOD was calculated based on 3 Sb/m (where, Sb and m are the standard deviation of the blank and slop ratio of the calibration curve respectively was 0.000008 μg mL-1. The procedure was applied to saffron samples and the good recovery percent for the saffron samples was obtained.

Latent potyvirus infections in Crocus sativus artwrightianus: an underestimated problem in saffron?

Directory of Open Access Journals (Sweden)

Maria GRILLI CAIOLA

2011-09-01

Full Text Available Normal 0 14 false false false IT X-NONE X-NONE MicrosoftInternetExplorer4 In over two decades, while studying saffron reproductive biology, we frequently found ultrastructural alterations typical of potyvirus infection in stigmas, styles and leaves of Crocus sativus (saffron and C. cartwrightianus (wild and ornamental species, a putative ancestor of saffron from different provenance. This suggests that these viruses are widely diffused in cultivated Crocus spp., possibly causing latent infections. The few data found in literature, while highlighting the general lack of attention given by plant virologists to Crocus spp., nevertheless confi rm that potyviruses, particularly Bean yellow mosaic virus (BYMV, can cause asymptomatic infections in these host species. The reasons and possible implications of widely distributed potyvirus latent infections in Crocus spp. are reported and discussed, with the aim of increasing general awareness of these viruses, and of encouraging sanitary selection programs focused on saffron, that could improve the quantity and quality of yields of the most expensive spice commodity grown.

Effects of auxin and copper on growth of saffron

Directory of Open Access Journals (Sweden)

Mozafar Sharifi

2014-03-01

Full Text Available Saffron is known as one of the most common spices and medicinal plant in the world. Little information is available on the effects of copper and growth regulators on morphological characteristics of saffron. The aim of this study was to evaluate the influence of different concentrations of copper and auxin on morphological properties of root and leaf of saffron. This study was arranged as a factorial experiment in greenhouse condition and in hydroponic system. Copper was used in copper sulfate (CuSO4 form (0, 0.02, 0.1 and 0.2 mg/L and auxin in naphthalene acetic acid (NAA form (0, 1 and 2 g/L. Results showed that interaction of Naphthalene acetic acid 1 g/L and copper sulfate 0.1 mg/L increased root number, as well as root and leaf dry weight. Furthermore, naphthalene acetic acid 1 and 2 g/L in most treatments reduced the number of buds. Copper concentration of corm was increased in 0.2 mg/L copper sulfate.

Effect of climatic factors affecting saffron using analytic hierarchy process(AHP; (Case Study Roshtkhar Region, Iran

Directory of Open Access Journals (Sweden)

Saeid Kamyabi

2014-06-01

Full Text Available The present paper aimed to determine the criteria for understanding climate and ranking factors influencing saffron and assess its impact on Roshtkhoar city of Khorasan Razavi province. The city of Roshtkhar has potential for increasing saffron cultivation; therefore, the main hypothesis during the research was, which climatic factors had the most influence on the cultivation of saffron in the city Roshtkhar. The research methodology was based on a period of ten years cross-sectional data collected from meteorological stations in the studied area. In this study, with taking into account of climatic factors affecting the cultivation of saffron, Analytical Hierarchy Process (AHP method was used to prioritize rural and regional municipalities Roshtkhar cultivated land. Research process included data collection, analysis, statistical analysis, data entry software Expert choice, clustering and selection criteria, and integrating information. The results showed that, among environmental factors, precipitation index (0.281 and temperature coefficient (0.137 had the greatest impact in saffron cultivation. Water resources and evaporation of water had the lowest score in the survey accounted. In the municipalities of the city, Hossein-Abad districts had favorable conditions for growing saffron.

The Effect of Increased Temperature on Flowering Behaviour of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

A. Koocheki

2011-01-01

Full Text Available Abstract Flowering in saffron requires a period of incubation at high temperatures for flower differentiation followed by a period of low temperatures for flower emergence. Global warming could adversely affect the flowering of saffron because of its high sensitivity to temperature. Flowering behaviour of saffron in response to rising temperature was studied in an experiment conducted in controlled environment. Corms with identical sizes were collected form green or fully withered field grown plants and sown in plastic pots. Pots were incubated in 25, 27 and 30 °C for 70, 90 and 120 days. By the end of each incubation period, pots incubated in 25, 27 and 30 °C were transferred to 17, 19 and 21 °C, respectively. Days to flowering, development rate and growth characteristics of saffron were measured in alternative temperature regimes of 25/17, 27/19 and 30/21 °C in combination with 3 incubation periods and in 3 replications. The results indicated that increasing incubation temperature up to 27 °C had no significant effects on saffron flowering behaviour however, no flower was appeared from corms incubated in 30°C. Increased duration of incubation period had adverse effects on flower emergence and corms incubated for 120 days were only flowered in 27/19 °C temperature regime. The optimal flowering response and the highest number of vegetative buds was obtained when 90 days incubation period at 27 °C was followed by a period for flower emergence at 17°C. Corms lifted from green or withered plants showed similar response to temperature regimes and incubation periods. However, in average duration of sowing to flowering was 5 days longer in corms lifted from green plants. Comparing the results of this research with daily temperature in the main saffron production areas of Khorasan provinces showed that increasing mean daily temperature by 2 °C during summer and autumn results in a considerable delay in flowering of saffron.

Investigation of weed species diversity and community structure in saffron fields of Khorasan

Directory of Open Access Journals (Sweden)

Surur Khorramdel

2017-09-01

Full Text Available Weedy flora of agroecosystems is composed of many species that have evolved in response to cropping system practices by occupying the niches left available in agroecosystems. In order to study weed species diversity and community structure in the saffron fields of Khorasan province, a survey trial was carried out in seven counties (including Mashhad, Neyshabur, Birjandn, Ghaen, Gonabad, Torbat-e Jam and Torbat-e Heydari during 2014 and 2015 from vegetative growth, dormant to flowering stages of saffron randomly dropped 1×1 m2 quadrates in 50 fields based on a systematic method as W pattern. The counties were clustered by the hierarchical complete linkage method based on Euclidean. Biodiversity indices such as stability coefficient, Simpson, Shannon–Wiener, Margalef and Menhinick were computed. The results indicated that the dominant weeds in saffron fields belong to 19 families and 50 species. Poaceae, Brassicaceae, Asteraceae and Fabaceae were dominant families with 11, 9, 8 and 6 species, respectively. The majority of weed species were dicotyledonous, C3, noxious and annual plants. The highest stability coefficients in the stages of growth of saffron were calculated in Alhagi camelorum, Avena fatua and Achillea millefolium to be 30.81, 24.11 and 12.14, respectively. All weed species except for Alhagi camelorum (sustainable species and Avena fatua (temporary species were recognized as causal species. The maximum diversity indices for weed species were recorded at the vegetative phase of saffron. Correlation coefficient between weed density and yield loss of saffron was computed as R2=0.98. Based on diversity indices for weed species, different counties were clustered in three groups at 75% similarity level.

Effects of Different Corm Densities and Bed Types on Flower Yield Components of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

A. Mollafilabi

2017-10-01

Full Text Available Introduction Saffron is among the most precious agricultural and medicinal plants of the world and has a specific placement in Iran exports. In Iran total cultivation area was 93000 ha in 2017 that from which about 96% devoted to two main provinces of saffron production including Khorasan-Razavi and South Khorasan with total production of 351 ton saffron. Saffron has unique characters including low water requirement, saffron irrigation in times that other crops do not need, farm utilization for some years, ease of transportation, lack of need to special machinery and complex technology, high capacity to use labor in time of picking flowers, occupation and in the end prevention from immigration and exchange income that make this crop becomes superior in those regions that lack of industrial perspectives and having water limitations. Organic fertilizers have effective role in saffron production including physical improvement of saffron soil, temperature relief, penetration improvement, porosity increase, and soil reducdtion in hardiness, and cause to saffron flowering. Several factors like climate, diseases, irrigation, storage, planting date, chemical and biological fertilizers and animal manure are very effective in saffron quantity and quality. Saffron yield depends on several factors like soil, crop density, planting method, corm size, geographical location, climatic factors like temperature fluctuations specially in time of flowering, rate of rainfall, cultural management and utilization period. The aim of this study was to determine possible effects of corm density and bed type on flower yield components and stigma yield of saffron. Materials and methods In order to evaluate effects of corm density and bed type on reproductive characters, yield components of flower and saffron stigma an experiment was conducted in the form of factorial as RCBD with three replicates at the research farm of Khorasan Science and Technology Part (KSTP during

Evaluation of the Extinction Coefficient, Radiation Absorption and Use Efficiency of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

Seyyedeh Maliheh Mirhashemi

2015-10-01

Full Text Available Leaf area index, light extinction coefficient and radiation use efficiency are important eco-physiological characteristics for realization of crops growth, development and radiation absorption. In order to determine the leaf area index (LAI, light extinction coefficient (K and radiation use efficiency (RUE of saffron during the first and second growing seasons, four experiments were started in 2011 and ended in 2014, at the Research Farm of the Agriculture Faculty, the Ferdowsi University of Mashhad, Iran. Saffron corms with weights between 13 to15 g and density of 50 plant.m2 were cultivated in 2011 and 2012. In all experimental years during the growing season, crop sampling was taken for required measurements including the leaf area index and shoot dry weight of saffron once every 14 days. The results showed that by increasing the age of saffron from 1 year to two years, the maximum LAI of saffron increased from 0.33 to 1.81, and light extinction coefficient decreased from 1.20 to 0.54. The increasing trend of LAI was coincident with fraction of absorbed radiation for all four years of the experiment. In the first and the second growing seasons, the amount of fraction of absorbed radiation gradually increased with increasing LAI and at 1083 and 1034 GDD reached its maximum value, respectively. In saffron farms when the plant was one year old and two years old, the mean value of RUE was 0.68 and 1.73 g.MJ-1 PAR, respectively. These results indicate that by increasing the saffron age and LAI, the value of K decreases and consequently radiation absorption and use efficiency will‎ increase.

A Comparative Analysis of Saffron and Methylprednisolone on Bleomycin-Induced Pulmonary Fibrosis in Rats

Directory of Open Access Journals (Sweden)

Mehrzad Bahtouee

2018-04-01

Full Text Available Background: The purpose of this study was to compare the effects of saffron and methylprednisolone on bleomycin-induced pulmonary fibrosis in rats. Methods: This study was conducted in Bushehr, southern Iran in 2017.The animals were divided into four groups of five rats each. Three groups were injected with a single intratracheal dose of bleomycin (5 mg/kg. The fourth group was administered with normal saline at the same volume (200 µl. Saffron extract dissolved in water was given to one group (100 mg /body weight orally while intraperitoneal injection of methylprednisolone (2.5 mg/kg injected to another one for 16 days. The rats were sacrificed 28 days following surgery and their right and left lungs were removed and washed for measuring lung indices, myeloperoxidase activities and finally histopathological examination. Results: Injection of bleomycin caused decrement of body weight aggravated by intraperitoneal methylprednisolone treatment. Lung indices were increased in the bleomycin-treated group compared with the control, while methylprednisolone, unlike saffron, had no preventive effects on it. Both saffron and methylprednisolone treatment prevented the increase in lung myeloperoxidase as a destructive enzyme. In addition, excessive collagen deposition and thickening of alveolar septa were significantly prevented with saffron treatment as compared to methylprednisolone injection following hematoxylin and eosin staining. Conclusion: Saffron with established antioxidant properties could prevent some detrimental effects in bleomycin-induced pulmonary fibrosis even more than methylprednisolone injection known as a standard therapy in this murine model. More investigations must be carried out to examine the beneficial or harmful effects of this remedy.

Effect of saffron petal extract on retention quality of fresh-cut watermelon cubes

Directory of Open Access Journals (Sweden)

hamed kaveh

2017-01-01

Full Text Available Saffron is considered as a valuable produce by producers and traders. Unfortunately, the use of its floral by products like petal which have proven to be antioxidant, antimicrobial and nutritional value is limited. In order to investigate the application of saffron petal extracts as an ameliorative on postharvest and processing quality of fresh-cut ‘Crimson Sweet’ watermelon, a completely randomized designed investigation was done on watermelon cubes with 1cm diameter (1±0.5 gram mean weight. Prepared watermelon cubes were divided into four groups and treated with saffron petal extract (10 % V/V for 10 minutes, UV irradiation (maximum wavelength 253.4 nm and 15W for 5 minutes, 10 minutes of saffron petal extract then UV irradiation for 5 minutes and control. After the application of treatments, fresh-cut watermelon cubes were stored at 5±0.5 ºC for 14 days. Sampling and observation of the studied characteristics (physiological loss in weight, soluble solid content, lycopene, microbial load and color quality (Chroma Hue was done every two days to find the trend of changes during the retention period. The results of experiment showed that petal extract of saffron could not decrease weight loss but it was significantly effective in lowering microbial load and increasing color quality, and prevention of lycopene degradation (P≤5%. Although treatment of UV+SPE had better efficiency to suppress microbial load significantly (P≤5%.

Evaluation of yield and identifying potential regions for Saffron (Crocus sativus L. cultivation in Khorasan Razavi province according to temperature parameters

Directory of Open Access Journals (Sweden)

Moein Tosan

2015-04-01

Full Text Available Saffron is cultivated in most part of Iran, because of low water requirement and well adaptation to diverse environmental condition. In recent years, for many reasons such as low water requirement, saffron cultivation areas has been increased especially in Khorasan Razavi province. Temperature is one of the most important factors in saffron flowering phenomena. The aim of this research was to evaluate the response of saffron to temperature in Khorasan Razavi province counties (Torbat-e-Heydarieh, Gonabad, Nishabour, Sabzevar and Ghoochan. Climatic data (monthly minimum, average, maximum temperatures and diurnal temperature range and saffron yield data were collected for past 20 years period. The stepwise regression methods were used to remove extra parameters and only keep the most important ones. By using these equations and ArcGIS software zoning, Spline method was find the best for saffron crop zoning. The results of linear regression in Gonabad showed that minimum, maximum and average temperature and also diurnal temperature range in March and April months had the greatest impact on saffron yield. For each of the four indices (the minimum, maximum and average temperature and also diurnal temperature range the best area for saffron cultivation was the southern part of the province (particularly Gonabad; so by increasing distance from this area to north areas (such as Kashmar, Torbat-e-Heydarieh, Sabzevar, Nishabour, Mashhad and finally Ghoochan saffron yield reduced by 30 to 50 percent. Therefore, the northern areas of the province had relatively low saffron yield. According to result of this research, saffron yield in Khorasan Razavi province was significantly influenced by temperature parameters. Flowering which basically is the most important stage of plant growth, is directly setting up with temperature.

Causing mutagenesis through the gamma rays upon the Saffron immature corm buds

International Nuclear Information System (INIS)

Rastegari, J.; Vedadi, S.; Ghafari, M.

2007-01-01

In this research five levels of Saffron Corm weights (6-8-10-12 and 14 grams) and five dose of gamma radiation (0-2.5-5-7.5 and 10 Gy) were used. There were 25 treatments with 4 replication. The statistical analysis were conducted on petiole and stigma length on both the irradiated and the controlled. There were no significant difference at 5% level and weight of Saffron Corms and the irradiation does on the petiole and stigma length. The chromosomal studies on the root tip showed the chromosome abnormality in corm weight of 8 and 10 grams and the doses of 7.5 and 10 Gy. It can be concluded that irradiation of more than 10 Gy will cause abnormality and stops the emergence of Saffron. The best does of irradiation was found to be 5-10 Gy

Stigma variability in saffron (Crocus sativus L.)

African Journals Online (AJOL)

STORAGESEVER

2009-02-18

Feb 18, 2009 ... mainly as a dye in industry, as a spice in cooking, as a food colorant, and as a .... stigmas and stored in different boxes for statistical analysis. In addition, the .... Biomedical properties of saffron and its potential use in cancer ...

Using ß-cyclodextrin and Arabic Gum as Wall Materials for Encapsulation of Saffron Essential Oil.

Science.gov (United States)

Atefi, Mohsen; Nayebzadeh, Kooshan; Mohammadi, Abdorreza; Mortazavian, Amir Mohammad

2017-01-01

Saffron essential oil has a pleasant aroma and medicinal activities. However, it is sensible into the environmental condition. Therefore, it should be protected against unwanted changes during storage or processing. Encapsulation is introduced as a process by which liable materials are protected from unwanted changes. In the present study, different ratios (0:100, 25:75, 50:50, 75:25, and 100:0) of ß-cyclodextrin (ß-CD) and arabic gum (GA) were used as wall martial for encapsulation saffron essential oil. In order to calculate of loading capacity (LC) and encapsulation efficiency (EE), and release (RE), safranal was determined as indicator of saffron essential oil using GC. According to the results, the highest LC and EE were related to the mixture of ß-CD/GA at a 75:25 ratio. In contrast, the lowest encapsulate hygroscopicity (EH) and RE were observed when only ß-CD was applied as wall material (P≤0.05). Comparing the differential scanning calorimetry (DSC) thermograms of the control and encapsulate of ß-CD/GA (75:25) confirmed encapsulation of saffron essential oil. Scanning electron microscopy (SEM) images with high magnifications showed the rhombic structure that partially coated by GA. The mixture of ß-CD/GA at a 75:25 ratio can be recommended for saffron essential oil encapsulation.

Climatic zonation and land suitability determination for saffron in Khorasan-Razavi province using data mining algorithms

Directory of Open Access Journals (Sweden)

mehdi Bashiri

2017-12-01

Full Text Available Yield prediction for agricultural crops plays an important role in export-import planning, purchase guarantees, pricing, secure profits and increasing in agricultural productivity. Crop yield is affected by several parameters especially climate. In this study, the saffron yield in the Khorasan-Razavi province was evaluated by different classification algorithms including artificial neural networks, regression models, local linear trees, decision trees, discriminant analysis, random forest, support vector machine and nearest neighbor analysis. These algorithms analyzed data for 20 years (1989-2009 including 11 climatological parameters. The results showed that a few numbers of climatological parameters affect the saffron yield. The minimum, mean and maximum of temperature, had the highest positive correlations and the relative humidity of 6.5h, sunny hours, relative humidity of 18.5h, evaporation, relative humidity of 12.5h and absolute humidity had the highest negative correlations with saffron cultivation areas, respectively. In addition, in classification of saffron cultivation areas, the discriminant analysis and support vector machine had higher accuracies. The correlation between saffron cultivation area and saffron yield values was relatively high (r=0.38. The nearest neighbor analysis had the best prediction accuracy for classification of cultivation areas. For this algorithm the coefficients of determination were 1 and 0.944 for training and testing stages, respectively. However, the algorithms accuracy for prediction of crop yield from climatological parameters was low (the average coefficients of determination equal to 0.48 and 0.05 for training and testing stages. The best algorithm i.e. nearest neighbor analysis had coefficients of determination equal to 1 and 0.177 for saffron yield prediction. Results showed that, using climatological parameters and data mining algorithms can classify cultivation areas. By this way it is possible

The effects of Crocus sativus (saffron and its constituents on nervous system: A review

Directory of Open Access Journals (Sweden)

Mohammad Reza Khazdair

2015-08-01

Full Text Available Saffron or Crocus sativus L. (C. sativus has been widely used as a medicinal plant to promote human health, especially in Asia. The main components of saffron are crocin, picrocrocin and safranal. The median lethal doses (LD50 of C. sativus are 200 mg/ml and 20.7 g/kg in vitro and in animal studies, respectively. Saffron has been suggested to be effective in the treatment of a wide range of disorders including coronary artery diseases, hypertension, stomach disorders, dysmenorrhea and learning and memory impairments. In addition, different studies have indicated that saffron has anti-inflammatory, anti-atherosclerotic, antigenotoxic and cytotoxic activities. Antitussive effects of stigmas and petals of C. sativus and its components, safranal and crocin have also been demonstrated. The anticonvulsant and anti-Alzheimer properties of saffron extract were shown in human and animal studies. The efficacy of C. sativus in the treatment of mild to moderate depression was also reported in clinical trial. Administration of C. sativus and its constituents increased glutamate and dopamine levels in the brain in a dose-dependent manner. It also interacts with the opioid system to reduce withdrawal syndrome. Therefore, in the present article, the effects of C. sativus and its constituents on the nervous system and the possible underlying mechanisms are reviewed. Our literature review showed that C. sativus and its components can be considered as promising agents in the treatment of nervous system disorders.

The toxicity of saffron (Crocus sativus L. and its constituents against normal and cancer cells

Directory of Open Access Journals (Sweden)

Alireza Milajerdi

2016-03-01

Conclusion: In conclusion, emerging evidence suggests that saffron extract and its crocin, crocetin and safranal have a selective toxicity effects against cancer cells and also may have cancer preventive functions. However, Saffron and its constituent's toxicity against normal cells is negligible and they are even non-toxic in oral administration.

Greek PDO saffron authentication studies using species specific molecular markers.

Science.gov (United States)

Bosmali, I; Ordoudi, S A; Tsimidou, M Z; Madesis, P

2017-10-01

Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Barcoding melting curve analysis for rapid, sensitive, and discriminating authentication of saffron (Crocus sativus L.) from its adulterants.

Science.gov (United States)

Jiang, Chao; Cao, Liang; Yuan, Yuan; Chen, Min; Jin, Yan; Huang, Luqi

2014-01-01

Saffron (Crocus sativus L.) is one of the most important and expensive medicinal spice products in the world. Because of its high market value and premium price, saffron is often adulterated through the incorporation of other materials, such as Carthamus tinctorius L. and Calendula officinalis L. flowers, Hemerocallis L. petals, Daucus carota L. fleshy root, Curcuma longa L. rhizomes, Zea may L., and Nelumbo nucifera Gaertn. stigmas. To develop a straightforward, nonsequencing method for rapid, sensitive, and discriminating detection of these adulterants in traded saffron, we report here the application of a barcoding melting curve analysis method (Bar-MCA) that uses the universal chloroplast plant DNA barcoding region trnH-psbA to identify adulterants. When amplified at DNA concentrations and annealing temperatures optimized for the curve analysis, peaks were formed at specific locations for saffron (81.92°C) and the adulterants: D. carota (81.60°C), C. tinctorius (80.10°C), C. officinalis (79.92°C), Dendranthema morifolium (Ramat.) Tzvel. (79.62°C), N. nucifera (80.58°C), Hemerocallis fulva (L.) L. (84.78°C), and Z. mays (84.33°C). The constructed melting curves for saffron and its adulterants have significantly different peak locations or shapes. In conclusion, Bar-MCA could be a faster and more cost-effective method to authenticate saffron and detect its adulterants.

Barcoding Melting Curve Analysis for Rapid, Sensitive, and Discriminating Authentication of Saffron (Crocus sativus L. from Its Adulterants

Directory of Open Access Journals (Sweden)

Chao Jiang

2014-01-01

Full Text Available Saffron (Crocus sativus L. is one of the most important and expensive medicinal spice products in the world. Because of its high market value and premium price, saffron is often adulterated through the incorporation of other materials, such as Carthamus tinctorius L. and Calendula officinalis L. flowers, Hemerocallis L. petals, Daucus carota L. fleshy root, Curcuma longa L. rhizomes, Zea may L., and Nelumbo nucifera Gaertn. stigmas. To develop a straightforward, nonsequencing method for rapid, sensitive, and discriminating detection of these adulterants in traded saffron, we report here the application of a barcoding melting curve analysis method (Bar-MCA that uses the universal chloroplast plant DNA barcoding region trnH-psbA to identify adulterants. When amplified at DNA concentrations and annealing temperatures optimized for the curve analysis, peaks were formed at specific locations for saffron (81.92°C and the adulterants: D. carota (81.60°C, C. tinctorius (80.10°C, C. officinalis (79.92°C, Dendranthema morifolium (Ramat. Tzvel. (79.62°C, N. nucifera (80.58°C, Hemerocallis fulva (L. L. (84.78°C, and Z. mays (84.33°C. The constructed melting curves for saffron and its adulterants have significantly different peak locations or shapes. In conclusion, Bar-MCA could be a faster and more cost-effective method to authenticate saffron and detect its adulterants.

Radioprotective effects saffron and its combination with green tea against γ-radiation-induced DNA damage in Swiss albino mice

International Nuclear Information System (INIS)

Koul, Apurva; Abraham, Suresh K.

2016-01-01

Protective effects of aqueous extract of saffron (dried stigmas of Crocus sativus L.) alone and its combination with green tea against γ-radiation-induced genotoxicity and oxidative stress were investigated in Swiss albino mice. Saffron (40 mg/kg bw) alone and in combination with green tea (40 mg/kg bw) were orally administered to mice for six consecutive days, followed by exposure to γ-radiation (2.25 Gy) on 6 th day after final feeding. Antigenotoxic effect of saffron was assayed using micronucleus test in bone marrow cells which showed a significant decrease in the number of micronucleated PCEs in saffron alone and its combination with green tea pre-treated animals when compared with the radiation alone treated animals. Saffron alone and its combination with green tea pre-treated animals showed a significant decrease in lipid peroxidation levels with a significant increase in the activity of antioxidant defense system enzymes, viz. acetylcholine esterase, glutathione-S-transferase, catalase, glutathione peroxidase, glutathione reductase and non-enzymatic antioxidant (GSH), when compared with the radiation alone treated animals. Our results suggested that saffron in combination with green tea exhibits radioprotective effects against γ-radiation induced DNA damage and oxidative stress in Swiss albino mice. (author)

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

Science.gov (United States)

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Effect of Saffron on Metabolic Profile and Retina in Apolipoprotein E-Knockout Mice Fed a High-Fat Diet.

Science.gov (United States)

Doumouchtsis, Evangelos K; Tzani, Aspasia; Doulamis, Ilias P; Konstantopoulos, Panagiotis; Laskarina-Maria, Korou; Agrogiannis, Georgios; Agapitos, Emmanouil; Moschos, Marilita M; Kostakis, Alkiviadis; Perrea, Despina N

2017-09-22

Saffron is a spice that has been traditionally used as a regimen for a variety of diseases due to its potent antioxidant attributes. It is well documented that impaired systemic oxidative status is firmly associated with diverse adverse effects including retinal damage. The aim of this study was to investigate the role of saffron administration against the retinal damage in apoE -/- mice fed a high-fat diet, since they constitute a designated experimental model susceptible to oxidative stress. Twenty-one mice were allocated into three groups: Group A (control, n = 7 c57bl/6 mice) received standard chow diet; Group B (high-fat, n = 7 apoE -/- mice) received a high-fat diet; and Group C (high-fat and saffron, n = 7 apoE -/- mice) received a high-fat diet and saffron (25 mg/kg/d) through their drinking water. The duration of the study was 20 weeks. Lipidemic profile, glucose, C-reactive protein (CRP), and total oxidative capacity (PerOX) were measured in blood serum. Histological analysis of retina was also conducted. Administration of saffron resulted in enhanced glycemic control and preservation of retinal thickness when compared with apoE -/- mice fed a high-fat diet. The outcomes of the study suggest the potential protective role of saffron against retinal damage induced by oxidative stress. Nevertheless, verification of these results in humans is required before any definite conclusions can be drawn.

BGDB: a database of bivalent genes.

Science.gov (United States)

Li, Qingyan; Lian, Shuabin; Dai, Zhiming; Xiang, Qian; Dai, Xianhua

2013-01-01

Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/

Ameliorative Effect of Saffron Aqueous Extract on Hyperglycemia, Hyperlipidemia, and Oxidative Stress on Diabetic Encephalopathy in Streptozotocin Induced Experimental Diabetes Mellitus

Directory of Open Access Journals (Sweden)

Saeed Samarghandian

2014-01-01

Full Text Available Diabetic encephalopathy is one of the severe complications in patients with diabetes mellitus. Findings indicate that saffron extract has antioxidant properties but its underlying beneficial effects on diabetic encephalopathy were unclear. In the present study, the protective activities of saffron were evaluated in diabetic encephalopathy. Saffron at 40 and 80 mg/kg significantly increased body weight and serum TNF-α and decreased blood glucose levels, glycosylated serum proteins, and serum advanced glycation endproducts (AGEs levels. Furthermore, significant increase in HDL and decrease (P<0.05 in cholesterol, triglyceride, and LDL were observed after 28 days of treatment. At the end of experiments, the hippocampus tissue was used for determination of glutathione content (GSH, superoxide dismutase (SOD, and catalase (CAT activities. Furthermore, saffron significantly increased GSH, SOD, and CAT but remarkably decreased cognitive deficit, serum TNF-α, and induced nitric oxide synthase (iNOS activity in hippocampus tissue. Our findings indicated that saffron extract may reduce hyperglycemia and hyperlipidemia risk and also reduce the oxidative stress in diabetic encephalopathy rats. This study suggested that saffron extract might be a promising candidate for the improvement of chemically induced diabetes and its complications.

Safety evaluation of saffron stigma (Crocus sativus L. aqueous extract and crocin in patients with schizophrenia

Directory of Open Access Journals (Sweden)

Bentolhoda Mousavi

2015-08-01

Full Text Available Objectives: Saffron is the stigma of Crocus sativus L., which has the potentials to play a role in the treatment of many diseases. Although many researches are now going on this precious spice, there are few data on saffron safety in human, especially in patients with chronic mental illnesses. This study aimed to evaluate the short-term safety and tolerability of both saffron and crocin (its major constituent in adult patients with schizophrenia. Materials and Methods: The capsules of saffron aqueous extract (SAE and crocin were used to evaluate short-term safety and tolerability in patients with schizophrenia. A double-blind, placebo-controlled study was performed on patients with schizophrenia. The patients were all male and were divided into three 22-patient groups. While receiving their normal treatment, they also received a 12 week treatment with SAE (15 mg twice daily, crocin (15 mg twice daily or placebo. Results: A total of 61 patients completed the trial; none of them reported a serious side effect. WBC count increased significantly in patients receiving saffron aqua extract (SAE, but it was within the normal range and had no clinical significance. Other hematologic components, markers of thyroid, liver and kidney or inflammation markers had no statistically significant difference among the groups. Conclusions: This study showed that SAE and crocin in doses of 15 mg twice daily were safely tolerated in patients with schizophrenia.

Identification and Prioritization of Marketing Mix Elements Affecting the Export of Saffron from the Perspective of Experts

Directory of Open Access Journals (Sweden)

Mohammad Ghodoosi

2016-01-01

Full Text Available The importance of saffron in the growth of non-oil exports makes it necessary to explain proper marketing systems based on expert priorities. The aim of this study is to identify and prioritize marketing mix elements influencing the increase in export of this product. In this regard, based on McCarthy's 4P model, different criteria for export marketing of this product were determined and prioritized using Analytical Hierarchy Process and interviews with 63 experts in the export of saffron. Based on the findings, product criteria with important sub criteria such as brands, the standard sign and packaging weighting 0.485, have the highest priority in saffron marketing. Promotion criteria (weight 0.281 are the next important in determining the marketing mix. Among the indicators of this criterion, advertisements (0.408, overseas sales (0.23 and specialized exhibitions (0.138 were the determining factors in maintaining Iran`s share of this market.  Finally, the criteria of price (weight 0.183 and distribution (0.068 have third and fourth priority in saffron marketing mix. Accordingly, identifying distribution channels in target markets, funding the establishment of an international distribution network for Iranian brands, supporting mechanized production process of saffron, and encouraging and requiring manufacturers to food-grade and health license are required and recommended.

Antihyperlipidemic effect of crude extract of saffron stigma (Crocus sativus in healthy male rats

Directory of Open Access Journals (Sweden)

Iliass Lahmass

2017-01-01

Full Text Available In this study, we investigated for the first time the antihyperlipidemic ef-fects of crude extract of stigmas from Crocus sativus (saffron against hyperlipidemia induced by tartrazine (synthetic dye in normal male rats. Thirty adult male albino rats weighing about 150 - 200 g, were divided into 5 groups (n = 6 and daily treatment was given orally. Clinical biochemis-try and metabolic parameters were evaluated at the end of the experiment and after 105 days. (n=6, for all groups. Our data revealed that the meta-bolic parameters like consumption of food and water, pH and urine vol-ume have not been affected; also the difference between liver, right kid-ney and heart weight was not significant. The levels of cholesterol and triglyceride were significantly increased in group 2 and group 3 compared to control group. There was no significant difference in the level of cholesterol and triglyceride in group 4. Treatment with saffron alone did not have any significant effects on the level of fat compared to control group. The oral administration of the crude extract of saffron revealed good hypolipidemic effects in adult male albino rats. These results suggest that aqueous saffron extract reduced plasma cholesterol and decreased triglyceride. Therefore, it could conceivably lead to suitable changes in blood lipid profiles. [J Med Allied Sci 2017; 7(1.000: 20-25

Geographical identification of saffron (Crocus sativus L.) by linear discriminant analysis applied to the UV-visible spectra of aqueous extracts.

Science.gov (United States)

D'Archivio, Angelo Antonio; Maggi, Maria Anna

2017-03-15

We attempted geographical classification of saffron using UV-visible spectroscopy, conventionally adopted for quality grading according to the ISO Normative 3632. We investigated 81 saffron samples produced in L'Aquila, Città della Pieve, Cascia, and Sardinia (Italy) and commercial products purchased in various supermarkets. Exploratory principal component analysis applied to the UV-vis spectra of saffron aqueous extracts revealed a clear differentiation of the samples belonging to different quality categories, but a poor separation according to the geographical origin of the spices. On the other hand, linear discriminant analysis based on 8 selected absorbance values, concentrated near 279, 305 and 328nm, allowed a good distinction of the spices coming from different sites. Under severe validation conditions (30% and 50% of saffron samples in the evaluation set), correct predictions were 85 and 83%, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Impact of Saffron on Symptoms of Withdrawal Syndrome in Patients Undergoing Maintenance Treatment for Opioid Addiction in Sabzevar Parish in 2017

Directory of Open Access Journals (Sweden)

Mohammad Nemat Shahi

2017-01-01

Full Text Available Background and Objective. Drug dependence is one of the serious problems around the world. Saffron is one of those beneficial medicinal plants which is embedded with a similar mechanism to methadone (e.g., inhibition of serotonin reuptake. Thus, it can be helpful in reducing the withdrawal symptoms. The aim of this study was to reduce the daily dose of methadone usage and reduce its side effects using saffron in the form of medicinal supplements. Methodology. This study was categorized as a clinical trial. Accordingly, 44 clients of addiction treatment centers in Sabzevar parish were randomly selected to participate in this study in 2016–2017. While the experimental group was treated with methadone syrup and self-made saffron capsules, the control group received methadone syrup and placebo capsules. Results. The results showed that the use of saffron and methadone alleviated the symptoms of withdrawal syndrome (p<0.001. Conclusion. Having reviewed the research participants, it was indicated that the introduction of saffron alleviated the symptoms of withdrawal syndrome in patients undergoing maintenance treatment for opioid addiction. Thus, it seems rational to make use of saffron in combination with methadone in order to alleviate the symptoms of withdrawal syndrome.

Study a possibility of saffron (Crocus sativus L. production in vertical culture

Directory of Open Access Journals (Sweden)

Lorin ali ahmad

2017-06-01

Full Text Available In recent years many research studies have been carried out to use a vertical planting system for production of some plants. Although saffron is one of the most expensive spices in the word, there is no investigation about saffron production in a vertical planting system. Therefore, the growth and production of saffron plant in two different systems (vertical and horizontal were studied in the agricultural research field of the Tarbiat Modares University during the 2013-2014 growing seasons. In the vertical system, saffron corms were planted in fabric bags containing potting soil. The fabric bags were hanged on a cube of metal with an area of each side of the cube being equal to 2.25 square meters. In the horizontal system, the corms were planted in three plots with the area of each plots being 2.25 square meters. The results showed that in the vertical planting system, the number of flowers, flower dry weight and dry weight of stigma per unit area of land (10 flower, 347.34 and 0.56 mg respectively were significantly higher than those obtained in the horizontal culture (They were almost three times higher .In contrast, the numbers and dry weight of lateral corms (2.4 corm and 0.36 g respectively and the dry weight of apical corm (0.88 g in the horizontal system were significantly greater than those obtained in the vertical system. Dry weight of leaf and root were significantly greater in the vertical system. The total number of buds and leaves were more in the horizontal culture. However, the maximum leaf length of the vertical planting system was higher than those of the horizontal system.

New Hydrogels Enriched with Antioxidants from Saffron Crocus Can Find Applications in Wound Treatment and/or Beautification.

Science.gov (United States)

Zeka, Keti; Ruparelia, Ketan C; Sansone, Claudia; Macchiarelli, Guido; Continenza, Maria Adelaide; Arroo, Randolph R J

2018-01-01

Saffron extracts have a long history of application as skin protectant, possibly due to their ability to scavenge free radicals. In this work, the performance of a hydrogel enriched with antioxidant compounds isolated from saffron crocus (Crocus sativus L.) petals was tested. These hydrogels could be considered as new drug delivery system. Hydrogels are crosslinked polymer networks that absorb large quantities of water but retain the properties of a solid, thus making ideal dressings for sensitive skin. We tested antioxidant-enriched hydrogels on primary mouse fibroblasts. Hydrogels enriched with kaempferol and crocin extracted from saffron petals showed good biocompatibility with in vitro cultured fibroblasts. These new types of hydrogels may find applications in wound treatment and/or beautification. © 2018 S. Karger AG, Basel.

Effects of gamma irradiation and silver nano particles on microbiological characteristics of saffron, using hurdle technology.

Science.gov (United States)

Hamid Sales, E; Motamedi Sedeh, F; Rajabifar, S

2012-03-01

Saffron, a plant from the Iridaceae family, is the world's most expensive spice. Gamma irradiation and silver nano particles whose uses are gradually increasing worldwide, have positive effects on preventing decay by sterilizing the microorganisms and by improving the safety without compromising the nutritional properties and sensory quality of the foods. In the present study combination effects of gamma irradiation and silver nano particles packaging on the microbial contamination of saffron were considered during storage. A combination of hurdles can ensure stability and microbial safety of foods. For this purpose, saffron samples were packaged by Poly Ethylene films that posses up to 300 ppm nano silver particles as antimicrobial agents and then irradiated in cobalt-60 irradiator (gamma cell PX30, dose rate 0.55 Gry/Sec) to 0, 1, 2,3 and 4 kGy at room temperature. The antimicrobial activities against Total Aerobic Mesophilic Bacteria, Entrobacteriace, Escherichia Coli and Clostridium Perfringines were higher in the irradiated samples, demonstrating the inhibition zone for their growth. Irradiation of the saffron samples packaged by Poly Ethylene films with nano silver particles showed the best results for decreasing microbial contamination at 2 kGy and for Poly Ethylene films without silver nano particles; it was 4 kGy.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

Science.gov (United States)

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

EPR study of the free radicals in the spices and pigments turmeric and saffron

International Nuclear Information System (INIS)

Troup, G.J.; Hutton, D.R.; Hunter, C.A.; Hewitt, D.; Mulinacci, N.; Romani, A.; Giaccherini, K. Anon

2000-01-01

Full text: The spices Turmeric (curcuma longa) and Saffron (crocus sativus) have also been used as pigments. The EPR spectrum of each shows a readily detectable free radical signal. EPR spectra of the available pure chief active colorants in solid form also give free radical signals. Curcumin (turmeric) is a 'linear' symmetric phenolic, so is expected to do so. The peptide turmerin (commercially unavailable), containing sulphur, may also contribute to the ESR signal. Crocetin (saffron) is a 'linear' molecule, related to the beta-carotenes, which do not give free radical signals: but it does, presumably because of its particular resonant structure properties

Analysis of the role of strategic products in sustainable rural livelihoods (Case study: saffron production in the Roshtkhar rural district

Directory of Open Access Journals (Sweden)

Sadegh Asghari Lafmejani

2017-09-01

Full Text Available Saffron is the most expensive agricultural and pharmaceutical product in the world. It is significant for several reasons such as having high water productivity compared to other crops. It is providing rural employment and preventing their migration, having high medicinal and spice values, ease of maintenance and transportation. Most importantly, it is producing a high revenue compared to other agricultural products. On this basis, due to the suitability of some parts of Iran to saffron production and the role of this product in the livelihood of rural households, assessment of the sustenance impacts of saffron production in the active villages seems absolutely necessary. Therefore, the aim of the present study is to assess the status of saffron production and its role in the livelihood of rural households of the Roshtkhar Rural District. This research was done based on a descriptive-analytic approach. In this regard, the role of saffron cultivation in 355 households living in 13 villages with over 100 households in the study rural district was investigated. To this goal, after conducting documentary studies and initial field visits, a wide range of measures proportional to the circumstances of the study villages were adopted. Then, data collection was performed based on the selected indices and questionnaires were distributed to be filled by villagers and households... To analyze the data, the relevant statistical and spatial analyses were done through the application of Expert choice, SPSS, and ArcGIS software packages. The research findings indicated that the annual revenues derived from saffron production in 43.9% of the households under study were more than they obtained from other sources of income. Through the analysis of the study data, it can be concluded that saffron production has a significant effect on the improvement of the residents’ livelihood in the Roshtkhar Rural District and this fact has reinforced the households�

Effects of Planting Dates, Irrigation Management and Cover Crops on Growth and Yield of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

A Koocheki

2017-08-01

Full Text Available Introduction Saffron as a winter active plant with low water requirement is the most strategic medicinal plant in arid and semi-arid parts of Iran. This slow-growing plant has narrow leaves and no aerial stem, hence weeds can be overcome it. Moreover, because of its root and canopy structure an important part of different resources is not used by this low input crop. Therefore, the use of associated crops could be an effective way for increasing resources use efficiencies (Koocheki et al., 2016. Appropriate corm planting date is another important factor that affects saffron growth and yield. Results of some studies show that late spring is the best time for corm planting (Ghasemi-Rooshnavand, 2009; Koocheki et al., 2016. In addition, irrigation management has been evaluated in some studies, but irrigation immediately after corm planting has not been investigated previously. Therefore, the aim of this study was to investigate the effect of irrigation management, planting date and the use of some companion crops on flowering of saffron during two growth cycles. Materials and methods This experiment was carried out as a split-split plot experiment based on a Randomized Complete Block Design with three replications at Research Station, Ferdowsi University of Mashhad, Iran in 2009-2011. Experimental factors included: planting date of saffron as main factor (first of June, first of August and first of October, 2009, the irrigation management as sub factor (irrigation and no irrigation after each planting date and the companion crops as sub-sub factor [Persian clover (Trifolium resupinatum, Bitter vetch (Lathyrus sativus and control. Corm planting was done in 10×25 cm distances with 12 cm depth. In the second year irrigation was done again in the plots which were irrigated after planting in the first year at the same previous dates. Companion crops were sown after first flower picking (November, 2009, then their residue were returned to the soil in

Examination of integration and central market hypothesis for saffron market in khorasan razavi, northern khorasan and southern khorasan

Directory of Open Access Journals (Sweden)

Alireza Karbasi

2014-10-01

Full Text Available Saffron is one of the important agricultural product and North Khorasan, Razavi and South is considered as the major producers in Iran. In this study Central Market Hypothesis or price leadership has been examined. For this purpose Johanson Co-integration test for monthly price data since 2006 to 2011 for these provinces has been used. Main results indicated that South Khorasan is a price leader between these provinces. In addition, saffron market is unit in South Khorasan and Khorasan Razavi and the law of one price is indefeasible. Moreover, North Khorasan has a separate market and in long run saffron market in this province is not an impressible market. The adoption of a policy on each of the three provinces, affects the other two the product market provinces.

LINE FUSION GENES: a database of LINE expression in human genes

Directory of Open Access Journals (Sweden)

Park Hong-Seog

2006-06-01

Full Text Available Abstract Background Long Interspersed Nuclear Elements (LINEs are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. Description We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. Conclusion We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. Availability http://www.primate.or.kr/line

WGDB: Wood Gene Database with search interface.

Science.gov (United States)

Goyal, Neha; Ginwal, H S

2014-01-01

Wood quality can be defined in terms of particular end use with the involvement of several traits. Over the last fifteen years researchers have assessed the wood quality traits in forest trees. The wood quality was categorized as: cell wall biochemical traits, fibre properties include the microfibril angle, density and stiffness in loblolly pine [1]. The user friendly and an open-access database has been developed named Wood Gene Database (WGDB) for describing the wood genes along the information of protein and published research articles. It contains 720 wood genes from species namely Pinus, Deodar, fast growing trees namely Poplar, Eucalyptus. WGDB designed to encompass the majority of publicly accessible genes codes for cellulose, hemicellulose and lignin in tree species which are responsive to wood formation and quality. It is an interactive platform for collecting, managing and searching the specific wood genes; it also enables the data mining relate to the genomic information specifically in Arabidopsis thaliana, Populus trichocarpa, Eucalyptus grandis, Pinus taeda, Pinus radiata, Cedrus deodara, Cedrus atlantica. For user convenience, this database is cross linked with public databases namely NCBI, EMBL & Dendrome with the search engine Google for making it more informative and provides bioinformatics tools named BLAST,COBALT. The database is freely available on www.wgdb.in.

The estimation of phenological thresholds of Saffron cultivation in Isfahan province based on the daily temperature statistics

Directory of Open Access Journals (Sweden)

Gholamabbas Fallahghalhary

2015-04-01

Full Text Available In this research, the statistics of daily temperature of meteorology stations for estimating the probable occurrence of the first and last frost temperature, the phonological thresholds of saffron and its flowering and irrigation dates were explored. Furthermore, by applying different methods, the probabilities of the attained dates in different probability levels were fit in Smada software. The estimated probability level of 95 percent, as the optimum date, was donated for the entire Isfahan province in ArcGIS9/3 software environment using the interpolation method of Cokriging. The time of occurrence of minimum temperatures is under the influence of the geographical and height condition of each region and the first fall season frost occurs in high regions of the eastern half of Isfahan province at the beginning of November and in the low-lying eastern regions in the late December. The occurrence of daily temperature is changeable from the first half of October and the second half of November. From the west to the east of Isfahan, the time of occurrence of this threshold has a delay of about one month. The optimum flowering date of saffron, based on climatic conditions, is from the first half of October to the late of November. By considering the flowering date and daily temperature requirement of saffron, the irrigation date prior to flowering continues from the second half of September in the western parts and the beginning of November in the eastern regions. From the perspective of thermal condition, the western, central, northern and eastern parts of Isfahan province are more suited to the cultivation and development of saffron product. The amount of water requirement in the study area based on evapotranspiration and crop coefficients of saffron occurred in the mid-season, late season and Initial.

HRGFish: A database of hypoxia responsive genes in fishes

Science.gov (United States)

Rashid, Iliyas; Nagpure, Naresh Sahebrao; Srivastava, Prachi; Kumar, Ravindra; Pathak, Ajey Kumar; Singh, Mahender; Kushwaha, Basdeo

2017-02-01

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

Effect of aqueous extract of saffron (crocus sativus L.) against gamma radiation-induced skeletal muscles damage in rats

International Nuclear Information System (INIS)

El-Tahawy, N.A; Said, U.Z

2010-01-01

Muscular strength is important in sport as well as in daily activities. Reactive oxygen species (ROS) and oxidative damage are the most important factors in radiation-induced acute damage to muscle tissue. Saffron, obtained from dried stigmas of Crocus sativus L. (Iridaceae), is a highly valued spice, commonly used in flavouring and food colouring in different parts of the world and is known to possess the richest source of carotenoids. The present study was designed to investigate the efficacy of an aqueous extract of saffron to protect against radiation-induced oxidative damage in rat's skeletal muscle. Saffron was supplemented orally, via gavages to rats at a dose of 80 mg/ kg body wt/ day for 2 week pre- and 1 week post-exposure to 5 Gy (one shot dose) of whole body gamma-irradiation. Animals were sacrificed 1, 2 and 3 weeks post radiation exposure. The results revealed that whole body gamma-irradiation of rats induce oxidative stress in skeletal muscles obvious by significant elevation in the level of thiobarbituric acid reactive substances associated with significant decreases in superoxide dismutase and catalase activities. Also, radiation-induces skeletal muscles damage evidenced by significant decreases in the level of pyruvic acid, creatine phosphokinase, glutamate dehydrogenase and glucose-6-phosphate dehydrogenase activities as well as significant increases in lactic acid, total iron, and copper and calcium levels. Saffron treated-irradiated rats showed significantly less severe damage and remarkable improvement in all the measured parameters, compared to irradiated rats. It could be concluded that saffron by attenuating radiation-induced oxidative stress might play a role in maintaining skeletal muscle integrity.

The Androgen Receptor Gene Mutations Database.

Science.gov (United States)

Gottlieb, B; Lehvaslaiho, H; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1998-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 272 to 309 in the past year. We have expanded the database: (i) by giving each entry an accession number; (ii) by adding information on the length of polymorphic polyglutamine (polyGln) and polyglycine (polyGly) tracts in exon 1; (iii) by adding information on large gene deletions; (iv) by providing a direct link with a completely searchable database (courtesy EMBL-European Bioinformatics Institute). The addition of the exon 1 polymorphisms is discussed in light of their possible relevance as markers for predisposition to prostate or breast cancer. The database is also available on the internet (http://www.mcgill. ca/androgendb/ ), from EMBL-European Bioinformatics Institute (ftp. ebi.ac.uk/pub/databases/androgen ), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca).

Effects of Saffron on Cognition, Anxiety, and Depression in Patients Undergoing Coronary Artery Bypass Grafting: A Randomized Double-Blind Placebo-Controlled Trial.

Science.gov (United States)

Moazen-Zadeh, Ehsan; Abbasi, Seyed Hesameddin; Safi-Aghdam, Hamideh; Shahmansouri, Nazila; Arjmandi-Beglar, Akram; Hajhosseinn Talasaz, Azita; Salehiomran, Abbas; Forghani, Saeedeh; Akhondzadeh, Shahin

2018-04-01

Cognitive decline, depression, and anxiety are among the major concerns in patients undergoing coronary artery bypass grafting (CABG). Crocus sativus L. (saffron) seems to be a promising candidate for treatment of these conditions. In this 12-week, randomized, double-blind, placebo-controlled clinical trial, men and women with on-pump CABG, who had Wechsler Memory Scale (WMS) score >70 and age Patients were excluded if they had history of treatment with saffron or acetylcholinesterase inhibitors, comorbid neuropsychiatric disorders, serious medical conditions other than cardiovascular diseases, and hypersensitivity to herbal compounds. The primary outcome was defined as the difference in mean total score changes for WMS-Revised from the baseline to week 12 between the saffron and placebo groups. Secondary outcomes included difference in mean score changes from baseline to endpoint between the two treatment groups for Mini Mental Status Examination and subscales of Hospital Anxiety and Depression Scale ( www.irct.ir ; IRCT201408071556N63). No significant difference was detected in primary or secondary outcomes between the saffron and placebo groups. Also, no significant time × treatment interaction effect was found for any of the scales. The results of this trial do not support the hypothesis of potential benefits of saffron in treatment of CABG-related neuropsychiatric conditions.

A comparative gene expression database for invertebrates

Directory of Open Access Journals (Sweden)

Ormestad Mattias

2011-08-01

Full Text Available Abstract Background As whole genome and transcriptome sequencing gets cheaper and faster, a great number of 'exotic' animal models are emerging, rapidly adding valuable data to the ever-expanding Evo-Devo field. All these new organisms serve as a fantastic resource for the research community, but the sheer amount of data, some published, some not, makes detailed comparison of gene expression patterns very difficult to summarize - a problem sometimes even noticeable within a single lab. The need to merge existing data with new information in an organized manner that is publicly available to the research community is now more necessary than ever. Description In order to offer a homogenous way of storing and handling gene expression patterns from a variety of organisms, we have developed the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons. The database can be queried by gene name, developmental stage and/or expression domains. Conclusions This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species. In addition, this database enables a quick identification of putative syn-expression groups that can be used to initiate, among other things, gene regulatory network (GRN projects.

Barcoding Melting Curve Analysis for Rapid, Sensitive, and Discriminating Authentication of Saffron (Crocus sativus L.) from Its Adulterants

OpenAIRE

Jiang, Chao; Cao, Liang; Yuan, Yuan; Chen, Min; Jin, Yan; Huang, Luqi

2014-01-01

Saffron (Crocus sativus L.) is one of the most important and expensive medicinal spice products in the world. Because of its high market value and premium price, saffron is often adulterated through the incorporation of other materials, such as Carthamus tinctorius L. and Calendula officinalis L. flowers, Hemerocallis L. petals, Daucus carota L. fleshy root, Curcuma longa L. rhizomes, Zea may L., and Nelumbo nucifera Gaertn. stigmas. To develop a straightforward, nonsequencing method for rapi...

Effects of humic acid application and mother corm weight on yield and growth of saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

A Koocheki

2016-03-01

Full Text Available Introduction Saffron as a food, spicy and medicinal plant has more than 62000 ha under cultivation with about 250 tons annual dry stigma production in Iran, which includes about 90% of its world production. Therefore, this plant has a specific value in agricultural export products of Iran (Fallahi et al., 2014. Due to the important role of saffron in Iran’s agroecosystems, the improvement of its agronomic practices is essential. Nutritional management and mother corms size are two of the main factors affecting growth and yield of saffron. Humic acid is an eco-friendly fertilizer that improves the physical, chemical and biological properties of soil. This nutritional source has hormonal compounds and exerts a positive effect on elements absorption, quality and yield of plants. In addition, in saffron cultivation, it is possible to produce considerable amounts of stigma by using of standard mother corms with a minimum weight of 8 g. Because, large corms have a positive effect on stigma yield especially in the first growth cycle and the weight of replacement corms and consequently saffron flowering in the other growth cycles (Nassiri Mahallati et al., 2008. Therefore, the aim of this research was to investigate the interaction effects of mother corm size and different rates of humic acid on growth and yield of saffron. Materials and methods This experiment was carried out as factorial based on randomized completely block design with three replications in research farm of Ferdowsi University of Mashhad, Iran, during two growing season (2009-2011. Experimental factors were consisted of mother corm weight (4-5, 6-8 and 9-10 g and application of humic acid (0, 20, 40, 60, 80 and 100 kg.ha-1. Mother corm planting was in early October, 2009 with 10×20 cm corms distances and planting depth of 10cm. Humic acid (dissolved in water was used along with the first autumnal irrigation in two season growth. Flower and stigma yield of saffron were measured

LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

Science.gov (United States)

Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

2012-01-01

Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene

Study on Effect of Type of Explant and Hormone on Callus Induction and Regeneration in Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

Mohsen Sajjadi

2015-10-01

Full Text Available Saffron (Crocus sativus L. is one of the medicinal plants that contain active components and medicinal materials. Tissue culture of saffron can improve the quality and quantity of the saffron product, increase its export and the farmers’ income. In this study, 36 different types of hormone combinations in the dark and 9 different treatments of hormone combinations in cold (4°C, using different saffron explants (bulb, leaf, scales around leaf and distal parts of the leaf were studied in tissue culture. To investigate the growth of corms, the callus formation and the regeneration rate, three replications for each treatment were used and the length of shoot (cm, the callus formation percentage and the regeneration percentage were measured and statistical analysis was performed. Among the types of explants, only explants from bulbs produced the callus on MS medium containing 2 mg.l-1 BAP and 1 mg.l-1 IBA in both the dark and cold conditions. The highest percentage of regeneration was obtained in MS medium with hormonal composition of 0.3 mg.l-1 TDZ, 1 mg.l-1 BAP, 2 mg.l-1 IBA and 0.01 mg.l-1 GA3 in the cold conditions.

The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice.

Science.gov (United States)

Abbott, Kenneth L; Nyre, Erik T; Abrahante, Juan; Ho, Yen-Yi; Isaksson Vogel, Rachel; Starr, Timothy K

2015-01-01

Identification of cancer driver gene mutations is crucial for advancing cancer therapeutics. Due to the overwhelming number of passenger mutations in the human tumor genome, it is difficult to pinpoint causative driver genes. Using transposon mutagenesis in mice many laboratories have conducted forward genetic screens and identified thousands of candidate driver genes that are highly relevant to human cancer. Unfortunately, this information is difficult to access and utilize because it is scattered across multiple publications using different mouse genome builds and strength metrics. To improve access to these findings and facilitate meta-analyses, we developed the Candidate Cancer Gene Database (CCGD, http://ccgd-starrlab.oit.umn.edu/). The CCGD is a manually curated database containing a unified description of all identified candidate driver genes and the genomic location of transposon common insertion sites (CISs) from all currently published transposon-based screens. To demonstrate relevance to human cancer, we performed a modified gene set enrichment analysis using KEGG pathways and show that human cancer pathways are highly enriched in the database. We also used hierarchical clustering to identify pathways enriched in blood cancers compared to solid cancers. The CCGD is a novel resource available to scientists interested in the identification of genetic drivers of cancer. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Therapeutic Potential of Saffron Crocus (Crocus sativus L.

Directory of Open Access Journals (Sweden)

Zeliha Selamoglu

2016-12-01

Full Text Available Herbal plants are using for folk medicine since immemorial times. Hippocrates who is the father of medicine, refer to 400 medicinal plants and advised ‘‘let food be your medicine and let medicine be your food’’. Most of plants are using today for medicine. It is still acceptable today that prevention is more important than treatment. Saffron was utilized in folk remedy against scarlet fever, smallpox, colds, asthma, eye and heart diseases, tumours, and cancer.

Saffron improved depression and reduced homocysteine level in patients with major depression: A Randomized, double-blind study

Directory of Open Access Journals (Sweden)

Gholamali Jelodar

2017-12-01

Full Text Available Objectives: A correlation between hyperhomocysteinemia, and depression has been reported. Saffron (Crocus sativus is recommended for treatment of depression; hence, in this study the effect of co-administration of saffron and fluoxetine on plasma homocysteine and depression was evaluated. Material and methods: This was a 4-week randomized and double-blind clinical trial which was conducted from March 2013 to February 2014. In this trial, 40 male and females (20-55 years old diagnosed with severe depression were selected and following filing the Beck form, were randomly divided into two groups.  Experimental group was treated with fluoxetine 20 mg/day and saffron 30 mg /day and the control group received placebo and fluoxetine 20 mg/day for four weeks. Before treatment and at the end of the study, fasting blood samples were collected. For females, blood samples were collected on the third day of their menstrual cycle. Results: A significant reduction of homocysteine levels was observed in both sex in the experimental group compared to before treatment (p

Using the TIGR gene index databases for biological discovery.

Science.gov (United States)

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

Enhanced Bioaccessibility of Crocetin Sugar Esters from Saffron in Infusions Rich in Natural Phenolic Antioxidants

Directory of Open Access Journals (Sweden)

Stella A. Ordoudi

2015-09-01

Full Text Available The present study aims to examine whether and to what extent the bioaccessibility of the major saffron apocarotenoids, namely crocetin sugar esters (CRTSEs, is affected by the presence of strong water-soluble antioxidants, ingredients of the herbs found in commercial tea blends with saffron. An in vitro digestion model was applied to infusions from these products to investigate the possible changes. All of the studied infusions were rich in total phenols (9.9–22.5 mg caffeic acid equivalents/100 mg dry infusion and presented strong DPPH radical scavenging activity regardless of the composition of the corresponding herbal blends. RP-HPLC-DAD and LC-MS analysis enabled the grouping of the infusions into hydroxycinnamic acid-rich and in flavan-3-ol-rich ones. CRTSEs in herbal tea infusions were found to be significantly more bioaccessible (66.3%–88.6% than those in the reference saffron infusion (60.9%. The positive role of strong phenolic antioxidants (caffeic acid, rosmarinic acid on the stability of CRTSEs was also evidenced in model binary mixtures. On the contrary, cinnamic acid, exerting no antioxidant activity, did not have such an effect. Our findings suggest that strong radical scavengers may protect the crocetin sugar esters from oxidation during digestion when present in excess.

Enhanced Bioaccessibility of Crocetin Sugar Esters from Saffron in Infusions Rich in Natural Phenolic Antioxidants.

Science.gov (United States)

Ordoudi, Stella A; Kyriakoudi, Anastasia; Tsimidou, Maria Z

2015-09-25

The present study aims to examine whether and to what extent the bioaccessibility of the major saffron apocarotenoids, namely crocetin sugar esters (CRTSEs), is affected by the presence of strong water-soluble antioxidants, ingredients of the herbs found in commercial tea blends with saffron. An in vitro digestion model was applied to infusions from these products to investigate the possible changes. All of the studied infusions were rich in total phenols (9.9-22.5 mg caffeic acid equivalents/100 mg dry infusion) and presented strong DPPH radical scavenging activity regardless of the composition of the corresponding herbal blends. RP-HPLC-DAD and LC-MS analysis enabled the grouping of the infusions into hydroxycinnamic acid-rich and in flavan-3-ol-rich ones. CRTSEs in herbal tea infusions were found to be significantly more bioaccessible (66.3%-88.6%) than those in the reference saffron infusion (60.9%). The positive role of strong phenolic antioxidants (caffeic acid, rosmarinic acid) on the stability of CRTSEs was also evidenced in model binary mixtures. On the contrary, cinnamic acid, exerting no antioxidant activity, did not have such an effect. Our findings suggest that strong radical scavengers may protect the crocetin sugar esters from oxidation during digestion when present in excess.

Safranal, a saffron constituent, attenuates retinal degeneration in P23H rats.

Directory of Open Access Journals (Sweden)

Laura Fernández-Sánchez

Full Text Available Saffron, an extract from Crocus sativus, has been largely used in traditional medicine for its antiapoptotic and anticarcinogenic properties. In this work, we investigate the effects of safranal, a component of saffron stigmas, in attenuating retinal degeneration in the P23H rat model of autosomal dominant retinitis pigmentosa. We demonstrate that administration of safranal to homozygous P23H line-3 rats preserves both photoreceptor morphology and number. Electroretinographic recordings showed higher a- and b-wave amplitudes under both photopic and scotopic conditions in safranal-treated versus non-treated animals. Furthermore, the capillary network in safranal-treated animals was preserved, unlike that found in untreated animals. Our findings indicate that dietary supplementation with safranal slows photoreceptor cell degeneration and ameliorates the loss of retinal function and vascular network disruption in P23H rats. This work also suggests that safranal could be potentially useful to retard retinal degeneration in patients with retinitis pigmentosa.

Inner Alienation: Diasporic Consciousness in Kamila Shamsie’s Salt and Saffron

Directory of Open Access Journals (Sweden)

Humaira Riaz

2015-10-01

Full Text Available The purpose of this study is to investigate the ‘diasporic consciousness ‘of the fictional characters, incorporated in selected work of Pakistani expatriate writer Kamila Shamsie through the portrayal of cross-cultural differences. This study attempts to unravel the inner-alienation that sustains through specific discourses and events occurring in the lives of the expatriate fictional characters represented in Salt and Saffron (2000. The composite term used for this study is ‘diasporic consciousness’ that refers to a specific kind of awareness dominant among the contemporary transnational communities. It is also said to possess a dual nature. More specifically, it is defined in relationship to the memories of the homeland. It emphasizes on describing a myriad of experiences showing a particular state of mind and most prominently a sense of identity. Shamsie’s Salt and Saffron portrays the cross-cultural differences between Karachi and New York, and explores an irrational fear of place in which the characters initially find themselves trapped in. Keywords: Diaspora, Consciousness, Inner-Alienation, Culture

Integrated olfactory receptor and microarray gene expression databases

Directory of Open Access Journals (Sweden)

Crasto Chiquito J

2007-06-01

Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence.

Science.gov (United States)

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-05-05

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided.

Efficiency of Saffron Farmers in Shahyk Region of Ghaen City, Iran (Application of Data Envelopment Analysis Using the Efficient and Inefficient Frontiers

Directory of Open Access Journals (Sweden)

Karim Naderi Mahdei

2015-10-01

Full Text Available Addressing the special conditions of saffron growing areas, and planning the optimum use of its production factors need specific attention and determination of the efficiency of saffron farms seems to be necessary. Thus, the current study attempts to measure the efficiency of saffron fields by using bounded data envelopment analysis to give an overall assessment of the performance of the farms. The necessary data was collected by interviewing and filling 36 questionnaires by the saffron farmers of the city of Ghaen, Iran and the data were analyzed by GAMS software. The results showed that average optimistic output and input oriented efficiency is 1.259 and 0.849, respectively. Also, 13.8% of the farms are located on the inefficiency frontiers. 47 percent of the farms are surrounded by efficient and inefficient frontier that reflects the overuse of inputs and potential to produce more and reduce the use of inputs. According to the results, it may be suggested that the efficient farms should be considered as a pattern and we should present training of need assessment in inefficient farms in order to enhance farmers’ efficiency with appropriate and scientific planning.

TiGER: a database for tissue-specific gene expression and regulation.

Science.gov (United States)

Liu, Xiong; Yu, Xueping; Zack, Donald J; Zhu, Heng; Qian, Jiang

2008-06-09

Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

TiGER: A database for tissue-specific gene expression and regulation

Directory of Open Access Journals (Sweden)

Zack Donald J

2008-06-01

Full Text Available Abstract Background Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. Results The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation. The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. Conclusion We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

The Effects of Saffron Economic Stability of Rural Residents in the Darbeghazi District City of Nishabur

Directory of Open Access Journals (Sweden)

Seyed Amir Mohamad Alavizade

2016-08-01

Full Text Available Agricultural sustainability is undoubtedly one of the most important parts of sustainable development. The main source of income for the residents of villages of the Khorasan Razavi province is based on agricultural and horticultural products especially sale of saffron. In this regard the turquoise shades of the flowers of this plant encompass all of the fields in Nishabur and they have been much welcomed by farmers in this city. In this study, the cultivation of saffron in creating economic stability of the rural district Derbghazi in the central part of the city of Nishabur city will be examined. The research method in this paper is based on library, documentary, field and analytical – descriptive studies. In this context and in order to determine the economic stability of rural areas, the Morris Davis model has been used. This model contains three matrices that separately calculate and analyze the economic indicators. The statistical population under study consists of more than one hundred households from the rural villages in the Derbghazi rural district and the sample population studied consists of 308 households based on the Cochran formula. The results of the Morris Davis model indicate that among ten villages that were studied, Behroudi, Jilo, Khojan and Norouazabad have low economic stability, and Rouhabad, Haghiye, Shadmiyane, Karizak plus the villages of Jafarabad garden and Karizak Sabbah have average economic stability. In the end and based on the results of the research study some recommendations are presented in order to maintain employment in the region and support the farmers who are cultivating saffron to encourage the till of saffron and help the economic stability of the residents of the villages that were studied.

A Longitudinal Follow-Up Study of Saffron Supplementation in Early Age-Related Macular Degeneration: Sustained Benefits to Central Retinal Function

Directory of Open Access Journals (Sweden)

M. Piccardi

2012-01-01

Full Text Available Objectives. In a previous randomized clinical trial (Falsini et al. (2010, it was shown that short-term Saffron supplementation improves retinal flicker sensitivity in early age-related macular degeneration (AMD. The aim of this study was to evaluate whether the observed functional benefits from Saffron supplementation may extend over a longer follow-up duration. Design. Longitudinal, interventional open-label study. Setting. Outpatient ophthalmology setting. Participants. Twenty-nine early AMD patients (age range: 55–85 years with a baseline visual acuity >0.3. Intervention. Saffron oral supplementation (20 mg/day over an average period of treatment of 14 (±2 months. Measurements. Clinical examination and focal-electroretinogram-(fERG- derived macular (18° flicker sensitivity estimate (Falsini et al. (2010 every three months over a followup of 14 (±2 months. Retinal sensitivity, the reciprocal value of the estimated fERG amplitude threshold, was the main outcome measure. Results. After three months of supplementation, mean fERG sensitivity improved by 0.3 log units compared to baseline values (P<0.01, and mean visual acuity improved by two Snellen lines compared to baseline values (0.75 to 0.9, P<0.01. These changes remained stable over the follow-up period. Conclusion. These results indicate that in early AMD Saffron supplementation induces macular function improvements from baseline that are extended over a long-term followup.

Effects of Bed Type, Corm Weight and Lifting Time on Quantitative and Qualitative Criteria of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

A. Mollafiilabi

2017-12-01

Full Text Available Introduction Saffron (Crocus sativus L. as the most important medicinal and agricultural crop of the world has therapeutic properties including laxative, stomach stimulant, anti cancer, anti inflammation and against spasm. One of the reasons of lower yield in traditional farms of Iran is using small corms of old farms. Combining the date of corm lifting and the duration of 25°C incubation, corms could be flowered from early September to mid-December. The results showed that corm weight of saffron affects significantly on flowering and yield. Soils covered by mulch or surface mulch compared with soils lack of mulch have a higher thermal adjustment so that in higher ambient temperature the soil can be warm later and at night they lose their warmth later. This research was conducted to find the effects of corm weight, planting beds under hydroponics at commercial level and determination of the best time of corm lifting from farm and its transfer for production and their interaction under controlled conditions on yield and other characters of this precious crop. Material and Methods In order to study effects of corm weight and time of its lifting from farm in planting beds an experiment was conducted as factorial in the form of RCBD in three replicates at the agric. Research complex of Fadak and Research Institute of Food Science and Technology (RIFST in 2010. Factors under study were: two corm weights (8 to 10 and more than 10 g, two planting beds (stone wool and peat moss and six lifting times (mid June, early July, mid July, early August , mid August and early October. For 40 days, 457 corms per m-2 were stored in incubation with 85% relative humidity and 25°C temperature at the darkness. Then, saffron corms were transferred in growth chamber with 17° C in 8/16 h light and dark. Characteristics such as number of flower, fresh weight of flower, dry weight of flower, fresh and dry weight of stigma, fresh and dry weight of style, fresh and dry

Smooth muscle relaxant activity of Crocus sativus (saffron and its constituents: possible mechanisms

Directory of Open Access Journals (Sweden)

Amin Mokhtari-Zaer

2015-08-01

Full Text Available Saffron, Crocus sativus L. (C. sativus is rich in carotenoids and used in traditional medicine for treatment of various conditions such as coughs, stomach disorders, amenorrhea, asthma and cardiovascular disorders. These therapeutic effects of the plant are suggested to be due to its relaxant effect on smooth muscles. The effect of C. sativus and its constituents on different smooth muscles and the underlying mechanisms have been studied. Several studies have shown the relaxant effects of C. sativus and its constituents including safranal, crocin, crocetin and kaempferol on blood vessels. In addition, it was reported that saffron stigma lowers systolic blood pressure. The present review highlights the relaxant effects of C. sativus and its constituents on various smooth muscles. The possible mechanisms of this relaxing effect including activation of ß2-adrenoceptors, inhibition of histamine H1 and muscarinic receptors and calcium channels and modulation of nitric oxide (NO are also reviewed.

Candidate enzymes for saffron crocin biosynthesis are localized in multiple cellular compartments

KAUST Repository

Demurtas, Olivia Costantina

2018-05-29

Saffron is composed of the dried stigmas of Crocus sativus and is the most expensive spice on Earth. Its red color is due to the apocarotenoid glycosides, crocins, which accumulate in the vacuole and reach up to 10% of the stigma dry weight. We have previously characterized the first dedicated enzyme in crocin biosynthesis, CsCCD2, which cleaves zeaxanthin to yield crocetin dialdehyde. In this work, we identified six putative aldehyde dehydrogenase (ALDH) transcripts expressed in saffron stigmas. When expressed in E. coli, only one of corresponding proteins (CsALDH3I1), was able to convert crocetin dialdehyde into the crocin precursor, crocetin. CsALDH3I1 carries a C-terminal hydrophobic domain, similar to that of a Neurospora membrane-associated apocarotenoid dehydrogenase, YLO-1. We also characterized a UDP-glycosyltransferase enzyme, CsUGT74AD1, able to convert crocetin to crocins 1 and 2\\'. In vitro assays showed high specificity of CsALDH3I1 for crocetin dialdehyde and long chain apocarotenals, and of CsUGT74AD1 for crocetin. Upon extract fractionation, the CsCCD2, CsALDH3I1 and CsUGT74AD1 enzymes partitioned in the insoluble fraction, suggesting that they are associated to membranes or to large insoluble complexes. Immunogold labeling of saffron stigmas and confocal microscopy of fusions to Green Fluorescent Protein expressed in N. benthamiana leaves revealed that CsCCD2 localizes to plastids, CsALDH3I1 to the endoplasmic reticulum (ER) and CsUGT74AD1 to the cytoplasm, in association with cytoskeletal-like structures. Based on our and on literature data, we propose that the ER and cytoplasm function as

Candidate enzymes for saffron crocin biosynthesis are localized in multiple cellular compartments

KAUST Repository

Demurtas, Olivia Costantina; Frusciante, Sarah; Ferrante, Paola; Diretto, Gianfranco; Azad, Noraddin Hosseinpour; Pietrella, Marco; Aprea, Giuseppe; Taddei, Anna Rita; Romano, Elena; Mi, Jianing; Al-Babili, Salim; Frigerio, Lorenzo; Giuliano, Giovanni

2018-01-01

Saffron is composed of the dried stigmas of Crocus sativus and is the most expensive spice on Earth. Its red color is due to the apocarotenoid glycosides, crocins, which accumulate in the vacuole and reach up to 10% of the stigma dry weight. We have previously characterized the first dedicated enzyme in crocin biosynthesis, CsCCD2, which cleaves zeaxanthin to yield crocetin dialdehyde. In this work, we identified six putative aldehyde dehydrogenase (ALDH) transcripts expressed in saffron stigmas. When expressed in E. coli, only one of corresponding proteins (CsALDH3I1), was able to convert crocetin dialdehyde into the crocin precursor, crocetin. CsALDH3I1 carries a C-terminal hydrophobic domain, similar to that of a Neurospora membrane-associated apocarotenoid dehydrogenase, YLO-1. We also characterized a UDP-glycosyltransferase enzyme, CsUGT74AD1, able to convert crocetin to crocins 1 and 2'. In vitro assays showed high specificity of CsALDH3I1 for crocetin dialdehyde and long chain apocarotenals, and of CsUGT74AD1 for crocetin. Upon extract fractionation, the CsCCD2, CsALDH3I1 and CsUGT74AD1 enzymes partitioned in the insoluble fraction, suggesting that they are associated to membranes or to large insoluble complexes. Immunogold labeling of saffron stigmas and confocal microscopy of fusions to Green Fluorescent Protein expressed in N. benthamiana leaves revealed that CsCCD2 localizes to plastids, CsALDH3I1 to the endoplasmic reticulum (ER) and CsUGT74AD1 to the cytoplasm, in association with cytoskeletal-like structures. Based on our and on literature data, we propose that the ER and cytoplasm function as

Mining biological databases for candidate disease genes

Science.gov (United States)

Braun, Terry A.; Scheetz, Todd; Webster, Gregg L.; Casavant, Thomas L.

2001-07-01

The publicly-funded effort to sequence the complete nucleotide sequence of the human genome, the Human Genome Project (HGP), has currently produced more than 93% of the 3 billion nucleotides of the human genome into a preliminary `draft' format. In addition, several valuable sources of information have been developed as direct and indirect results of the HGP. These include the sequencing of model organisms (rat, mouse, fly, and others), gene discovery projects (ESTs and full-length), and new technologies such as expression analysis and resources (micro-arrays or gene chips). These resources are invaluable for the researchers identifying the functional genes of the genome that transcribe and translate into the transcriptome and proteome, both of which potentially contain orders of magnitude more complexity than the genome itself. Preliminary analyses of this data identified approximately 30,000 - 40,000 human `genes.' However, the bulk of the effort still remains -- to identify the functional and structural elements contained within the transcriptome and proteome, and to associate function in the transcriptome and proteome to genes. A fortuitous consequence of the HGP is the existence of hundreds of databases containing biological information that may contain relevant data pertaining to the identification of disease-causing genes. The task of mining these databases for information on candidate genes is a commercial application of enormous potential. We are developing a system to acquire and mine data from specific databases to aid our efforts to identify disease genes. A high speed cluster of Linux of workstations is used to analyze sequence and perform distributed sequence alignments as part of our data mining and processing. This system has been used to mine GeneMap99 sequences within specific genomic intervals to identify potential candidate disease genes associated with Bardet-Biedle Syndrome (BBS).

AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L. germplasm.

Directory of Open Access Journals (Sweden)

Matteo Busconi

Full Text Available The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence and epigenetic (cytosine methylation level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12 effective different genotypes, the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28 different effective epigenotypes. The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real and accessions from the East (Cuenca and Teruel were clearly recognised.

The Effect of Pre-emergence Application of some Common Herbicides on Weed Population, Vegetative Growth, Flower and Corm Characteristics of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

R. Sadrabadi Haghighi

2016-06-01

Full Text Available Intoduction: Saffron (Corocus sativus L. as the most expensive crop has special position among export products of Iran. Currently, Iran is the biggest saffron producer and exporter in the world. Much of saffron in Iran produced in South and Razavi provinces (6. One of the problems in saffron production of these regions is weed control. Weed competing with saffron for water, nutrients, light cause reduction of product (3, 7. Among control methods of weed, use of herbicides is not common in saffron fields. The main reason is the evidences about herbicides damage. For example, Zare Hosseini et al (14 observed application of herbicides of Iodosulfuron methyl sodium + Mesosulfuron- methyl+ Mefenpyr-diethyl destroyed grasses and broadleaf, but it destroyed saffron plant too. Haloxyfop- R methyl ester damaged grasses, but decreased stigma yield. This study aimed to investigate the effect of pre-emergence herbicides on weed population changes; the performance characteristics of saffron and saffron corms were implemented. Materials and Methods: An experiment was conducted in a 4-year saffron farm located in Shahn Abad village, Zaveh city in Khorasan Razavi province in 2011- 2012. It was in a completely randomized block design with eight treatments and three replications. The treatments included six pre-emergence herbicides including Metribuzin 70% WP (850 g.ha-1, Oxyfluorfen24% EC (1 l.ha-1, Ioxynil 22.5% EC (1.5 l.ha-1, Etalfluorelin 33.3%EC (3 l.ha-1, Trifluoralin 48%EC (2 l.ha-1 and Chloridazon 80 %WP (5 Kg.ha-1 + Desmedipham 15.7% EC (5 l.ha-1 along with weed free and weedy check. Herbicides applied after irrigation simultaneously with crust breaking. The measurement characteristics included the number of flowers, fresh and dry weight of flower and stigma, leaf dry weight, leaf length, corm number and weight of saffron, weed type and wet and dry weight of dominant weeds. Herbicide treatments after irrigation were performed simultaneously with Crust

CCDB: a curated database of genes involved in cervix cancer.

Science.gov (United States)

Agarwal, Subhash M; Raghav, Dhwani; Singh, Harinder; Raghava, G P S

2011-01-01

The Cervical Cancer gene DataBase (CCDB, http://crdd.osdd.net/raghava/ccdb) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. In spite of the large women population that is presently affected from this malignancy still at present, no database exists that catalogs information on genes associated with cervical cancer. Therefore, we have compiled 537 genes in CCDB that are linked with cervical cancer causation processes such as methylation, gene amplification, mutation, polymorphism and change in expression level, as evident from published literature. Each record contains details related to gene like architecture (exon-intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search, thereby providing researchers with easy access to the latest information on genes involved in cervix cancer.

Update of the androgen receptor gene mutations database.

Science.gov (United States)

Gottlieb, B; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1999-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 309 to 374 during the past year. We have expanded the database by adding information on AR-interacting proteins; and we have improved the database by identifying those mutation entries that have been updated. Mutations of unknown significance have now been reported in both the 5' and 3' untranslated regions of the AR gene, and in individuals who are somatic mosaics constitutionally. In addition, single nucleotide polymorphisms, including silent mutations, have been discovered in normal individuals and in individuals with male infertility. A mutation hotspot associated with prostatic cancer has been identified in exon 5. The database is available on the internet (http://www.mcgill.ca/androgendb/), from EMBL-European Bioinformatics Institute (ftp.ebi.ac.uk/pub/databases/androgen), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca). Copyright 1999 Wiley-Liss, Inc.

Antitumor Effects of Saffron-Derived Carotenoids in Prostate Cancer Cell Models

Directory of Open Access Journals (Sweden)

Claudio Festuccia

2014-01-01

Full Text Available Crocus sativus L. extracts (saffron are rich in carotenoids. Preclinical studies have shown that dietary intake of carotenoids has antitumor effects suggesting their potential preventive and/or therapeutic roles. We have recently reported that saffron (SE and crocin (CR exhibit anticancer activity by promoting cell cycle arrest in prostate cancer (PCa cells. It has also been demonstrated that crocetin esters are produced after SE gastrointestinal digestion by CR hydrolysis. The aim of the present report was to investigate if SE, crocetin (CCT, and CR affected in vivo tumor growth of two aggressive PCa cell lines (PC3 and 22rv1 which were xenografted in male nude mice treated by oral gavage with SE, CR, and CCT. We demonstrated that the antitumor effects of CCT were higher when compared to CR and SE and treatments reverted the epithelial-mesenchymal transdifferentiation (EMT as attested by the significant reduction of N-cadherin and beta-catenin expression and the increased expression of E-cadherin. Additionally, SE, CR, and CCT inhibited PCa cell invasion and migration through the downmodulation of metalloproteinase and urokinase expression/activity suggesting that these agents may affect metastatic processes. Our findings suggest that CR and CCT may be dietary phytochemicals with potential antitumor effects in biologically aggressive PCa cells.

DDEC: Dragon database of genes implicated in esophageal cancer

International Nuclear Information System (INIS)

Essack, Magbubah; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B

2009-01-01

Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports. We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic

A survey on technical efficiency, marketing and market structure of saffron crop, Iran

Directory of Open Access Journals (Sweden)

Mahmoud Shaban

2014-03-01

Full Text Available The current study attempted to determine technical efficiency as well as study the marketing and market structure of Saffarn crop in Iran. To access the research goals 140 farms, 25 retailers and 14 wholesalers randomly selected. The necessary data collected through interview and filling questionarie. Apart from this, some agricultural Expert from selected cities of Razavi province have been chosen to interview. To determine the market time-series data for the period of 1995-12 was used. To determine technical efficiency DEA method, to calculate marketing margins Digbi method and to find market structure concentration ratio and Herfindal index were used. The results indicated that, the average technical efficiency was 63.49 and minimum and maximum technical efficiency respectively 19.04 and 100, retailer margin mean of Saffron was more than wholesale margin mean and average marketing cost coefficient of Saffron was about 14.78. It means that, marketing factors share in final price is 14.78. Address to the results the Saffaran’s market structure is oligopoly.

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

Science.gov (United States)

Liberzon, Arthur; Birger, Chet; Thorvaldsdóttir, Helga; Ghandi, Mahmoud; Mesirov, Jill P; Tamayo, Pablo

2015-12-23

The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.

Analysis of the effects of change in cropping pattern due to drought on saffron production in rural areas of the Zebarkhan district villages

Directory of Open Access Journals (Sweden)

Hamdollah Sojasi Qidari

2017-04-01

Full Text Available Selection of a given cropping pattern can have serious results on the farmers’ life and rural society because of the multi dimensionality of agriculture. However, in many cases, farmers are inclined to change the cropping pattern because of changes in natural situations, changes in demand and consumption, etc. One of the most important and effective factors of change cropping pattern amongst Iranian farmers in recent years is the drought problem. One of the more current cultural method changes in the Khorasan region is inclination to saffron cultivation that can have various economic, social and environmental effects. Thus, this research paid attention to the investigation of changes from cultivation method from drought to the economic, social and environmental dimensions of saffron production amongst the villagers of the Zebarkhan district of the Khorasan Razavi province. Analytical-description methodology was used for this purpose. Data collection was done using the library- field methodology with researcher’s questionnaire whose narrative is 0.78 according to Cronbach's alpha method. Therefore, by using the Cochran formula with the intended level of 0.05, 142 farmers have been selected by available sampling method that have changed their cropping pattern to saffron production because of water shortages and drought. Then, their ideas were analyzed considering cases of economic, social and environmental effects of cropping pattern change to saffron production. The results showed meaningful changes in all research indices except for increase of cultivation surface area. Moreover, the most important changes of cropping pattern and switching over to saffron production have been identified using the Shannon entropy weighing method. In addition, the shown the revealed with continuation of differences of the changes in cropping pattern of saffron between the various villages were analyzed by using the multi-index TOPSIS. Finally, it was shown

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

Directory of Open Access Journals (Sweden)

Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

An Interactive Database of Cocaine-Responsive Gene Expression

Directory of Open Access Journals (Sweden)

Willard M. Freeman

2002-01-01

Full Text Available The postgenomic era of large-scale gene expression studies is inundating drug abuse researchers and many other scientists with findings related to gene expression. This information is distributed across many different journals, and requires laborious literature searches. Here, we present an interactive database that combines existing information related to cocaine-mediated changes in gene expression in an easy-to-use format. The database is limited to statistically significant changes in mRNA or protein expression after cocaine administration. The Flash-based program is integrated into a Web page, and organizes changes in gene expression based on neuroanatomical region, general function, and gene name. Accompanying each gene is a description of the gene, links to the original publications, and a link to the appropriate OMIM (Online Mendelian Inheritance in Man entry. The nature of this review allows for timely modifications and rapid inclusion of new publications, and should help researchers build second-generation hypotheses on the role of gene expression changes in the physiology and behavior of cocaine abuse. Furthermore, this method of organizing large volumes of scientific information can easily be adapted to assist researchers in fields outside of drug abuse.

License - Gene Name Thesaurus | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Gene Name Thesaurus License to Use This Database Last updated : 2012/01/17 The license for this database... is the license specified in the Creative Commons Attribution-Share Alike 2.1 Japan . If you use data from this database..., please be sure attribute this database as follows: Gene Name Thesaurus, © The Data...he summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here . With regard to this database..., you are licensed to: freely access part or whole of this database, and acquire data; freely redistrib

Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde

Directory of Open Access Journals (Sweden)

Lourdes Gómez-Gómez

2018-05-01

Full Text Available In saffron, the cleavage of zeaxanthin by means of CCD2 generates crocetin dialdehyde, which is then converted by an unknown aldehyde dehydrogenase to crocetin. A proteome from saffron stigma was released recently and, based on the expression pattern and correlation analyses, five aldehyde dehydrogenases (ALDHs were suggested as possible candidates to generate crocetin from crocetin dialdehydes. We selected four of the suggested ALDHs and analyzed their expression in different tissues, determined their activity over crocetin dialdehyde, and performed structure modeling and docking calculation to find their specificity. All the ALDHs were able to convert crocetin dialdehyde to crocetin, but two of them were stigma tissue-specific. Structure modeling and docking analyses revealed that, in all cases, there was a high coverage of residues in the models. All of them showed a very close conformation, indicated by the low root-mean-square deviation (RMSD values of backbone atoms, which indicate a high similarity among them. However, low affinity between the enzymes and the crocetin dialdehyde were observed. Phylogenetic analysis and binding affinities calculations, including some ALDHs from Gardenia jasmonoides, Crocus sieberi, and Buddleja species that accumulate crocetin and Bixa orellana synthetizing the apocarotenoid bixin selected on their expression pattern matching with the accumulation of either crocins or bixin, pointed out that family 2 C4 members might be involved in the conversion of crocetin dialdehyde to crocetin with high specificity.

DDEC: Dragon database of genes implicated in esophageal cancer

KAUST Repository

Essack, Magbubah

2009-07-06

Background: Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Description: Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new \\'association hypotheses\\' generated based on the precompiled reports. Conclusion: We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is

To Evaluate the Effect of Soil Physical and Chemical Characteristics on the Growth Characteristics of Saffron (Crocus sativus L. Corms in Tornbat-e Heydariyeh Area

Directory of Open Access Journals (Sweden)

Fariba Zarghani

2016-07-01

Full Text Available Introduction Saffron is one of the most economically important plants across Iran and all over the world. The most important cultivated areas of saffron are in Khorasan-e Razavi and Southern Khorasan provinces (Jihad Keshavarzi Khorasan Razavi, 2013. The corm is the reservoir of photosynthetic materials and plays an important role in the saffron life cycle. Corm size and physicochemical characteristics of soil determine the growth and yield of saffron (Aytekin et al., 2008. It has been advised to use corms with diameter more than 2.5 cm (Kafi et al., 2002. Despite the importance of this plant, few studies have been conducted on the effects of soil characteristics on the growth of the plant in natural field conditions. Therefore, the objective which we will try to achieve is: to evaluate the effect of soil physical and chemical characteristics of the growth of saffron corm and determine the most important effect characteristics. Materials and methods In September 2012, 30 samples of 3 to 5 years old saffron corms were taken from the fields with similar management in Torbat Heydariyeh. The surrounding soil corms (depth of 0 to 30 cm were sampled, too. Dry weight of corms was measured in the laboratory. Air dried soil samples were passed through a 2 mm sieve and used for physical-chemical analyses. Soil texture was determined by using pipet method. Total nitrogen, available phosphorous, available potassium, soil organic carbon and calcium carbonate equivalent were measured in bulk soil samples. Calcium, magnesium, sodium, EC and pH were measured in the saturated soil paste. Fe, Cu and Zn were extracted by DTPA and measured by atomic adsorption spectroscopy. Correlation, regression and neural network technique were used to analyze the data and to identify the most important soil characteristics on the corms characteristics. Results and discussion Diameter and dry weight of corms with mean values of 34.04 mm and 3.72 g, ranged from 22.8 to 51.7 mm

Effect of Stevia (Stevia rebaudiana as a Substitute for Sugar on Physicochemical, Rheological and Sensory Properties of Dietary Saffron Syrup

Directory of Open Access Journals (Sweden)

Neda Hashemi

2015-01-01

Full Text Available In recent years production and usage of functional food and drinks is one of the public and scientist’s interest. Since carbohydrates have been recognizedas the major calorie source in many food baskets, most attention has been focused on substitution of sucrose with non-caloric sweeteners. Although both natural and synthetic sweeteners have been used in the formulation of food stuffs, deep concern is raised regarding safety aspects of synthetic ones. Stevia is a natural suitable sweetener that is currently being used as a substitute for sugar in many dietary and functional foods and drinks. In the present study the effect of using stevia sugar as a replacement for sucrose in the preparation of saffron beverages was investigated. Accordingly, saffron syrup was prepared with 5 treatments in which100%, 75%, 50%, 25% and 0% of stevia sugar replaced sucrose. Then, the physicochemical, rheological and sensory properties of saffron functional syrup were investigated. The results indicated that by increasing stevia brix level, density and viscosity increased but the syrups’ pH decreases. The best treatment was the sample containing 25% steviaand 75% sucrose that compared to other samples regarding sensory characteristics had a higher acceptance by consumer and regarding physicochemical and rheological characteristics more similar to the control sample.

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

Science.gov (United States)

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

DDEC: Dragon database of genes implicated in esophageal cancer

KAUST Repository

Essack, Magbubah; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B.

2009-01-01

expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined

Organic saffron position in the future household consumption basket and effective structures (Case study

Directory of Open Access Journals (Sweden)

Ahmadreza Shahpouri

2014-09-01

Full Text Available Considering the importance of planning at the production level, it is necessary to identify the consumer's future behavior towards organic products. Thus, using seemingly unrelated regression and data of 2012 for 200 households in mashhad, in the present study we have tried to determine the future share of these products in the household's basket and also survey the effective factors on this share in organic saffron. The results showed that households in mashhad tend to allocate an average of 34 percent of their future consumption basket for organic saffron. The regression results illustrated that while children below 10 years old in the households, willingness to pay the price differential compared with non-organic products and organic labeling positively affected the willingness to pay for organic products, environmental concerns variables created by non-organic products had a negative effect on their willingness. Considering the research results, helping to raise people's awareness about food through different educational and advertising approaches, providing a mechanism to label organic products and assessing the strengths and weaknesses of producing and distributing the organic products are provided as suggestions.

Effect of Corm Density on Yield and Qualitative Traits of Saffron (Crocus sativus L. under Different Urea and Biological Fertilizers in Shahr-e-Rey Region

Directory of Open Access Journals (Sweden)

Alireza pazoki

2017-07-01

Full Text Available To study the effect of corm density on yield and qualitative traits of saffron (Crocus sativus L. under different biological and chemical nitrogen fertilizers, a factorial experiment based on completely randomized block design with 3 replications was done in 2014 at Shahr-e-Rey region (Ghomi Abad. The experimental factors were: corm density in 3 levels (60, 120 and 180 corm per square meter and biological and chemical nitrogen fertilizers in 4 levels (without fertilizer application, 150 kg.ha-1 of Urea, 5 L.ha-1 of Nitroxin and 75 kg.ha-1 of Urea +5 L.ha-1 of Nitroxin. The results indicated that the corm density affects number of daughter corm, fresh daughter corm weight, corm diameter, dry stigma and style weight, dry and fresh flower weight significantly. Mean comparisons also indicated that by increasing corm density from 6o to 180, saffron dry yield of saffron improved by 2.7 fold. However, increasing corm density reduced corm diameter, fresh corm daughter weight and their numbers per square meter. It can be concluded that nitroxin as an organic fertilizer, increases vegetative traits and saffron dry yield (stigma + style weight to 2.08 kg.ha-1 and highly improves in qualitative traits like Safranal, Picrocrocin, and Crocin. It can be also said that combined use of nitroxin and urea would be an alternative method to reduce application of urea.

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases

Directory of Open Access Journals (Sweden)

Ma'ayan Avi

2007-10-01

Full Text Available Abstract Background In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP, generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. Results Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Conclusion Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Science.gov (United States)

Li, Li; Brunk, Brian P.; Kissinger, Jessica C.; Pape, Deana; Tang, Keliang; Cole, Robert H.; Martin, John; Wylie, Todd; Dante, Mike; Fogarty, Steven J.; Howe, Daniel K.; Liberator, Paul; Diaz, Carmen; Anderson, Jennifer; White, Michael; Jerome, Maria E.; Johnson, Emily A.; Radke, Jay A.; Stoeckert, Christian J.; Waterston, Robert H.; Clifton, Sandra W.; Roos, David S.; Sibley, L. David

2003-01-01

Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%–20% represent putative homologs with a conservative cutoff of p neurona: , , , , , , , , , , , , , –, –, –, –, –. Eimeria tenella: –, –, –, –, –, –, –, –, – , –, –, –, –, –, –, –, –, –, –, –. Neospora caninum: –, –, , – , –, –.] PMID:12618375

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.

Science.gov (United States)

Kawamura, Takashi; Ohtsubo, Masafumi; Mitsuyama, Susumu; Ohno-Nakamura, Saho; Shimizu, Nobuyoshi; Minoshima, Shinsei

2010-06-01

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

Science.gov (United States)

Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

2012-01-01

Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and

Identification of Apo- Carotenoids' Crocin and Crocetin Isomers in Saffron Crude Extracts by HPLC Coupled to Atmospheric Pressure Chemical Ionization and High Resolution Orbitrap Mass Spectrometry

Directory of Open Access Journals (Sweden)

Noraddin Hosseinpour azad

2017-01-01

Full Text Available The main metabolites in saffron are the Apo- carotenoids’ Crocin and Crocetin. Color intensity and quality of saffron mostly depend on the presence of Crocins that are glycosylated steric form of Crocetin by glycosyltransferase enzyme. The aim of this study is the characterization of these metabolites in methanolic and chloroformic extracts of saffron stigmas during anthesis stage by LC-APCI-MS. Identification of cis and trans isomers of Crocin and Crocetin was done by three parameters such as mass spectra registered in the negative ion mode, retention time and absorption ratio related to each metabolites. The variability of these parameters made it possible to detect the Crocins isomer with regard to the attached position and the number of UDP- glucose and Gentiobiosyl molecules to Crocetin structure. Crocins was the mainly detected components as there are polar components that are classified in the carotenoeids groups and the strified form of Crocetin Glucose (β-D-Glucopyranosyl and Gentiobiose (β-D-Glucopyranosyl-D-Glucose. Also doubly charged ions were found for trans-isomers of Crocin-4, due to the high symmetry of their molecules. Based on the data gathered, the applied chromatograph Machin in this project is accurate and it is most sensitive tools to investigate about plants’ natural components like saffron, also the used APCI-MS in negative ions mode is the most efficient method to distinguish different steric forms of Crocin based on the ion’s fragments related to united reduction of glycosyl and gentiobiosyl as well as molecular fractions.

DDPC: Dragon database of genes associated with prostate cancer

KAUST Repository

Maqungo, Monique

2010-09-29

Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc .kaust.edu.sa/ddpc/. The Author(s) 2010.

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

Science.gov (United States)

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database

Gene Name Thesaurus - Gene Name Thesaurus | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available 08/lsdba.nbdc00966-001 Description of data contents Curators who have expertize in biological research edit ...onym information fields in various gene/genome databases. 2. The curators who have expertise in biological research

Autism genetic database (AGD: a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites

Directory of Open Access Journals (Sweden)

Talebizadeh Zohreh

2009-09-01

Full Text Available Abstract Background Autism is a highly heritable complex neurodevelopmental disorder, therefore identifying its genetic basis has been challenging. To date, numerous susceptibility genes and chromosomal abnormalities have been reported in association with autism, but most discoveries either fail to be replicated or account for a small effect. Thus, in most cases the underlying causative genetic mechanisms are not fully understood. In the present work, the Autism Genetic Database (AGD was developed as a literature-driven, web-based, and easy to access database designed with the aim of creating a comprehensive repository for all the currently reported genes and genomic copy number variations (CNVs associated with autism in order to further facilitate the assessment of these autism susceptibility genetic factors. Description AGD is a relational database that organizes data resulting from exhaustive literature searches for reported susceptibility genes and CNVs associated with autism. Furthermore, genomic information about human fragile sites and noncoding RNAs was also downloaded and parsed from miRBase, snoRNA-LBME-db, piRNABank, and the MIT/ICBP siRNA database. A web client genome browser enables viewing of the features while a web client query tool provides access to more specific information for the features. When applicable, links to external databases including GenBank, PubMed, miRBase, snoRNA-LBME-db, piRNABank, and the MIT siRNA database are provided. Conclusion AGD comprises a comprehensive list of susceptibility genes and copy number variations reported to-date in association with autism, as well as all known human noncoding RNA genes and fragile sites. Such a unique and inclusive autism genetic database will facilitate the evaluation of autism susceptibility factors in relation to known human noncoding RNAs and fragile sites, impacting on human diseases. As a result, this new autism database offers a valuable tool for the research

Antihyperlipidemic effect of crude extract of saffron stigma (Crocus sativus) in healthy male rats

OpenAIRE

Iliass Lahmass; Sabir Ouahhoud; Assia Sabouni; Mohammed Elyoubi; Redouane Benabbas; Rachid Elmoussaoui; Mohammed Choukri; Ennouamane Saalaoui

2017-01-01

In this study, we investigated for the first time the antihyperlipidemic ef-fects of crude extract of stigmas from Crocus sativus (saffron) against hyperlipidemia induced by tartrazine (synthetic dye) in normal male rats. Thirty adult male albino rats weighing about 150 - 200 g, were divided into 5 groups (n = 6) and daily treatment was given orally. Clinical biochemis-try and metabolic parameters were evaluated at the end of the experiment and after 105 days. (n=6, for all groups). Our data ...

MAGIC Database and Interfaces: An Integrated Package for Gene Discovery and Expression

Directory of Open Access Journals (Sweden)

Lee H. Pratt

2006-03-01

Full Text Available The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs, and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.

Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

Science.gov (United States)

Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

2011-12-01

The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Directory of Open Access Journals (Sweden)

Baseler Michael W

2007-11-01

Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

AGEMAP: a gene expression database for aging in mice.

Directory of Open Access Journals (Sweden)

Jacob M Zahn

2007-11-01

Full Text Available We present the AGEMAP (Atlas of Gene Expression in Mouse Aging Project gene expression database, which is a resource that catalogs changes in gene expression as a function of age in mice. The AGEMAP database includes expression changes for 8,932 genes in 16 tissues as a function of age. We found great heterogeneity in the amount of transcriptional changes with age in different tissues. Some tissues displayed large transcriptional differences in old mice, suggesting that these tissues may contribute strongly to organismal decline. Other tissues showed few or no changes in expression with age, indicating strong levels of homeostasis throughout life. Based on the pattern of age-related transcriptional changes, we found that tissues could be classified into one of three aging processes: (1 a pattern common to neural tissues, (2 a pattern for vascular tissues, and (3 a pattern for steroid-responsive tissues. We observed that different tissues age in a coordinated fashion in individual mice, such that certain mice exhibit rapid aging, whereas others exhibit slow aging for multiple tissues. Finally, we compared the transcriptional profiles for aging in mice to those from humans, flies, and worms. We found that genes involved in the electron transport chain show common age regulation in all four species, indicating that these genes may be exceptionally good markers of aging. However, we saw no overall correlation of age regulation between mice and humans, suggesting that aging processes in mice and humans may be fundamentally different.

New mutations and an updated database for the patched-1 (PTCH1) gene.

Science.gov (United States)

Reinders, Marie G; van Hout, Antonius F; Cosgun, Betûl; Paulussen, Aimée D; Leter, Edward M; Steijlen, Peter M; Mosterd, Klara; van Geel, Michel; Gille, Johan J

2018-05-01

Basal cell nevus syndrome (BCNS) is an autosomal dominant disorder characterized by multiple basal cell carcinomas (BCCs), maxillary keratocysts, and cerebral calcifications. BCNS most commonly is caused by a germline mutation in the patched-1 (PTCH1) gene. PTCH1 mutations are also described in patients with holoprosencephaly. We have established a locus-specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). We included 117 new PTCH1 variations, in addition to 331 previously published unique PTCH1 mutations. These new mutations were found in 141 patients who had a positive PTCH1 mutation analysis in either the VU University Medical Centre (VUMC) or Maastricht University Medical Centre (MUMC) between 1995 and 2015. The database contains 331 previously published unique PTCH1 mutations and 117 new PTCH1 variations. We have established a locus-specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). The database provides an open collection for both clinicians and researchers and is accessible online at http://www.lovd.nl/PTCH1. © 2018 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.

DDPC: Dragon database of genes associated with prostate cancer

KAUST Repository

Maqungo, Monique; Kaur, Mandeep; Kwofie, Samuel K.; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Oppon, Ekow; Christoffels, Alan; Bajic, Vladimir B.

2010-01-01

associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise

The "GeneTrustee": a universal identification system that ensures privacy and confidentiality for human genetic databases.

Science.gov (United States)

Burnett, Leslie; Barlow-Stewart, Kris; Proos, Anné L; Aizenberg, Harry

2003-05-01

This article describes a generic model for access to samples and information in human genetic databases. The model utilises a "GeneTrustee", a third-party intermediary independent of the subjects and of the investigators or database custodians. The GeneTrustee model has been implemented successfully in various community genetics screening programs and has facilitated research access to genetic databases while protecting the privacy and confidentiality of research subjects. The GeneTrustee model could also be applied to various types of non-conventional genetic databases, including neonatal screening Guthrie card collections, and to forensic DNA samples.

Saffron extracts effect on processes in brain structures under exposure to x-ray irradiation of medium dose

International Nuclear Information System (INIS)

Rzaeva, A.

2012-01-01

Full text : Process of ionizing radiation on live organism is accompanied by interaction of free radicals (FR) with molecules of proteins, nucleic acids and lipids. In its turn, FR occurs subsequently by excitation and ionization of molecules. Besides all, ionizing radiation becomes the reason of accumulation in body tissues of toxic products (radio toxic) that strengthen beam effect. Endogenous antioxidatic system (EAS) of an organism plays a significant role in detoxication of redundant quantity of FR formed in cells. Ionizing radiation influences negatively to high-grade functioning of basic EAS enzymes. Besides, during radiation injuries, the level of FR increases. In case of its exhaustion and lack insertion of natural antioxidants (bioantioxidants) to organism plays a therapeutic role. Thus, in our work we used saffron extract in experiments with the purpose of studying its effect on the activity of antioxidant enzymes at radiation influence. Determination of proteins has been carried out with Lowry method. In the result of carried-out researches, it has been detected fixed dynamics of activity change of antioxidant enzymes in various brain structures of white rats within x-ray irradiation at medium dose, and joint impact of x-ray radiation of saffron extract. Under exposure to X-ray irradiation of medium dose in some brain structures decreasing of catalase activity was revealed. Tendency towards decreasing is more developed on the 3th day of irradiation. As opposed to catalase activity GPO activity was increased. Insertion of saffron extract to experimental animals (for 21 days before irradiation) conducive to prevention the decreasing of catalase activity stabilizes GPO activity and exerts an effective influence. Thereby, bioantioxidants have significant role in the regulation of processes occurred in tissues and cells under the influence of extreme factors. Antioxidant protection system of organism carries out continuous protection of organism from toxic

Online Analytical Processing (OLAP: A Fast and Effective Data Mining Tool for Gene Expression Databases

Directory of Open Access Journals (Sweden)

Alkharouf Nadim W.

2005-01-01

Full Text Available Gene expression databases contain a wealth of information, but current data mining tools are limited in their speed and effectiveness in extracting meaningful biological knowledge from them. Online analytical processing (OLAP can be used as a supplement to cluster analysis for fast and effective data mining of gene expression databases. We used Analysis Services 2000, a product that ships with SQLServer2000, to construct an OLAP cube that was used to mine a time series experiment designed to identify genes associated with resistance of soybean to the soybean cyst nematode, a devastating pest of soybean. The data for these experiments is stored in the soybean genomics and microarray database (SGMD. A number of candidate resistance genes and pathways were found. Compared to traditional cluster analysis of gene expression data, OLAP was more effective and faster in finding biologically meaningful information. OLAP is available from a number of vendors and can work with any relational database management system through OLE DB.

Online analytical processing (OLAP): a fast and effective data mining tool for gene expression databases.

Science.gov (United States)

Alkharouf, Nadim W; Jamison, D Curtis; Matthews, Benjamin F

2005-06-30

Gene expression databases contain a wealth of information, but current data mining tools are limited in their speed and effectiveness in extracting meaningful biological knowledge from them. Online analytical processing (OLAP) can be used as a supplement to cluster analysis for fast and effective data mining of gene expression databases. We used Analysis Services 2000, a product that ships with SQLServer2000, to construct an OLAP cube that was used to mine a time series experiment designed to identify genes associated with resistance of soybean to the soybean cyst nematode, a devastating pest of soybean. The data for these experiments is stored in the soybean genomics and microarray database (SGMD). A number of candidate resistance genes and pathways were found. Compared to traditional cluster analysis of gene expression data, OLAP was more effective and faster in finding biologically meaningful information. OLAP is available from a number of vendors and can work with any relational database management system through OLE DB.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

Science.gov (United States)

Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

2018-01-04

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

A Serial Analysis of Gene Expression (SAGE) database analysis of chemosensitivity

DEFF Research Database (Denmark)

Stein, Wilfred D; Litman, Thomas; Fojo, Tito

2004-01-01

are their corresponding solid tumors. We used the Serial Analysis of Gene Expression (SAGE) database to identify differences between solid tumors and cell lines, hoping to detect genes that could potentially explain differences in drug sensitivity. SAGE libraries were available for both solid tumors and cell lines from...

Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

KAUST Repository

Frusciante, Sarah; Diretto, Gianfranco; Bruno, Mark; Ferrante, Paola; Pietrella, Marco; Prado-Cabrero, Alfonso; Rubio-Moraga, Á ngela L.; Beyer, Peter D.; Gó mez-Gó mez, Lourdes; Al-Babili, Salim; Giuliano, Giovanni

2014-01-01

Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7′,8′ double bonds adjacent to a 3-OH-β-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-β-apo-8′-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-β-apo-8′-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the β-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope.

Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

KAUST Repository

Frusciante, Sarah

2014-08-05

Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7′,8′ double bonds adjacent to a 3-OH-β-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-β-apo-8′-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-β-apo-8′-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the β-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope.

GeneBins: a database for classifying gene expression data, with application to plant genome arrays

Directory of Open Access Journals (Sweden)

Weiller Georg

2007-03-01

Full Text Available Abstract Background To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms. Results We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG ontology. The GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula. An online analysis tool to identify relevant functions is also provided. Conclusion GeneBins provides resources to interpret gene expression results from microarray experiments. It is available at http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/

Effects of Cinnamon, Cardamom, Saffron, and Ginger Consumption on Markers of Glycemic Control, Lipid Profile, Oxidative Stress, and Inflammation in Type 2 Diabetes Patients.

Science.gov (United States)

Azimi, Paria; Ghiasvand, Reza; Feizi, Awat; Hariri, Mitra; Abbasi, Behnoud

2014-01-01

Type 2 diabetes (T2D) may be caused by elevated oxidative stress, inflammation, and hyperglycemia. The phytochemicals in several herbal medicines are reported to effectively improve diabetes and to ameliorate diabetic complications. The aim of the present study was to determine the effects of cinnamon, cardamom, saffron, and ginger as supplementary remedies in T2D. This randomized controlled, clinical trial included 204 T2D patients. The participants were randomly assigned to four intervention groups receiving 3 glasses of black tea and either 3 g cardamom, or cinnamon, or ginger, or 1 g saffron and one control group which consumed only 3 tea glasses without any herbal medicine for 8 weeks. Markers of inflammation, oxidative stress, fasting blood sugar, lipid profile, and anthropometric measures were evaluated at baseline and after 8 weeks of intervention. After 8 weeks of intervention, cinnamon, cardamom, ginger, and saffron consumption had significant effects on total cholesterol, LDL, and HDL levels (p < 0.05) compared with controls. However, the herbal products did not have significant effects on measures of glycemic control, anthropometry, inflammation, and oxidative stress. In within-group comparisons only, cinnamon intake significantly decreased fasting blood sugar (FBS). The herbal remedies examined had significantly beneficial effects on cholesterol, but not on measures of glycemic control, oxidative stress, and inflammation. Based on the contradictory results reported in the literature, the effects of herbal medicine in diabetic patients should undergo further detailed investigation.

Aspergillus flavus Blast2GO gene ontology database: elevated growth temperature alters amino acid metabolism

Science.gov (United States)

The availability of a representative gene ontology (GO) database is a prerequisite for a successful functional genomics study. Using online Blast2GO resources we constructed a GO database of Aspergillus flavus. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mea...

Investigation of mutations in the HBB gene using the 1,000 genomes database.

Science.gov (United States)

Carlice-Dos-Reis, Tânia; Viana, Jaime; Moreira, Fabiano Cordeiro; Cardoso, Greice de Lemos; Guerreiro, João; Santos, Sidney; Ribeiro-Dos-Santos, Ândrea

2017-01-01

Mutations in the HBB gene are responsible for several serious hemoglobinopathies, such as sickle cell anemia and β-thalassemia. Sickle cell anemia is one of the most common monogenic diseases worldwide. Due to its prevalence, diverse strategies have been developed for a better understanding of its molecular mechanisms. In silico analysis has been increasingly used to investigate the genotype-phenotype relationship of many diseases, and the sequences of healthy individuals deposited in the 1,000 Genomes database appear to be an excellent tool for such analysis. The objective of this study is to analyze the variations in the HBB gene in the 1,000 Genomes database, to describe the mutation frequencies in the different population groups, and to investigate the pattern of pathogenicity. The computational tool SNPEFF was used to align the data from 2,504 samples of the 1,000 Genomes database with the HG19 genome reference. The pathogenicity of each amino acid change was investigated using the databases CLINVAR, dbSNP and HbVar and five different predictors. Twenty different mutations were found in 209 healthy individuals. The African group had the highest number of individuals with mutations, and the European group had the lowest number. Thus, it is concluded that approximately 8.3% of phenotypically healthy individuals from the 1,000 Genomes database have some mutation in the HBB gene. The frequency of mutated genes was estimated at 0.042, so that the expected frequency of being homozygous or compound heterozygous for these variants in the next generation is approximately 0.002. In total, 193 subjects had a non-synonymous mutation, which 186 (7.4%) have a deleterious mutation. Considering that the 1,000 Genomes database is representative of the world's population, it can be estimated that fourteen out of every 10,000 individuals in the world will have a hemoglobinopathy in the next generation.

HAEdb: a novel interactive, locus-specific mutation database for the C1 inhibitor gene.

Science.gov (United States)

Kalmár, Lajos; Hegedüs, Tamás; Farkas, Henriette; Nagy, Melinda; Tordai, Attila

2005-01-01

Hereditary angioneurotic edema (HAE) is an autosomal dominant disorder characterized by episodic local subcutaneous and submucosal edema and is caused by the deficiency of the activated C1 esterase inhibitor protein (C1-INH or C1INH; approved gene symbol SERPING1). Published C1-INH mutations are represented in large universal databases (e.g., OMIM, HGMD), but these databases update their data rather infrequently, they are not interactive, and they do not allow searches according to different criteria. The HAEdb, a C1-INH gene mutation database (http://hae.biomembrane.hu) was created to contribute to the following expectations: 1) help the comprehensive collection of information on genetic alterations of the C1-INH gene; 2) create a database in which data can be searched and compared according to several flexible criteria; and 3) provide additional help in new mutation identification. The website uses MySQL, an open-source, multithreaded, relational database management system. The user-friendly graphical interface was written in the PHP web programming language. The website consists of two main parts, the freely browsable search function, and the password-protected data deposition function. Mutations of the C1-INH gene are divided in two parts: gross mutations involving DNA fragments >1 kb, and micro mutations encompassing all non-gross mutations. Several attributes (e.g., affected exon, molecular consequence, family history) are collected for each mutation in a standardized form. This database may facilitate future comprehensive analyses of C1-INH mutations and also provide regular help for molecular diagnostic testing of HAE patients in different centers.

Cry-Bt identifier: a biological database for PCR detection of Cry genes present in transgenic plants.

Science.gov (United States)

Singh, Vinay Kumar; Ambwani, Sonu; Marla, Soma; Kumar, Anil

2009-10-23

We describe the development of a user friendly tool that would assist in the retrieval of information relating to Cry genes in transgenic crops. The tool also helps in detection of transformed Cry genes from Bacillus thuringiensis present in transgenic plants by providing suitable designed primers for PCR identification of these genes. The tool designed based on relational database model enables easy retrieval of information from the database with simple user queries. The tool also enables users to access related information about Cry genes present in various databases by interacting with different sources (nucleotide sequences, protein sequence, sequence comparison tools, published literature, conserved domains, evolutionary and structural data). http://insilicogenomics.in/Cry-btIdentifier/welcome.html.

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.

Science.gov (United States)

Gaby, John Christian; Buckley, Daniel H

2014-01-01

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder.

Science.gov (United States)

Zhang, Shuyun; Deng, Libin; Jia, Qiyue; Huang, Shaoting; Gu, Junwang; Zhou, Fankun; Gao, Meng; Sun, Xinyi; Feng, Chang; Fan, Guangqin

2017-11-16

Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples). Then, we applied R language software and developed an interactive shared and updated database (dbMDEGA) displaying the results of meta-analysis of data from ASD studies regarding differentially expressed genes (DEGs) in the brain. This database, dbMDEGA ( https://dbmdega.shinyapps.io/dbMDEGA/ ), is a publicly available web-portal for manual annotation and visualization of DEGs in the brain from data from ASD studies. This database uniquely presents meta-analysis values and homologous forest plots of DEGs in brain tissues. Gene entries are annotated with meta-values, statistical values and forest plots of DEGs in brain samples. This database aims to provide searchable meta-analysis results based on the current reported brain gene expression datasets of ASD to help detect candidate genes underlying this disorder. This new analytical tool may provide valuable assistance in the discovery of DEGs and the elucidation of the molecular pathogenicity of ASD. This database model may be replicated to study other disorders.

CRDB: database of chemosensory receptor gene families in vertebrate.

Directory of Open Access Journals (Sweden)

Dong Dong

Full Text Available Chemosensory receptors (CR are crucial for animals to sense the environmental changes and survive on earth. The emergence of whole-genome sequences provides us an opportunity to identify the entire CR gene repertoires. To completely gain more insight into the evolution of CR genes in vertebrates, we identified the nearly all CR genes in 25 vertebrates using homology-based approaches. Among these CR gene repertoires, nearly half of them were identified for the first time in those previously uncharacterized species, such as the guinea pig, giant panda and elephant, etc. Consistent with previous findings, we found that the numbers of CR genes vary extensively among different species, suggesting an extreme form of 'birth-and-death' evolution. For the purpose of facilitating CR gene analysis, we constructed a database with the goals to provide a resource for CR genes annotation and a web tool for exploring their evolutionary patterns. Besides a search engine for the gene extraction from a specific chromosome region, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of CR genes. Our work can provide a rigorous platform for further study on the evolution of CR genes in vertebrates.

Effect of Zeolite Rates and Irrigation Management on Some Properties of Saffron Corms

Directory of Open Access Journals (Sweden)

Abbas Khashei Siuki

2016-11-01

Full Text Available Saffron (Crocus sativus L. is a subtropical and valuable crop which is reproduced by corms. Due to the importance of corm weight in saffron yield, it is important to study the different factors that affect yield such as drought stress. For this purpose, this research was conducted as a factorial design based on completely randomized design (CRD in the Agricultural Research Station of the University of Birjand during the period 2013-2015. The treatments consisted of Zeolite at four rates (0: Z0, 0.5: Z1, 1: Z2 and 2: Z3 as weight percentage and irrigation management at three levels (traditional: I1, deficit irrigation as 70% moisture depletion: I2 and full irrigation: I3 with three replications. The results showed that zeolite rates has a significant effect on corm weight, number of corms less than 2gr, number of 6-8gr corms and number of replacement corms (P≤0.01. Irrigation management also has a significant effect on corm weight (P≤0.01, number of corms 6-8gr and number of replacement corms (P≤0.05. The treatments with no zeolite amended (Z0I1, Z0I2 and Z0I3 showed a reduction in corm weight compared to Z3I3 (P≤0.05. Z3I3, Z3I2 and Z3I3 showed an increase in the number of replacement corms while Z0I1 and Z0I2 had the least number of replacement corms. In conclusion, Z2I1 is recommended as the best treatment by considering the reduction in zeolite and water used, which increased corm weight by 26.64%, 23.88% and 17.81% compared to Z0I1, Z0I2 and Z0I3, respectively.

aeGEPUCI: a database of gene expression in the dengue vector mosquito, Aedes aegypti

Directory of Open Access Journals (Sweden)

James Anthony A

2010-10-01

Full Text Available Abstract Background Aedes aegypti is the principal vector of dengue and yellow fever viruses. The availability of the sequenced and annotated genome enables genome-wide analyses of gene expression in this mosquito. The large amount of data resulting from these analyses requires efficient cataloguing before it becomes useful as the basis for new insights into gene expression patterns and studies of the underlying molecular mechanisms for generating these patterns. Findings We provide a publicly-accessible database and data-mining tool, aeGEPUCI, that integrates 1 microarray analyses of sex- and stage-specific gene expression in Ae. aegypti, 2 functional gene annotation, 3 genomic sequence data, and 4 computational sequence analysis tools. The database can be used to identify genes expressed in particular stages and patterns of interest, and to analyze putative cis-regulatory elements (CREs that may play a role in coordinating these patterns. The database is accessible from the address http://www.aegep.bio.uci.edu. Conclusions The combination of gene expression, function and sequence data coupled with integrated sequence analysis tools allows for identification of expression patterns and streamlines the development of CRE predictions and experiments to assess how patterns of expression are coordinated at the molecular level.

The Effect of Different Hormones on Callus Induction, Regeneration and Multiplication of Saffron (Crocus Sativus L. Corms

Directory of Open Access Journals (Sweden)

Abbas Safarnejad

2016-08-01

Full Text Available Saffron (Crocus sativus; Iridaceae is an important economic and medicinal crop in Iran. The saffron that is an herbaceous triploid geophyte is used mainly as a source of secondary metabolites having aromatic and medicinal value. The plant develops annually from buds on the mother corm – i.e. a thickened stem - which acts as a resting, perennating storage organ. In this research in vitro propagation of Crocus sativus through direct and indirect methods has been studied. Corm slices as explants were sterilized and transferred to MS media with different concentrations of plant growth regulators. The results showed that use of HgCl2 0.15% for 20 minutes is the best treatment for sterilization. The results of ANOVA of direct regeneration indicated that the most corm formation was observed in 2 mg/l BAP. Maximum callus induction was achieved on MS supplemented with 1 mg/l 2,4-D + 2 mg/l BAP. As results indicate the most number of embryos were obtained in MS medium containing 0.15 mg/ l NAA. Also this medium was suitable for germination of embryo. Corm formation was only observed in MS supplemented with1 mg/l 2, 4-D + 2 mg/l BAP in the indirect method. The corm was transferred to JF pot for adaptation and then it was transferred to the pot and soil for growing.

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine).

Science.gov (United States)

Wong, Darren C J; Sweetman, Crystal; Drew, Damian P; Ford, Christopher M

2013-12-16

Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.

Science.gov (United States)

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch.

Allelopathic effects of leaf and corm water extract of saffron (Crocus sativus L. on germination and seedling growth of flixweed (Descurainia sophia L. and downy brome (Bromus tectorum L.

Directory of Open Access Journals (Sweden)

Zeinab Alipoor

2015-04-01

Full Text Available This study was conducted in two factorial experiment based on completely randomized design with three replications at research laboratory of faculty of agriculture in University of Birjand in 2013. Factors included saffron organs at 2 levels (leaves and corms and water extract concentrations at 5 levels (0, 0.5, 1, 1.5 and 2 percent.The allelopathic effects of saffron leaves and corms on seed germination and seedling growth characteristics of flixweed (Descurainia sophia L. and downy brome (Bromus tectorum L. were studied in two separate experiments. Results indicated lowest seed germination percentage of downy brome and flixweed were observed at concentration of 2% of corm extract (by 65% and 66% reduce compared to control, respectively. The rate of germination of downy brome decreased (by 71% compared to control with concentration of 2% of leaf extract but the rate of germination on flixweed was not significantly affected by extract concentrations. Different concentrations of leaf and corm extracts significantly decreased length and weight of plumule and radicals of two weeds. A logistic model provided a successful estimation of relationship between leaf water extract and germination percentage of two weeds. Based on orthogonal comparison tests, the allelopathic inhibition effects of saffron leaves and corms were more on downy brome and flixweed, respectively.

Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

LENUS (Irish Health Repository)

OhEigeartaigh, Sean S

2011-07-26

Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external

PRODORIC2: the bacterial gene regulation database in 2018

Science.gov (United States)

Dudek, Christian-Alexander; Hartlich, Juliane; Brötje, David; Jahn, Dieter

2018-01-01

Abstract Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de. PMID:29136200

Effects of enzymatic extraction on anthocyanins yield of saffron tepals (Crocos sativus along with its color properties and structural stability

Directory of Open Access Journals (Sweden)

Leila Lotfi

2015-06-01

Full Text Available An aqueous solution of Pectinex (containing cellulase, hemicellulase, and pectinase at 1%, 2.5%, 5%, 7%, and 10% concentrations and 40°C was used to extract anthocyanins (Acys of saffron tepals at 20, 40, 60, 120 and 180 min reaction times and compared with ethanol solvent under similar conditions. The Acys of the Pectinex solution reached 6.7 mg/g of tepal powder (∼40% more than the ethanol method when the enzyme concentrations and extraction times were, respectively, 5% and 60 min. The Acys of aqueous enzymes had three times slower degradation rates and 50% more attractive chroma color than the ones recovered by ethanol solution after 3 h of extraction time. Additionally, the Acys of the ethanol solution lost its content sharply (>45% and its chroma changed quickly (due to the browning and polymerization. High performance liquid chromatography (HPLC analysis showed that Acys extracted with mixed enzymes had about 80% more cyanidin 3-glucosides and 20% less pelargonidin 3,5-glucosides than with the ethanol method. Most probably, the high content of cyanidin 3-glycosides in enzyme-extracted Acys of saffron tepals was the key factor for its high stability.

Effect of Nutrient Solution Concentration, Time and Frequency of Foliar Application on Growth of Leaf and Daughter Corms of Saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

R Khorasani

2015-07-01

Full Text Available In order to investigate the effect of different levels of nutrient solution concentration and times and frequencies of foliar applications on dry weight, nitrogen, phosphorus and potassium concentrations of leaf and corm of saffron, a pot experiment was conducted as a completely randomized design with factorial arrangement and three replications under open door conditions in research garden of ferdowsi university, faculty of agriculture. The experimental treatments were included 4 levels of solution concentration (0, 4, 8 and 12 per 1000 and 7 levels of time and frequency of foliar applications (F1: foliar application on 3th February, F2: foliar application on 18th February, F3: foliar application on 5th March, F4: foliar applications on 3th and 18th February, F5: foliar applications on 3th February and 5th March, F6: foliar applications on 18th February and 5th March, F7: foliar applications on 3th and 18th February and 5th March. Results of variance analysis showed that fresh and dry weight of corm and leaf were not influenced by concentration, time and frequency of foliar applications. Also, comparison of nitrogen, phosphorus and potassium concentrations of leaf and corm showed that there was no significant difference between levels of foliar treatments and control. Therefore, it seems that due attention to pattern of leaf and low nutrient demand of saffron, foliar applications in different levels of nutrient solution concentrations and times and frequencies of foliar applications could not increase vegetative growth and consequently, could not improve the growth and nutritional properties of saffron corms.

Putative resistance genes in the CitEST database

Directory of Open Access Journals (Sweden)

Simone Guidetti-Gonzalez

2007-01-01

Full Text Available Disease resistance in plants is usually associated with the activation of a wide variety of defense responses to prevent pathogen replication and/or movement. The ability of the host plant to recognize the pathogen and to activate defense responses is regulated by direct or indirect interaction between the products of plant resistance (R and pathogen avirulence (Avr genes. Attempted infection of plants by avirulent pathogens elicits a battery of defenses often followed by the collapse of the challenged host cells. Localized host cell death may help to prevent the pathogen from spreading to uninfected tissues, known as hypersensitive response (HR. When either the plant or the pathogen lacks its cognate gene, activation of the plant’s defense responses fails to occur or is delayed and does not prevent pathogen colonization. In the CitEST database, we identified 1,300 reads related to R genes in Citrus which have been reported in other plant species. These reads were translated in silico, and alignments of their amino acid sequences revealed the presence of characteristic domains and motifs that are specific to R gene classes. The description of the reads identified suggests that they function as resistance genes in citrus.

SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

Directory of Open Access Journals (Sweden)

Vleeshouwers Vivianne GAA

2011-08-01

Full Text Available Abstract Background The cultivated potato (Solanum tuberosum L. is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato. Description The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications. Conclusion Solanum section Petota forms the basis of the SolRgene database, which contains a

Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

Directory of Open Access Journals (Sweden)

Belmamoune Mounia

2008-06-01

Full Text Available The Gene Expression Management System (GEMS is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative platform that addresses one of the important challenges of developmental biology: how to integrate genetic data that underpin morphological changes during embryogenesis. Our motivation to build this system was by the need to be able to organize and compare multiple patterns of gene expression at tissue level. Integration with other developmental and biomolecular databases will further support our understanding of development. The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS. The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term. These terms are extracted from a formal anatomical ontology, i.e. the Developmental Anatomy Ontology of Zebrafish (DAOZ. In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration and retrieval . The annotations are the glue for integration of patterns of gene expression in GEMS as well as in other biomolecular databases. At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development. At the other hand, GO terms extend GEMS expression patterns integration to a wide range of bioinformatics resources.

Database Description - DGBY | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available base Description General information of database Database name DGBY Alternative name Database...EL: +81-29-838-8066 E-mail: Database classification Microarray Data and other Gene Expression Databases Orga...nism Taxonomy Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Database descripti...-called phenomics). We uploaded these data on this website which is designated DGBY(Database for Gene expres...ma J, Ando A, Takagi H. Journal: Yeast. 2008 Mar;25(3):179-90. External Links: Original website information Database

The Co-regulation Data Harvester: Automating gene annotation starting from a transcriptome database

Science.gov (United States)

Tsypin, Lev M.; Turkewitz, Aaron P.

Identifying co-regulated genes provides a useful approach for defining pathway-specific machinery in an organism. To be efficient, this approach relies on thorough genome annotation, a process much slower than genome sequencing per se. Tetrahymena thermophila, a unicellular eukaryote, has been a useful model organism and has a fully sequenced but sparsely annotated genome. One important resource for studying this organism has been an online transcriptomic database. We have developed an automated approach to gene annotation in the context of transcriptome data in T. thermophila, called the Co-regulation Data Harvester (CDH). Beginning with a gene of interest, the CDH identifies co-regulated genes by accessing the Tetrahymena transcriptome database. It then identifies their closely related genes (orthologs) in other organisms by using reciprocal BLAST searches. Finally, it collates the annotations of those orthologs' functions, which provides the user with information to help predict the cellular role of the initial query. The CDH, which is freely available, represents a powerful new tool for analyzing cell biological pathways in Tetrahymena. Moreover, to the extent that genes and pathways are conserved between organisms, the inferences obtained via the CDH should be relevant, and can be explored, in many other systems.

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.

Science.gov (United States)

Hassani-Pak, Keywan; Rawlings, Christopher

2017-06-13

Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.

A database of annotated promoters of genes associated with common respiratory and related diseases

KAUST Repository

Chowdhary, Rajesh

2012-07-01

Many genes have been implicated in the pathogenesis of common respiratory and related diseases (RRDs), yet the underlying mechanisms are largely unknown. Differential gene expression patterns in diseased and healthy individuals suggest that RRDs affect or are affected by modified transcription regulation programs. It is thus crucial to characterize implicated genes in terms of transcriptional regulation. For this purpose, we conducted a promoter analysis of genes associated with 11 common RRDs including allergic rhinitis, asthma, bronchiectasis, bronchiolitis, bronchitis, chronic obstructive pulmonary disease, cystic fibrosis, emphysema, eczema, psoriasis, and urticaria, many of which are thought to be genetically related. The objective of the present study was to obtain deeper insight into the transcriptional regulation of these disease-associated genes by annotating their promoter regions with transcription factors (TFs) and TF binding sites (TFBSs). We discovered many TFs that are significantly enriched in the target disease groups including associations that have been documented in the literature. We also identified a number of putative TFs/TFBSs that appear to be novel. The results of our analysis are provided in an online database that is freely accessible to researchers at http://www.respiratorygenomics.com. Promoter-associated TFBS information and related genomic features, such as histone modification sites, microsatellites, CpG islands, and SNPs, are graphically summarized in the database. Users can compare and contrast underlying mechanisms of specific RRDs relative to candidate genes, TFs, gene ontology terms, micro-RNAs, and biological pathways for the conduct of metaanalyses. This database represents a novel, useful resource for RRD researchers. Copyright © 2012 by the American Thoracic Society.

A database of annotated promoters of genes associated with common respiratory and related diseases

KAUST Repository

Chowdhary, Rajesh; Tan, Sinlam; Pavesi, Giulio; Jin, Gg; Dong, Difeng; Mathur, Sameer K.; Burkart, Arthur; Narang, Vipin; Glurich, Ingrid E.; Raby, Benjamin A.; Weiss, Scott T.; Limsoon, Wong; Liu, Jun; Bajic, Vladimir B.

2012-01-01

Many genes have been implicated in the pathogenesis of common respiratory and related diseases (RRDs), yet the underlying mechanisms are largely unknown. Differential gene expression patterns in diseased and healthy individuals suggest that RRDs affect or are affected by modified transcription regulation programs. It is thus crucial to characterize implicated genes in terms of transcriptional regulation. For this purpose, we conducted a promoter analysis of genes associated with 11 common RRDs including allergic rhinitis, asthma, bronchiectasis, bronchiolitis, bronchitis, chronic obstructive pulmonary disease, cystic fibrosis, emphysema, eczema, psoriasis, and urticaria, many of which are thought to be genetically related. The objective of the present study was to obtain deeper insight into the transcriptional regulation of these disease-associated genes by annotating their promoter regions with transcription factors (TFs) and TF binding sites (TFBSs). We discovered many TFs that are significantly enriched in the target disease groups including associations that have been documented in the literature. We also identified a number of putative TFs/TFBSs that appear to be novel. The results of our analysis are provided in an online database that is freely accessible to researchers at http://www.respiratorygenomics.com. Promoter-associated TFBS information and related genomic features, such as histone modification sites, microsatellites, CpG islands, and SNPs, are graphically summarized in the database. Users can compare and contrast underlying mechanisms of specific RRDs relative to candidate genes, TFs, gene ontology terms, micro-RNAs, and biological pathways for the conduct of metaanalyses. This database represents a novel, useful resource for RRD researchers. Copyright © 2012 by the American Thoracic Society.

A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database

Energy Technology Data Exchange (ETDEWEB)

Dehal, Paramvir S.; Boore, Jeffrey L.

2005-08-25

We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining

Directory of Open Access Journals (Sweden)

Chen Hsin-Hsi

2008-10-01

Full Text Available Abstract Background Traditional Chinese Medicine (TCM, a complementary and alternative medical system in Western countries, has been used to treat various diseases over thousands of years in East Asian countries. In recent years, many herbal medicines were found to exhibit a variety of effects through regulating a wide range of gene expressions or protein activities. As available TCM data continue to accumulate rapidly, an urgent need for exploring these resources systematically is imperative, so as to effectively utilize the large volume of literature. Methods TCM, gene, disease, biological pathway and protein-protein interaction information were collected from public databases. For association discovery, the TCM names, gene names, disease names, TCM ingredients and effects were used to annotate the literature corpus obtained from PubMed. The concept to mine entity associations was based on hypothesis testing and collocation analysis. The annotated corpus was processed with natural language processing tools and rule-based approaches were applied to the sentences for extracting the relations between TCM effecters and effects. Results We developed a database, TCMGeneDIT, to provide association information about TCMs, genes, diseases, TCM effects and TCM ingredients mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information are also available for exploring the regulations of genes associated with TCM curative effects. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in understanding the possible therapeutic mechanisms of TCMs via gene regulations and deducing synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. The database is now available at http://tcm.lifescience.ntu.edu.tw/. Conclusion TCMGeneDIT is a unique database

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

Science.gov (United States)

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

Directory of Open Access Journals (Sweden)

Mixon Mark

2009-04-01

Full Text Available Abstract Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene

Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses

Directory of Open Access Journals (Sweden)

Rayapadi G. Swetha

2016-01-01

Full Text Available Ebola Virus Disease (EVD is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. This prompted us to develop the Ebolavirus Database (EDB and we have provided links to various tools that will aid researchers to locate important regions in both the genomes and proteomes of Ebolavirus. The genomic analyses of ebolaviruses will provide important clues for locating the essential and core functional genes. The aim of EDB is to act as an integrated resource for ebolaviruses and we strongly believe that the database will be a useful tool for clinicians, microbiologists, health care workers, and bioscience researchers.

Database Description - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us SKIP Stemcell Database Database Description General information of database Database name SKIP Stemcell Database...rsity Journal Search: Contact address http://www.skip.med.keio.ac.jp/en/contact/ Database classification Human Genes and Diseases Dat...abase classification Stemcell Article Organism Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database...ks: Original website information Database maintenance site Center for Medical Genetics, School of medicine, ...lable Web services Not available URL of Web services - Need for user registration Not available About This Database Database

Effect of corm planting density, organic and chemical fertilizers on formation and phosphorus uptake of saffron (Crocus sativus L. replacement corms during phonological stages

Directory of Open Access Journals (Sweden)

Hassan Feizi

2015-01-01

Full Text Available Saffron (Crocus sativus L. propagates by replacement corms producing from the mother corm after flowering during each season. In order to investigate the effect of corm planting density, organic and chemical fertilizers on formation and phosphorus uptake of saffron replacement corms during phonological stages, a field experiment was conducted as factorial layout based on randomized complete block design with three replications, at Faculty of Agriculture, Ferdowsi University of Mashhad, Iran, during 2013 and 2014 growing seasons. The experimental treatments were all combination of different levels of planting density (25, 50, 75 and 100 corms per m2 and fertilizer sources (manure 25 t. ha-1, chemical fertilizer (N 150 kg ha-1 + P 75 kg ha-1 and control. Due to different sampling dates of replacement corms during phonological stages (21 November, 21 December, 20 January, 20 April and 21 May, respectively, the experimental data were analyzed as factorial - split in time based on a randomized complete block design. Based on results, the highest number of replacement corms lower than 4 g (5.8 corms per plant were observed in fifth sampling stage and then decreased. In all levels of planting density (25 to 100 corms per m2, the effects of manure on increasing the number, weight and phosphorus content of replacement corms in range of 4.1 to 8 and 8.1 to 12 g per plant were significantly higher than chemical fertilizer. In fifth sampling stage, by applying the manure, the weight and phosphorus content of replacement corms in range of 8.1 to 12 g per plant were significantly increased (approximately twice, as compared to chemical fertilizer. It seems the decrease in saffron yield as result to decreasing the corm planting density can be slightly offset by increasing the percentage of larger corms formation per plant.

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

Directory of Open Access Journals (Sweden)

Baumbach Jan

2007-11-01

Full Text Available Abstract Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user can be analyzed in the context of known

Candidate gene database and transcript map for peach, a model species for fruit trees.

Science.gov (United States)

Horn, Renate; Lecouls, Anne-Claire; Callahan, Ann; Dandekar, Abhaya; Garay, Lilibeth; McCord, Per; Howad, Werner; Chan, Helen; Verde, Ignazio; Main, Doreen; Jung, Sook; Georgi, Laura; Forrest, Sam; Mook, Jennifer; Zhebentyayeva, Tatyana; Yu, Yeisoo; Kim, Hye Ran; Jesudurai, Christopher; Sosinski, Bryon; Arús, Pere; Baird, Vance; Parfitt, Dan; Reighard, Gregory; Scorza, Ralph; Tomkins, Jeffrey; Wing, Rod; Abbott, Albert Glenn

2005-05-01

Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].

rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

Science.gov (United States)

Guo, Liyuan; Wang, Jing

2018-01-04

Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

TreeFam: a curated database of phylogenetic trees of animal gene families

DEFF Research Database (Denmark)

Li, Heng; Coghlan, Avril; Ruan, Jue

2006-01-01

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively......, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins...

Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.

Science.gov (United States)

Hiscock, D; Upton, C

2000-05-01

The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters. The software and additional figures and information are available at http://athena.bioc.uvic.ca/genomes/index.html .

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

Science.gov (United States)

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

2018-02-22

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

Science.gov (United States)

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific

An elm EST database for identifying leaf beetle egg-induced defense genes

Directory of Open Access Journals (Sweden)

Büchel Kerstin

2012-06-01

Full Text Available Abstract Background Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor, egg laying by the elm leaf beetle ( Xanthogaleruca luteola activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes. Results Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i untreated control elms, and elms treated with (ii egg laying and feeding by elm leaf beetles, (iii feeding, (iv artificial transfer of egg clutches, and (v methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs were identified which clustered into 52,823 unique transcripts (Unitrans and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction

An elm EST database for identifying leaf beetle egg-induced defense genes.

Science.gov (United States)

Büchel, Kerstin; McDowell, Eric; Nelson, Will; Descour, Anne; Gershenzon, Jonathan; Hilker, Monika; Soderlund, Carol; Gang, David R; Fenning, Trevor; Meiners, Torsten

2012-06-15

Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor), egg laying by the elm leaf beetle ( Xanthogaleruca luteola) activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes. Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i) untreated control elms, and elms treated with (ii) egg laying and feeding by elm leaf beetles, (iii) feeding, (iv) artificial transfer of egg clutches, and (v) methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs) were identified which clustered into 52,823 unique transcripts (Unitrans) and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant) database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism

Apparent expression of flower colours and internal variation of enzyme activities in some typical phenotypes of dyer's saffron cultivars

Directory of Open Access Journals (Sweden)

Koshi Saito

2014-01-01

Full Text Available Phytochemical screening of four Carthamus pigments in phenotypically different cultivars of dyer's saffron was carried out by means of chromatographic techniques. The pigment composition in the floral part correlated well with the flower colour, supporting these components as idoneous chemotaxonomic markers. Among seven cultivars examined, three were orange-yellow and contained carthamin (red and precarthamin, safflor yellow A and safflor yellow B (orange-yellow (type 0. There were bright-yellow and also had the above four pigments (type Y. The seventh cultivar was ivory-white and produced no quinoidal chalcones in the florets (type W. Relative activities of three different enzymes were examined in soluble protein extracts from etiolated seedlings of the garden varieties. Monophenol monooxygenase (EC 1.14.18.1 and peroxidase (EC 1.11.1.7. were distributed over all cultivars tested. The relative level of the enzyme activities could be ordered as follows: type 0, type W and type Y. The activity of a carthamin-synthesizing enzyme was found in the protein extracts from all garden forms examined. Its activity was most prominent in type O. The activity level in type W was inferior to that of type O. The catalytic intensity in type Y was found to even lower. The results were discussed as to the composition of the phenotypic markers and the distribution of the enzyme activities in three different garden forms of dyer's saffron cultivars.

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina

Directory of Open Access Journals (Sweden)

Léveillard Thierry

2008-05-01

Full Text Available Abstract Background The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electrical impulses that travel along the optic nerve to the brain where they are turned into images. It consists of neurons, nourishing blood vessels and different cell types, of which neural cells predominate. Defects in any of these cells can lead to a variety of retinal diseases, including age-related macular degeneration, retinitis pigmentosa, Leber congenital amaurosis and glaucoma. Recent progress in genomics and microarray technology provides extensive opportunities to examine alterations in retinal gene expression profiles during development and diseases. However, there is no specific database that deals with retinal gene expression profiling. In this context we have built RETINOBASE, a dedicated microarray database for retina. Description RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina. It provides access to gene expression meta-data and offers significant insights into gene networks in retina, resulting in better hypothesis framing for biological problems that can subsequently be tested in the laboratory. Public and proprietary data are automatically analyzed with 3 distinct methods, RMA, dChip and MAS5, then clustered using 2 different K-means and 1 mixture models method. Thus, RETINOBASE provides a framework to compare these methods and to optimize the retinal data analysis. RETINOBASE has three different modules, "Gene Information", "Raw Data System Analysis" and "Fold change system Analysis" that are interconnected in a relational schema, allowing efficient retrieval and cross comparison of data. Currently, RETINOBASE contains datasets from 28 different microarray experiments performed

DDMGD: the database of text-mined associations between genes methylated in diseases from different species

KAUST Repository

Raies, A. B.

2014-11-14

Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD\\'s scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases.

Database Description - ASTRA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available abase Description General information of database Database name ASTRA Alternative n...tics Journal Search: Contact address Database classification Nucleotide Sequence Databases - Gene structure,...3702 Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The database represents classified p...(10):1211-6. External Links: Original website information Database maintenance site National Institute of Ad... for user registration Not available About This Database Database Description Dow

DDMGD: the database of text-mined associations between genes methylated in diseases from different species.

Science.gov (United States)

Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir B

2015-01-01

Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Database Description - RMOS | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available base Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...19&lang=en Whole data download - Referenced database Rice Expression Database (RED) Rice full-length cDNA Database... (KOME) Rice Genome Integrated Map Database (INE) Rice Mutant Panel Database (Tos17) Rice Genome Annotation Database

Impact of use of different sources of humic, bio and nano fertilizers and nitrogen levels on saffron (.Crocus sativus L flower yield

Directory of Open Access Journals (Sweden)

aliasghar armak

2017-12-01

Full Text Available This study is aimed at investigating the effect of using humic, bio and nano fertilizers and levels of nitrogen fertilizers in flower yield of saffron (Crocus sativus L. at the University of Torbat Heydarieh research farm located in Zaveh in 2014-2015. Treatments consisted of three levels of nitrogen application and use of fertilizer sources as the main factor, including Bioumik, Super Humic, combined Super Humic and Bioumik, Humi Ful, Nitrokara and no fertilizer as sub plots as split plot based on randomized complete block design with 18 treatments and three replications. Analysis of data showed that the effect of year and fertilizer sources on all traits measured was significant. The effect of nitrogen treatments was significant (at 1% except on number of flowers, dry style, mean dry weight stigma, and mean dry weight. Fertilizer sources increased all measured traits significantly. Application of Biomic increased petals and sepals dry weight (736.34 g/m2 by 46.78% in comparison with the control (464.19 g/m2. The highest dry weight stigma (524.2 g/m2 was seen in Super Humic + Bioumik treatment compared to the control group (443.1 g/m2. Super Humic treatment increased dry weight stigma by 86.49% relative to control. It seems that the use of humic, bio and nano fertilizers has a good effect on saffron performance.

Database Description - RED | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ase Description General information of database Database name RED Alternative name Rice Expression Database...enome Research Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Database classifi...cation Microarray, Gene Expression Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database descripti... Article title: Rice Expression Database: the gateway to rice functional genomics...nt Science (2002) Dec 7 (12):563-564 External Links: Original website information Database maintenance site

A methodology to establish a database to study gene environment interactions for childhood asthma

Directory of Open Access Journals (Sweden)

McCormick Jonathan

2010-12-01

Full Text Available Abstract Background Gene-environment interactions are likely to explain some of the heterogeneity in childhood asthma. Here, we describe the methodology and experiences in establishing a database for childhood asthma designed to study gene-environment interactions (PAGES - Paediatric Asthma Gene Environment Study. Methods Children with asthma and under the care of a respiratory paediatrician are being recruited from 15 hospitals between 2008 and 2011. An asthma questionnaire is completed and returned by post. At a routine clinic visit saliva is collected for DNA extraction. Detailed phenotyping in a proportion of children includes spirometry, bronchodilator response (BDR, skin prick reactivity, exhaled nitric oxide and salivary cotinine. Dietary and quality of life questionnaires are completed. Data are entered onto a purpose-built database. Results To date 1045 children have been invited to participate and data collected in 501 (48%. The mean age (SD of participants is 8.6 (3.9 years, 57% male. DNA has been collected in 436 children. Spirometry has been obtained in 172 children, mean % predicted (SD FEV1 97% (15 and median (IQR BDR is 5% (2, 9. There were differences in age, socioeconomic status, severity and %FEV1 between the different centres (p≤0.024. Reasons for non-participation included parents not having time to take part, children not attending clinics and, in a small proportion, refusal to take part. Conclusions It is feasible to establish a national database to study gene-environment interactions within an asthmatic paediatric population; there are barriers to participation and some different characteristics in individuals recruited from different centres. Recruitment to our study continues and is anticipated to extend current understanding of asthma heterogeneity.

Safety Evaluation of Crocin (a constituent of saffron Tablets in Healthy Volunteers

Directory of Open Access Journals (Sweden)

Amir Houshang Mohamadpour

2013-01-01

Full Text Available Objective(s: Crocin is the chemical ingredient primarily responsible for the color of saffron. It has different pharmacological effects such as antioxidant, anticancer and memory improving activities. Crocin tablets were evaluated for short-term safety and tolerability in healthy adult volunteers. Materials and Methods: The study was a randomized, double-blind, placebo-controlled design consisting of one month treatment of crocin tablets. Volunteers who fulfilled inclusion and exclusion criteria were randomized into 2 groups of 22 each (males and females and received 20 mg crocin tablets or placebo. General measures of health were recorded during the study such as hematological, biochemical, hormonal and urinary parameters in pre and post-treatment periods. Results: No major adverse events were reported during the trial. Crocin tablets did not change the above parameters except that it decreased amylase, mixed white blood cells and PTT in healthy volunteers after one month. Conclusion: This clinical safety evaluation showed a relatively safe and normal profile for crocin in healthy volunteers at the given doses within the trial period.

Screen for genes involved in radiation survival of Escherichia coli and construction of a reference database

Energy Technology Data Exchange (ETDEWEB)

Sargentini, Neil J., E-mail: nsargentini@atsu.edu; Gularte, Nicholas P.; Hudman, Deborah A.

2016-11-15

Highlights: • 3907 Keio knockout mutants of E. coli screened for UV and X-radiation sensitivity. • 76 mutants showed significantly increased radiation sensitivity. • A database of 9 screening studies listed 352 genes only once; 103 genes, 2–7 times. • 33 genes from this study are uncommon and potentially novel. • Common and uncommon genes differ in gene function profile. - Abstract: A set of 3907 single-gene knockout (Keio collection) strains of Escherichia coli K-12 was examined for strains with increased susceptibility to killing by X- or UV-radiation. After screening with a high-throughput resazurin-based assay and determining radiation survival with triplicate clonogenic assays, we identified 76 strains (and associated deleted genes) showing statistically-significant increased radiation sensitivity compared to a control strain. To determine gene novelty, we constructed a reference database comprised of genes found in nine similar studies including ours. This database contains 455 genes comprised of 103 common genes (found 2–7 times), and 352 uncommon genes (found once). Our 76 genes includes 43 common genes and 33 uncommon (potentially novel) genes, i.e., appY, atoS, betB, bglJ, clpP, cpxA, cysB, cysE, ddlA, dgkA, dppF, dusB, elfG, eutK, fadD, glnA, groL, guaB, intF, prpR, queA, rplY, seqA, sufC,yadG, yagJ, yahD, yahO, ybaK, ybfA, yfaL, yhjV, and yiaL. Of our 33 uncommon gene mutants, 4 (12%) were sensitive only to UV-radiation, 10 (30%) only to X-radiation, and 19 (58%) to both radiations. Our uncommon mutants vs. our common mutants showed more radiation specificity, i.e., 12% vs. 9% (sensitive only to UV-); 30% vs. 16% (X-) and 58% vs. 74% (both radiations). Considering just our radiation-sensitive mutants, the median UV-radiation survival (75 J m{sup −2}) for 23 uncommon mutants was 6.84E-3 compared to 1.85E-3 for 36 common mutants (P = 0.025). Similarly, the average X-radiation survival for 29 uncommon mutants was 1.08E-2, compared to 6.19E

GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes.

Science.gov (United States)

Catanho, Marcos; Mascarenhas, Daniel; Degrave, Wim; Miranda, Antonio Basílio de

2006-03-31

Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/or dynamic comparison of these data. GenoMycDB (http://www.dbbm.fiocruz.br/GenoMycDB) is a relational database built for large-scale comparative analyses of completely sequenced mycobacterial genomes, based on their predicted protein content. Its central structure is composed of the results obtained after pair-wise sequence alignments among all the predicted proteins coded by the genomes of six mycobacteria: Mycobacterium tuberculosis (strains H37Rv and CDC1551), M. bovis AF2122/97, M. avium subsp. paratuberculosis K10, M. leprae TN, and M. smegmatis MC2 155. The database stores the computed similarity parameters of every aligned pair, providing for each protein sequence the predicted subcellular localization, the assigned cluster of orthologous groups, the features of the corresponding gene, and links to several important databases. Tables containing pairs or groups of potential homologs between selected species/strains can be produced dynamically by user-defined criteria, based on one or multiple sequence similarity parameters. In addition, searches can be restricted according to the predicted subcellular localization of the protein, the DNA strand of the corresponding gene and/or the description of the protein. Massive data search and/or retrieval are available, and different ways of exporting the result are offered. GenoMycDB provides an on-line resource for the functional classification of mycobacterial proteins as well as for the analysis of genome structure, organization, and evolution.

Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers.

Science.gov (United States)

Kulaeva, Olga A; Zhernakov, Aleksandr I; Afonin, Alexey M; Boikov, Sergei S; Sulima, Anton S; Tikhonovich, Igor A; Zhukov, Vladimir A

2017-01-01

Pea (Pisum sativum L.) is the oldest model object of plant genetics and one of the most agriculturally important legumes in the world. Since the pea genome has not been sequenced yet, identification of genes responsible for mutant phenotypes or desirable agricultural traits is usually performed via genetic mapping followed by candidate gene search. Such mapping is best carried out using gene-based molecular markers, as it opens the possibility for exploiting genome synteny between pea and its close relative Medicago truncatula Gaertn., possessing sequenced and annotated genome. In the last 5 years, a large number of pea gene-based molecular markers have been designed and mapped owing to the rapid evolution of "next-generation sequencing" technologies. However, the access to the complete set of markers designed worldwide is limited because the data are not uniformed and therefore hard to use. The Pea Marker Database was designed to combine the information about pea markers in a form of user-friendly and practical online tool. Version 1 (PMD1) comprises information about 2484 genic markers, including their locations in linkage groups, the sequences of corresponding pea transcripts and the names of related genes in M. truncatula. Version 2 (PMD2) is an updated version comprising 15944 pea markers in the same format with several advanced features. To test the performance of the PMD, fine mapping of pea symbiotic genes Sym13 and Sym27 in linkage groups VII and V, respectively, was carried out. The results of mapping allowed us to propose the Sen1 gene (a homologue of SEN1 gene of Lotus japonicus (Regel) K. Larsen) as the best candidate gene for Sym13, and to narrow the list of possible candidate genes for Sym27 to ten, thus proving PMD to be useful for pea gene mapping and cloning. All information contained in PMD1 and PMD2 is available at www.peamarker.arriam.ru.

Using FlyBase, a Database of Drosophila Genes and Genomes.

Science.gov (United States)

Marygold, Steven J; Crosby, Madeline A; Goodman, Joshua L

2016-01-01

For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic, and high-throughput technologies add to the quantity and diversity of available data and resources.FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets, or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.This chapter provides an overview of the data content, organization, and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.

Effect of different levels of municipal waste compost and maternal corm weight on yield and vegetative characteristics of saffron (Crocus sativus L.

Directory of Open Access Journals (Sweden)

Zohre Gholizade

2016-11-01

Full Text Available In order to investigate the effects of different municipal waste compost levels of and maternal corm weights on yield and vegetative characteristics of saffron, an experiment was conducted with a factorial arrangement based on randomized complete block design with three replications at the Agricultural Research Station, University of Birjand during the growing season of 2014-2015. The treatments were four levels of municipal waste compost (0, 5, 10 and 20 t.ha-1 and three mother corm weights (0.1- 4, 4.1- 8 and 8.1- 12 g. The traits included the number of flower, fresh weight of flower, stigma and fresh weight of corm with scale, weight and diameter replacement and number of buds. The results showed that the effect of municipal waste compost was significant on total weight corm with scale, diameter of center corm and replacement corm, weight of fresh flower and stigma. The highest corm weight and number of replacement corms were obtained for treatment 10 t. ha-1 compost (21.33 g. plant -1 and 2.33 number, respectively, while the control had the lowest values (with 16.4 g. plant -1 and 1.66 number. The effect of mother corm weight was significant on the vegetative characteristics of saffron. The highest corm weight with scale, diameter of replacement, flower yield and fresh weight of flower and stigma were observed for 8.1-12 g. The most fresh  and dry weight of stigma (0.31 and 0.11 g. m -1, respectively were observed from treatment  mother corm weight 8.1-12 g, while the lowest values (0.06 and 0.03 g. m -1 were 0.1- 4g.  Interaction between municipal waste compost and corm weight had a significant effect on the weight of fresh flower, sepal, stigma and the number of lateral buds and the highest fresh weight of flower (9.36 g. m-2 and stigma (0.41 g. m-2 were observed for treatment 10 t. ha-1 and 8.1-12g. Generally, the findings of the current study revealed that the use of municipal waste compost (10 t. ha-1 and large mother corms (8/1-12 g

Phenological growth stages of saffron plant (Crocus sativus L.) according to the BBCH Scale

Energy Technology Data Exchange (ETDEWEB)

Lopez-Corcoles, H.; Brasa-Ramos, A.; Montero-Garcia, F.; Romero-Valverde, M.; Montero-Riquelme, F.

2015-07-01

Phenological studies are important for understanding the influence of climate dynamics on vegetative growth, flowering and fruiting on plants and can be used in many scientific subjects, such as Agronomy, Botany and Plant Biology, but also Climatology as a result of the current global interest in climate change monitoring. The purpose of the detailed specific culture descriptions of the principal growth stages in plants is to provide an instrument for standardization of data recording. To date, there was no coding method to describe developmental stages on saffron plant (Crocus sativus L.). Because of the increasing world-wide interest on this crop, a novel growth development code based on the BBCH extended scale is proposed in this paper. Six principal growth stages were set up, starting from sprouting, cataphylls and flowers appearance, plant appearance and development, replacement corms development, plant senescence and corm dormancy. Each principal growth stage is subdivided into secondary growth stages. Descriptive keys with illustrations are included to make effective use of the system. (Author)

Using the Pathogen-Host Interactions database (PHI-base to investigate plant pathogen genomes and genes implicated in virulence

Directory of Open Access Journals (Sweden)

Martin eUrban

2015-08-01

Full Text Available New pathogen-host interaction mechanisms can be revealed by integrating mutant phenotype data with genetic information. PHI-base is a multi-species manually curated database combining peer-reviewed published phenotype data from plant and animal pathogens and gene/protein information in a single database.

How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database.

Science.gov (United States)

Bouaziz, J; Mashiach, R; Cohen, S; Kedem, A; Baron, A; Zajicek, M; Feldman, I; Seidman, D; Soriano, D

2018-01-01

Endometriosis is a disease characterized by the development of endometrial tissue outside the uterus, but its cause remains largely unknown. Numerous genes have been studied and proposed to help explain its pathogenesis. However, the large number of these candidate genes has made functional validation through experimental methodologies nearly impossible. Computational methods could provide a useful alternative for prioritizing those most likely to be susceptibility genes. Using artificial intelligence applied to text mining, this study analyzed the genes involved in the pathogenesis, development, and progression of endometriosis. The data extraction by text mining of the endometriosis-related genes in the PubMed database was based on natural language processing, and the data were filtered to remove false positives. Using data from the text mining and gene network information as input for the web-based tool, 15,207 endometriosis-related genes were ranked according to their score in the database. Characterization of the filtered gene set through gene ontology, pathway, and network analysis provided information about the numerous mechanisms hypothesized to be responsible for the establishment of ectopic endometrial tissue, as well as the migration, implantation, survival, and proliferation of ectopic endometrial cells. Finally, the human genome was scanned through various databases using filtered genes as a seed to determine novel genes that might also be involved in the pathogenesis of endometriosis but which have not yet been characterized. These genes could be promising candidates to serve as useful diagnostic biomarkers and therapeutic targets in the management of endometriosis.

Transcriptome database resource and gene expression atlas for the rose

Science.gov (United States)

2012-01-01

Background For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. Results Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. Conclusions The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy. PMID:23164410

Mycobacteriophage genome database.

Science.gov (United States)

Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

2011-01-01

Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

Science.gov (United States)

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

Locus-Specific Databases and Recommendations to Strengthen Their Contribution to the Classification of Variants in Cancer Susceptibility Genes

NARCIS (Netherlands)

Greenblatt, Marc S.; Brody, Lawrence C.; Foulkes, William D.; Genuardi, Maurizio; Hofstra, Robert M. W.; Olivier, Magali; Plon, Sharon E.; Sijmons, Rolf H.; Sinilnikova, Olga; Spurdle, Amanda B.

2008-01-01

Locus-specific databases (LSDBs) are curated collections of sequence variants in genes associated with disease. LSDBs of cancer-related genes often serve as a critical resource to researchers, diagnostic laboratories, clinicians, and others in the cancer genetics community. LSDBs are poised to play

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

Science.gov (United States)

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Discovery of possible gene relationships through the application of self-organizing maps to DNA microarray databases.

Science.gov (United States)

Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

2014-01-01

DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques--an unsupervised artificial neural network called a Self-Organizing Map (SOM)-which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms.

Phenological growth stages of saffron plant (Crocus sativus L. according to the BBCH Scale

Directory of Open Access Journals (Sweden)

Horacio Lopez-Corcoles

2015-09-01

Full Text Available Phenological studies are important for understanding the influence of climate dynamics on vegetative growth, flowering and fruiting on plants and can be used in many scientific subjects, such as Agronomy, Botany and Plant Biology, but also Climatology as a result of the current global interest in climate change monitoring. The purpose of the detailed specific culture descriptions of the principal growth stages in plants is to provide an instrument for standardization of data recording. To date, there was no coding method to describe developmental stages on saffron plant (Crocus sativus L.. Because of the increasing world-wide interest on this crop, a novel growth development code based on the BBCH extended scale is proposed in this paper. Six principal growth stages were set up, starting from sprouting, cataphylls and flowers appearance, plant appearance and development, replacement corms development, plant senescence and corm dormancy. Each principal growth stage is subdivided into secondary growth stages. Descriptive keys with illustrations are included to make effective use of the system.

Database Description - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD...B-CE Database Description General information of database Database name tRNADB-CE Alter...CC BY-SA Detail Background and funding Name: MEXT Integrated Database Project Reference(s) Article title: tRNAD... 2009 Jan;37(Database issue):D163-8. External Links: Article title: tRNADB-CE 2011: tRNA gene database curat...n Download License Update History of This Database Site Policy | Contact Us Database Description - tRNADB-CE | LSDB Archive ...

Human Ageing Genomic Resources: new and updated databases

Science.gov (United States)

Tacutu, Robi; Thornton, Daniel; Johnson, Emily; Budovsky, Arie; Barardo, Diogo; Craig, Thomas; Diana, Eugene; Lehmann, Gilad; Toren, Dmitri; Wang, Jingwei; Fraifeld, Vadim E

2018-01-01

Abstract In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/). PMID:29121237

Full Data of Yeast Interacting Proteins Database (Original Version) - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Yeast Interacting Proteins Database Full Data of Yeast Interacting Proteins Database (Origin...al Version) Data detail Data name Full Data of Yeast Interacting Proteins Database (Original Version) DOI 10....18908/lsdba.nbdc00742-004 Description of data contents The entire data in the Yeast Interacting Proteins Database...eir interactions are required. Several sources including YPD (Yeast Proteome Database, Costanzo, M. C., Hoga...ematic name in the SGD (Saccharomyces Genome Database; http://www.yeastgenome.org /). Bait gene name The gen

Profiling of Escherichia coli Chromosome database.

Science.gov (United States)

Yamazaki, Yukiko; Niki, Hironori; Kato, Jun-ichi

2008-01-01

The Profiling of Escherichia coli Chromosome (PEC) database (http://www.shigen.nig.ac.jp/ecoli/pec/) is designed to allow E. coli researchers to efficiently access information from functional genomics studies. The database contains two principal types of data: gene essentiality and a large collection of E. coli genetic research resources. The essentiality data are based on data compilation from published single-gene essentiality studies and on cell growth studies of large-deletion mutants. Using the circular and linear viewers for both whole genomes and the minimal genome, users can not only gain an overview of the genome structure but also retrieve information on contigs, gene products, mutants, deletions, and so forth. In particular, genome-wide exhaustive mutants are an essential resource for studying E. coli gene functions. Although the genomic database was constructed independently from the genetic resources database, users may seamlessly access both types of data. In addition to these data, the PEC database also provides a summary of homologous genes of other bacterial genomes and of protein structure information, with a comprehensive interface. The PEC is thus a convenient and useful platform for contemporary E. coli researchers.

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila

Directory of Open Access Journals (Sweden)

Parrish Jodi R

2006-04-01

Full Text Available Abstract Background Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. Description Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes

Update History of This Database - RPD | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RPD Update History of This Database Date Update contents 2016/02/02 Rice Proteome Database English archi...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RPD | LSDB Archive ... ...ve site is opened. 2003/01/07 Rice Proteome Database ( http://gene64.dna.affrc.go.jp/RPD/ ) is opened. About Thi

Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB

Energy Technology Data Exchange (ETDEWEB)

DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.

2006-02-01

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni

Directory of Open Access Journals (Sweden)

Priyanka Patel

2016-03-01

Full Text Available A database that integrates all the information required for biological processing is essential to be stored in one platform. We have attempted to create one such integrated database that can be a one stop shop for the essential features required to fetch valuable result. LmSmdB (L. major and S. mansoni database is an integrated database that accounts for the biological networks and regulatory pathways computationally determined by integrating the knowledge of the genome sequences of the mentioned organisms. It is the first database of its kind that has together with the network designing showed the simulation pattern of the product. This database intends to create a comprehensive canopy for the regulation of lipid metabolism reaction in the parasite by integrating the transcription factors, regulatory genes and the protein products controlled by the transcription factors and hence operating the metabolism at genetic level. Keywords: L.major, S.mansoni, Regulatory networks, Transcription factors, Database

CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies

Directory of Open Access Journals (Sweden)

Furue Motoki

2010-07-01

Full Text Available Abstract Background Immunoglobulin (IG or antibody and the T-cell receptor (TR are pivotal proteins in the immune system of higher organisms. In cancer immunotherapy, the immune responses mediated by tumor-epitope-binding IG or TR play important roles in anticancer effects. Although there are public databases specific for immunological genes, their contents have not been associated with clinical studies. Therefore, we developed an integrated database of IG/TR data reported in cancer studies (the Cancer-related Immunological Gene Database [CIG-DB]. Description This database is designed as a platform to explore public human and murine IG/TR genes sequenced in cancer studies. A total of 38,308 annotation entries for IG/TR proteins were collected from GenBank/DDBJ/EMBL and the Protein Data Bank, and 2,740 non-redundant corresponding MEDLINE references were appended. Next, we filtered the MEDLINE texts by MeSH terms, titles, and abstracts containing keywords related to cancer. After we performed a manual check, we classified the protein entries into two groups: 611 on cancer therapy (Group I and 1,470 on hematological tumors (Group II. Thus, a total of 2,081 cancer-related IG and TR entries were tabularized. To effectively classify future entries, we developed a computational method based on text mining and canonical discriminant analysis by parsing MeSH/title/abstract words. We performed a leave-one-out cross validation for the method, which showed high accuracy rates: 94.6% for IG references and 94.7% for TR references. We also collected 920 epitope sequences bound with IG/TR. The CIG-DB is equipped with search engines for amino acid sequences and MEDLINE references, sequence analysis tools, and a 3D viewer. This database is accessible without charge or registration at http://www.scchr-cigdb.jp/, and the search results are freely downloadable. Conclusions The CIG-DB serves as a bridge between immunological gene data and cancer studies, presenting

Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

Science.gov (United States)

Naghdi, Mohammad Reza; Smail, Katia; Wang, Joy X; Wade, Fallou; Breaker, Ronald R; Perreault, Jonathan

2017-03-15

The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale. Here we present various approaches using the database RiboGap as a primary tool for finding known ncRNAs and for uncovering simple sequence motifs with regulatory roles. This database also can be used to easily extract intergenic sequences of eubacteria and archaea to find conserved RNA structures upstream of given genes. We also show how to extend analysis further to choose the best candidate ncRNAs for experimental validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Chemical processing of raw florets of dyer's saffron and successful extraction of a resulting product (carthamin: an approach to improve conventional methods

Directory of Open Access Journals (Sweden)

Koshi Saito

2014-01-01

Full Text Available Efficacy of KMnO4 on processing red florets of dyer's saffron was examined in the presence of micromolar concentrations of the metal salts. Apparent value for KMnO4 determined by double-reciprocal plots was 126 µM, whose value corresponds to a 1/154-fold of dried florets. Successful extraction of red carthamin was performed by using the processed matters with various solvent systems. HCl/NaOH, acetic acid/ammonia water and pyridine/methanol were found to be effective. For purification of carthamin, the cellulose adsorption technique was very promising. The data are assessed to standarize the new technique.

UMD-USHbases: a comprehensive set of databases to record and analyse pathogenic mutations and unclassified variants in seven Usher syndrome causing genes.

Science.gov (United States)

Baux, David; Faugère, Valérie; Larrieu, Lise; Le Guédard-Méreuze, Sandie; Hamroun, Dalil; Béroud, Christophe; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

2008-08-01

Using the Universal Mutation Database (UMD) software, we have constructed "UMD-USHbases", a set of relational databases of nucleotide variations for seven genes involved in Usher syndrome (MYO7A, CDH23, PCDH15, USH1C, USH1G, USH3A and USH2A). Mutations in the Usher syndrome type I causing genes are also recorded in non-syndromic hearing loss cases and mutations in USH2A in non-syndromic retinitis pigmentosa. Usher syndrome provides a particular challenge for molecular diagnostics because of the clinical and molecular heterogeneity. As many mutations are missense changes, and all the genes also contain apparently non-pathogenic polymorphisms, well-curated databases are crucial for accurate interpretation of pathogenicity. Tools are provided to assess the pathogenicity of mutations, including conservation of amino acids and analysis of splice-sites. Reference amino acid alignments are provided. Apparently non-pathogenic variants in patients with Usher syndrome, at both the nucleotide and amino acid level, are included. The UMD-USHbases currently contain more than 2,830 entries including disease causing mutations, unclassified variants or non-pathogenic polymorphisms identified in over 938 patients. In addition to data collected from 89 publications, 15 novel mutations identified in our laboratory are recorded in MYO7A (6), CDH23 (8), or PCDH15 (1) genes. Information is given on the relative involvement of the seven genes, the number and distribution of variants in each gene. UMD-USHbases give access to a software package that provides specific routines and optimized multicriteria research and sorting tools. These databases should assist clinicians and geneticists seeking information about mutations responsible for Usher syndrome.

Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

Directory of Open Access Journals (Sweden)

Raherison Elie

2012-08-01

Full Text Available Abstract Background Conifers have very large genomes (13 to 30 Gigabases that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.

Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology.

Science.gov (United States)

Vivar, Juan C; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

2013-08-01

Abstract Unparalleled technological advances have fueled an explosive growth in the scope and scale of biological data and have propelled life sciences into the realm of "Big Data" that cannot be managed or analyzed by conventional approaches. Big Data in the life sciences are driven primarily via a diverse collection of 'omics'-based technologies, including genomics, proteomics, metabolomics, transcriptomics, metagenomics, and lipidomics. Gene-set enrichment analysis is a powerful approach for interrogating large 'omics' datasets, leading to the identification of biological mechanisms associated with observed outcomes. While several factors influence the results from such analysis, the impact from the contents of pathway databases is often under-appreciated. Pathway databases often contain variously named pathways that overlap with one another to varying degrees. Ignoring such redundancies during pathway analysis can lead to the designation of several pathways as being significant due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies also result in correlated p values and overdispersion, leading to biased results. We investigated the level of redundancies in multiple pathway databases and observed large discrepancies in the nature and extent of pathway overlap. This prompted us to develop the application, ReCiPa (Redundancy Control in Pathway Databases), to control redundancies in pathway databases based on user-defined thresholds. Analysis of genomic and genetic datasets, using ReCiPa-generated overlap-controlled versions of KEGG and Reactome pathways, led to a reduction in redundancy among the top-scoring gene-sets and allowed for the inclusion of additional gene-sets representing possibly novel biological mechanisms. Using obesity as an example, bioinformatic analysis further demonstrated that gene-sets identified from overlap-controlled pathway databases show stronger evidence of prior association

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

Science.gov (United States)

Choubey, Jyotsna; Choudhari, Jyoti Kant; Patel, Ashish; Verma, Mukesh Kumar

2017-01-01

Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

The MAR databases: development and implementation of databases specific for marine metagenomics.

Science.gov (United States)

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

2018-01-04

We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Preventive effects of hydroalcoholic extract of saffron on hematological parameters of experimental asthmatic rats

Directory of Open Access Journals (Sweden)

Somayyeh Vosooghi

2013-05-01

Full Text Available Objective: Asthma is a chronic inflammatory disease of the respiratory airways distinguished by edema and infiltration of inflammatory immune cells. To test our hypothesis about the anti-inflammatory effect of saffron, we examined effects of Crocus sativus (C. sativus extract as a prophylactic anti-inflammatory agent in sensitized rats. Materials and Methods: To induce experimental asthma, rats were sensitized with injection and inhalation of ovalbumin (OA. Forty male Wistar rats were divided into 5 groups (n=8 for each: control, sensitized (asthma, and sensitized and pretreated with three different concentrations of extract, 50, 100, and 200 mg/kg, 2 times a week (group asthma+50EX, group asthma+100EX, and group asthma+200EX. After 32 days, total white blood cells (WBC counts, red blood cells (RBC, and platelet counts in blood were examined. Results: Total WBC number and eosinophil and neutrophil percentage in blood were increased, but lymphocyte decreased in sensitized animals compared with those of control group (pConclusion: Our findings indicated that the extract of C. sativus could be useful to prevent asthma as an anti-inflammatory treatment.

A searchable cross-platform gene expression database reveals connections between drug treatments and disease

Directory of Open Access Journals (Sweden)

Williams Gareth

2012-01-01

Full Text Available Abstract Background Transcriptional data covering multiple platforms and species is collected and processed into a searchable platform independent expression database (SPIED. SPIED consists of over 100,000 expression fold profiles defined independently of control/treatment assignment and mapped to non-redundant gene lists. The database is thus searchable with query profiles defined over genes alone. The motivation behind SPIED is that transcriptional profiles can be quantitatively compared and ranked and thus serve as effective surrogates for comparing the underlying biological states across multiple experiments. Results Drug perturbation, cancer and neurodegenerative disease derived transcriptional profiles are shown to be effective descriptors of the underlying biology as they return related drugs and pathologies from SPIED. In the case of Alzheimer's disease there is high transcriptional overlap with other neurodegenerative conditions and rodent models of neurodegeneration and nerve injury. Combining the query signature with correlating profiles allows for the definition of a tight neurodegeneration signature that successfully highlights many neuroprotective drugs in the Broad connectivity map. Conclusions Quantitative querying of expression data from across the totality of deposited experiments is an effective way of discovering connections between different biological systems and in particular that between drug action and biological disease state. Examples in cancer and neurodegenerative conditions validate the utility of SPIED.

The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

Directory of Open Access Journals (Sweden)

Lo Fang-Yi

2012-06-01

Full Text Available Abstract Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR, chromogenic in situ hybridization (CISH, reverse transcriptase-qPCR (RT-qPCR, and immunohistochemistry (IHC in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1 functioning in Rho activity control, FRAT2 (10q24.1 involved in Wnt signaling, PAFAH1B1 (17p13.3 functioning in motility control, and ZNF322A (6p22.1 involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (PP=0.06. In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of

The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

International Nuclear Information System (INIS)

Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

2012-01-01

Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

Huntington's disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database.

Science.gov (United States)

Kalathur, Ravi Kiran Reddy; Hernández-Prieto, Miguel A; Futschik, Matthias E

2012-06-28

Huntington's disease (HD) is a fatal progressive neurodegenerative disorder caused by the expansion of the polyglutamine repeat region in the huntingtin gene. Although the disease is triggered by the mutation of a single gene, intensive research has linked numerous other genes to its pathogenesis. To obtain a systematic overview of these genes, which may serve as therapeutic targets, CHDI Foundation has recently established the HD Research Crossroads database. With currently over 800 cataloged genes, this web-based resource constitutes the most extensive curation of genes relevant to HD. It provides us with an unprecedented opportunity to survey molecular mechanisms involved in HD in a holistic manner. To gain a synoptic view of therapeutic targets for HD, we have carried out a variety of bioinformatical and statistical analyses to scrutinize the functional association of genes curated in the HD Research Crossroads database. In particular, enrichment analyses were performed with respect to Gene Ontology categories, KEGG signaling pathways, and Pfam protein families. For selected processes, we also analyzed differential expression, using published microarray data. Additionally, we generated a candidate set of novel genetic modifiers of HD by combining information from the HD Research Crossroads database with previous genome-wide linkage studies. Our analyses led to a comprehensive identification of molecular mechanisms associated with HD. Remarkably, we not only recovered processes and pathways, which have frequently been linked to HD (such as cytotoxicity, apoptosis, and calcium signaling), but also found strong indications for other potentially disease-relevant mechanisms that have been less intensively studied in the context of HD (such as the cell cycle and RNA splicing, as well as Wnt and ErbB signaling). For follow-up studies, we provide a regularly updated compendium of molecular mechanism, that are associated with HD, at http://hdtt.sysbiolab.eu Additionally

Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database

Directory of Open Access Journals (Sweden)

Kalathur Ravi Kiran

2012-06-01

Full Text Available Abstract Background Huntington’s disease (HD is a fatal progressive neurodegenerative disorder caused by the expansion of the polyglutamine repeat region in the huntingtin gene. Although the disease is triggered by the mutation of a single gene, intensive research has linked numerous other genes to its pathogenesis. To obtain a systematic overview of these genes, which may serve as therapeutic targets, CHDI Foundation has recently established the HD Research Crossroads database. With currently over 800 cataloged genes, this web-based resource constitutes the most extensive curation of genes relevant to HD. It provides us with an unprecedented opportunity to survey molecular mechanisms involved in HD in a holistic manner. Methods To gain a synoptic view of therapeutic targets for HD, we have carried out a variety of bioinformatical and statistical analyses to scrutinize the functional association of genes curated in the HD Research Crossroads database. In particular, enrichment analyses were performed with respect to Gene Ontology categories, KEGG signaling pathways, and Pfam protein families. For selected processes, we also analyzed differential expression, using published microarray data. Additionally, we generated a candidate set of novel genetic modifiers of HD by combining information from the HD Research Crossroads database with previous genome-wide linkage studies. Results Our analyses led to a comprehensive identification of molecular mechanisms associated with HD. Remarkably, we not only recovered processes and pathways, which have frequently been linked to HD (such as cytotoxicity, apoptosis, and calcium signaling, but also found strong indications for other potentially disease-relevant mechanisms that have been less intensively studied in the context of HD (such as the cell cycle and RNA splicing, as well as Wnt and ErbB signaling. For follow-up studies, we provide a regularly updated compendium of molecular mechanism, that are

Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes.

Directory of Open Access Journals (Sweden)

Adam Y Ye

Full Text Available Transporters are essential in homeostatic exchange of endogenous and exogenous substances at the systematic, organic, cellular, and subcellular levels. Gene mutations of transporters are often related to pharmacogenetics traits. Recent developments in high throughput technologies on genomics, transcriptomics and proteomics allow in depth studies of transporter genes in normal cellular processes and diverse disease conditions. The flood of high throughput data have resulted in urgent need for an updated knowledgebase with curated, organized, and annotated human transporters in an easily accessible way. Using a pipeline with the combination of automated keywords query, sequence similarity search and manual curation on transporters, we collected 1,555 human non-redundant transporter genes to develop the Human Transporter Database (HTD (http://htd.cbi.pku.edu.cn. Based on the extensive annotations, global properties of the transporter genes were illustrated, such as expression patterns and polymorphisms in relationships with their ligands. We noted that the human transporters were enriched in many fundamental biological processes such as oxidative phosphorylation and cardiac muscle contraction, and significantly associated with Mendelian and complex diseases such as epilepsy and sudden infant death syndrome. Overall, HTD provides a well-organized interface to facilitate research communities to search detailed molecular and genetic information of transporters for development of personalized medicine.

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

Science.gov (United States)

Stenson, Peter D; Mort, Matthew; Ball, Edward V; Shaw, Katy; Phillips, Andrew; Cooper, David N

2014-01-01

The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.

Database Description - GenLibi | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ve name Gene Linker to bibliography DOI 10.18908/lsdba.nbdc01093-000 Creator Creator Name: Japan Science and Technology...mouse and rat genes. License CC BY-SA Detail Background and funding Name: JST (Japan Science and Technology ... site Japan Science and Technology Agency URL of the original website http://gene.biosciencedbc.jp/ Operatio...me(s): Journal: External Links: Original website information Database maintenance

Application of data envelopment analysis to evaluate the efficiency of saffron growers (Case study: Qaen county

Directory of Open Access Journals (Sweden)

Hadis Kavand

2014-06-01

Full Text Available Agricultural sector to meet the requests such as a higher yield, less pollution and fulfill consumer demands due to increasing scarcity of resources is under pressure. According to the importance of efficiency in productivity growth, this index can play an important rule, especially in developing countries, for the development of agricultural systems in order to meet these requests. The aim of this study was to evaluate the technical, economic and allocative efficiency of producers of saffron for Qaen region using data envelopment analysis. Information and data is collected through completion 50 questionnaires in year 2011-2012. Results show that average technical efficiency, allocative and economic in condition of constant return to scale are 0.86, 0.92, and 0.88 and in condition of variable return scale are 0.89, 0.92, and 0.80, respectively. Also, according to the results obtained, educating and advising farmers to the proper use of available resources, and promotion, and the use of appropriate technologies such as improved efficiency is recommended.

Tissue repair genes: the TiRe database and its implication for skin wound healing

OpenAIRE

Yanai, Hagai; Budovsky, Arie; Tacutu, Robi; Barzilay, Thomer; Abramovich, Amir; Ziesche, Rolf; Fraifeld, Vadim E.

2016-01-01

Wound healing is an inherent feature of any multicellular organism and recent years have brought about a huge amount of data regarding regular and abnormal tissue repair. Despite the accumulated knowledge, modulation of wound healing is still a major biomedical challenge, especially in advanced ages. In order to collect and systematically organize what we know about the key players in wound healing, we created the TiRe (Tissue Repair) database, an online collection of genes and proteins that ...

Open TG-GATEs: a large-scale toxicogenomics database

Science.gov (United States)

Igarashi, Yoshinobu; Nakatsu, Noriyuki; Yamashita, Tomoya; Ono, Atsushi; Ohno, Yasuo; Urushidani, Tetsuro; Yamada, Hiroshi

2015-01-01

Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological mechanisms in animal target organs. Over the past 10 years, the Japanese Toxicogenomics Project consortium (TGP) has been developing a large-scale toxicogenomics database consisting of data from 170 compounds (mostly drugs) with the aim of improving and enhancing drug safety assessment. Most of the data generated by the project (e.g. gene expression, pathology, lot number) are freely available to the public via Open TG-GATEs (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System). Here, we provide a comprehensive overview of the database, including both gene expression data and metadata, with a description of experimental conditions and procedures used to generate the database. Open TG-GATEs is available from http://toxico.nibio.go.jp/english/index.html. PMID:25313160

BBGD: an online database for blueberry genomic data

Directory of Open Access Journals (Sweden)

Matthews Benjamin F

2007-01-01

Full Text Available Abstract Background Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry. Description BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure. Conclusion By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.

GOBASE: an organelle genome database

OpenAIRE

O?Brien, Emmet A.; Zhang, Yue; Wang, Eric; Marie, Veronique; Badejoko, Wole; Lang, B. Franz; Burger, Gertraud

2008-01-01

The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (?913 000) and chloroplast-encoded sequences (?250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing...

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm

Directory of Open Access Journals (Sweden)

Allen Eric E

2008-10-01

Full Text Available Abstract Background The process of horizontal gene transfer (HGT is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. DarkHorse, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not. Description The DarkHorse algorithm has been applied to 955 microbial genome sequences, and the results organized into a web-searchable relational database, called the DarkHorse HGT Candidate Resource http://darkhorse.ucsd.edu. Users can select individual genomes or groups of genomes to screen by LPI score, search for protein functions by descriptive annotation or amino acid sequence similarity, or select proteins with unusual G+C composition in their underlying coding sequences. The search engine reports LPI scores for match partners as well as query sequences, providing the opportunity to explore whether potential HGT donor sequences are phylogenetically typical or atypical within their own genomes. This information can be used to predict whether or not sufficient information is available to build a well-supported phylogenetic tree using the potential donor sequence. Conclusion The DarkHorse HGT Candidate database provides a powerful, flexible set of tools for identifying phylogenetically atypical proteins, allowing researchers to explore both individual HGT events in single genomes, and

Human Variome Project Quality Assessment Criteria for Variation Databases.

Science.gov (United States)

Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter

2016-06-01

Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.

Scarab/Saffron Development Project Case study: Material Selection Criteria for the Monoethylene Glycol Recovery Package

International Nuclear Information System (INIS)

Moussa, A.M.; Habib, S.; Shinaishin, A.

2004-01-01

MEG Recovery Unit for Scarab/Saffron development project is the first application in gas production. The Mono Ethylene Glycol Recovery Unit (MEG) recovers MEG from Water/MEG stream and removes salts and other contaminants. MEG Recovery Unit Equipment Design Criteria were designed for two parallel trains A and B, each train is capable to treat 500 bbl MEG, 1500 bbl water and 9 ton salt. The MEG unit is a combination of two unit operations; MEG Recovery unit is normally applicable in the oil and gas industries that is applying distillation technique, while the new technology is salt treatment and handling. The MEG Unit material selection is made to be suitable for the entire design life which is 25 years, the materials for MEG Recovery Unit have been selected among the available corrosion resistance alloys, where requested by the service and ambient conditions. Therefore all. the parts of the MEG unit that are in saline service are in either (2205 duplex, AISI 316L) and in Inconel alloy 625 related to operating temperature. This case study focused at Inconel alloy 625, which is selected for salt service and their operation problem occurred during the construction and operating conditions

Natural Compounds from Saffron and Bear Bile Prevent Vision Loss and Retinal Degeneration

Directory of Open Access Journals (Sweden)

Laura Fernández-Sánchez

2015-07-01

Full Text Available All retinal disorders, regardless of their aetiology, involve the activation of oxidative stress and apoptosis pathways. The administration of neuroprotective factors is crucial in all phases of the pathology, even when vision has been completely lost. The retina is one of the most susceptible tissues to reactive oxygen species damage. On the other hand, proper development and functioning of the retina requires a precise balance between the processes of proliferation, differentiation and programmed cell death. The life-or-death decision seems to be the result of a complex balance between pro- and anti-apoptotic signals. It has been recently shown the efficacy of natural products to slow retinal degenerative process through different pathways. In this review, we assess the neuroprotective effect of two compounds used in the ancient pharmacopoeia. On one hand, it has been demonstrated that administration of the saffron constituent safranal to P23H rats, an animal model of retinitis pigmentosa, preserves photoreceptor morphology and number, the capillary network and the visual response. On the other hand, it has been shown that systemic administration of tauroursodeoxycholic acid (TUDCA, the major component of bear bile, to P23H rats preserves cone and rod structure and function, together with their contact with postsynaptic neurons. The neuroprotective effects of safranal and TUDCA make these compounds potentially useful for therapeutic applications in retinal degenerative diseases.

Natural Compounds from Saffron and Bear Bile Prevent Vision Loss and Retinal Degeneration.

Science.gov (United States)

Fernández-Sánchez, Laura; Lax, Pedro; Noailles, Agustina; Angulo, Antonia; Maneu, Victoria; Cuenca, Nicolás

2015-07-31

All retinal disorders, regardless of their aetiology, involve the activation of oxidative stress and apoptosis pathways. The administration of neuroprotective factors is crucial in all phases of the pathology, even when vision has been completely lost. The retina is one of the most susceptible tissues to reactive oxygen species damage. On the other hand, proper development and functioning of the retina requires a precise balance between the processes of proliferation, differentiation and programmed cell death. The life-or-death decision seems to be the result of a complex balance between pro- and anti-apoptotic signals. It has been recently shown the efficacy of natural products to slow retinal degenerative process through different pathways. In this review, we assess the neuroprotective effect of two compounds used in the ancient pharmacopoeia. On one hand, it has been demonstrated that administration of the saffron constituent safranal to P23H rats, an animal model of retinitis pigmentosa, preserves photoreceptor morphology and number, the capillary network and the visual response. On the other hand, it has been shown that systemic administration of tauroursodeoxycholic acid (TUDCA), the major component of bear bile, to P23H rats preserves cone and rod structure and function, together with their contact with postsynaptic neurons. The neuroprotective effects of safranal and TUDCA make these compounds potentially useful for therapeutic applications in retinal degenerative diseases.

DistiLD Database

DEFF Research Database (Denmark)

Palleja, Albert; Horn, Heiko; Eliasson, Sabrina

2012-01-01

Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of hundreds of diseases. However, there is currently no database that enables non-specialists to answer the following simple questions: which SNPs associated...... with diseases are in linkage disequilibrium (LD) with a gene of interest? Which chromosomal regions have been associated with a given disease, and which are the potentially causal genes in each region? To answer these questions, we use data from the HapMap Project to partition each chromosome into so-called LD...... blocks, so that SNPs in LD with each other are preferentially in the same block, whereas SNPs not in LD are in different blocks. By projecting SNPs and genes onto LD blocks, the DistiLD database aims to increase usage of existing GWAS results by making it easy to query and visualize disease...

SoyFN: a knowledge database of soybean functional networks.

Science.gov (United States)

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

Update History of This Database - GenLibi | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us GenLibi Update History of This Database Date Update contents 2014/03/25 GenLibi English archi...base Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - GenLibi | LSDB Archive ... ...ve site is opened. 2007/03/01 GenLibi ( http://gene.biosciencedbc.jp/ ) is opened. About This Database Data

BIOSPIDA: A Relational Database Translator for NCBI.

Science.gov (United States)

Hagen, Matthew S; Lee, Eva K

2010-11-13

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.

Development and application of a database of food ingredient fraud and economically motivated adulteration from 1980 to 2010.

Science.gov (United States)

Moore, Jeffrey C; Spink, John; Lipp, Markus

2012-04-01

Food ingredient fraud and economically motivated adulteration are emerging risks, but a comprehensive compilation of information about known problematic ingredients and detection methods does not currently exist. The objectives of this research were to collect such information from publicly available articles in scholarly journals and general media, organize into a database, and review and analyze the data to identify trends. The results summarized are a database that will be published in the US Pharmacopeial Convention's Food Chemicals Codex, 8th edition, and includes 1305 records, including 1000 records with analytical methods collected from 677 references. Olive oil, milk, honey, and saffron were the most common targets for adulteration reported in scholarly journals, and potentially harmful issues identified include spices diluted with lead chromate and lead tetraoxide, substitution of Chinese star anise with toxic Japanese star anise, and melamine adulteration of high protein content foods. High-performance liquid chromatography and infrared spectroscopy were the most common analytical detection procedures, and chemometrics data analysis was used in a large number of reports. Future expansion of this database will include additional publically available articles published before 1980 and in other languages, as well as data outside the public domain. The authors recommend in-depth analyses of individual incidents. This report describes the development and application of a database of food ingredient fraud issues from publicly available references. The database provides baseline information and data useful to governments, agencies, and individual companies assessing the risks of specific products produced in specific regions as well as products distributed and sold in other regions. In addition, the report describes current analytical technologies for detecting food fraud and identifies trends and developments. © 2012 US Pharmacupia Journal of Food Science �

Identification of Anhydrobiosis-related Genes from an Expressed Sequence Tag Database in the Cryptobiotic Midge Polypedilum vanderplanki (Diptera; Chironomidae)*

Science.gov (United States)

Cornette, Richard; Kanamori, Yasushi; Watanabe, Masahiko; Nakahara, Yuichi; Gusev, Oleg; Mitsumasu, Kanako; Kadono-Okuda, Keiko; Shimomura, Michihiko; Mita, Kazuei; Kikawada, Takahiro; Okuda, Takashi

2010-01-01

Some organisms are able to survive the loss of almost all their body water content, entering a latent state known as anhydrobiosis. The sleeping chironomid (Polypedilum vanderplanki) lives in the semi-arid regions of Africa, and its larvae can survive desiccation in an anhydrobiotic form during the dry season. To unveil the molecular mechanisms of this resistance to desiccation, an anhydrobiosis-related Expressed Sequence Tag (EST) database was obtained from the sequences of three cDNA libraries constructed from P. vanderplanki larvae after 0, 12, and 36 h of desiccation. The database contained 15,056 ESTs distributed into 4,807 UniGene clusters. ESTs were classified according to gene ontology categories, and putative expression patterns were deduced for all clusters on the basis of the number of clones in each library; expression patterns were confirmed by real-time PCR for selected genes. Among up-regulated genes, antioxidants, late embryogenesis abundant (LEA) proteins, and heat shock proteins (Hsps) were identified as important groups for anhydrobiosis. Genes related to trehalose metabolism and various transporters were also strongly induced by desiccation. Those results suggest that the oxidative stress response plays a central role in successful anhydrobiosis. Similarly, protein denaturation and aggregation may be prevented by marked up-regulation of Hsps and the anhydrobiosis-specific LEA proteins. A third major feature is the predicted increase in trehalose synthesis and in the expression of various transporter proteins allowing the distribution of trehalose and other solutes to all tissues. PMID:20833722

Discovering gene annotations in biomedical text databases

Directory of Open Access Journals (Sweden)

Ozsoyoglu Gultekin

2008-03-01

Full Text Available Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i automating the annotation of genomic entities with Gene Ontology concepts, and (ii providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate

GiSAO.db: a database for ageing research

Directory of Open Access Journals (Sweden)

Grillari Johannes

2011-05-01

Full Text Available Abstract Background Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily. Description GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing. Conclusions We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at https://gisao.genome.tugraz.at and all the stored data can be viewed with a guest account.

YMDB: the Yeast Metabolome Database

Science.gov (United States)

Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S.

2012-01-01

The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated ‘metabolomic’ database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast.

Science.gov (United States)

Chuartzman, Silvia G; Schuldiner, Maya

2018-03-25

In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice ('hits') are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen - all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community. © 2018 The Authors Yeast Published by John Wiley & Sons Ltd.

The protective role of saffron petal extracts on gentamicininduced nephrotoxicity in rats

Directory of Open Access Journals (Sweden)

Arash Omidi

2016-07-01

Full Text Available Different potentially therapeutic approaches to prevent or attenuate gentamicin sulfate (GM induced nephrotoxicity have been proposed. The present study was conducted to investigate the effect of the saffron petals extracts (Crocus sativus (SPE on male Wistar rats with kidney failure. Rats (40 were randomly assigned into five groups of 8 animals each: i the control group, that received normal saline (0.5 mL/kg; ii the GM group, that received GM (80 mg/kg by intraperitoneal (i.p. injection on a daily basis; iii the GM+SPE group that received the same dose of GM and SPE (40 mg/kg by i.p. injection on a daily basis; iv the GM+2SPE group, that received the same dose of GM and twofold of SPE (80 mg/kg by i.p. injection on a daily basis; whereas v 2SPE+GM group, that received 80 mg/kg of SPE a week before initiating the treatment with GM (prevention group. Significant differences were seen in the concentration of glucose, blood urea nitrogen (BUN, and creatinine between treatment groups and control in the male Wistar rats. GM was observed to cause nephrotoxicity, which was evidenced by an elevation of serum BUN and creatinine levels. The biochemical findings of the current study are concordant with those of histopathologic findings. The results of this study indicate that SPE especially in dose of 40 mg/kg can ameliorate harmful effects of GM on the kidney. The present results may suggest that the SPE have ameliorative effects on kidney failures induced by GM.

ProOpDB: Prokaryotic Operon DataBase.

Science.gov (United States)

Taboada, Blanca; Ciria, Ricardo; Martinez-Guerrero, Cristian E; Merino, Enrique

2012-01-01

The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: (i) organism name, (ii) metabolic pathways, as defined by the KEGG database, (iii) gene orthology, as defined by the COG database, (iv) conserved protein domains, as defined by the Pfam database, (v) reference gene and (vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient method to select the most representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool to visualize their genomic context and retrieve the sequence of their corresponding 5' regulatory regions, as well as the nucleotide or amino acid sequences of their genes.

ECMDB: The E. coli Metabolome Database

OpenAIRE

Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S.

2012-01-01

The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ?1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. E...

Comparative efficacy and safety of Crocus sativus L. for treating mild to moderate major depressive disorder in adults: a meta-analysis of randomized controlled trials

Directory of Open Access Journals (Sweden)

Yang XY

2018-05-01

Full Text Available Xiangying Yang,1 Xiaolu Chen,1 Yixiao Fu,2 Qinghua Luo,2 Lian Du,2 Haitang Qiu,2 Tian Qiu,2 Li Zhang,1 Huaqing Meng2 1The First Branch, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China Purpose: To investigate the efficacy and safety of saffron in the treatment of major depressive disorder (MDD in comparison to placebo and synthetic antidepressants. Patients and methods: We conducted a systematic search in several electronic databases as well as manual search in bibliographies of relevant studies. We included randomized controlled trials that investigated the efficacy and safety of saffron for treating MDD in adults in comparison to either placebo or synthetic antidepressants. Primary outcome was change in scores on depressive symptoms from baseline. Secondary outcomes included remission rate, response rate, and drop-out rate for all reasons. We chose a random-effects model in order to obtain more conservative results. Standardized mean differences (SMDs and odds ratios (ORs with 95% confidence intervals (CIs were estimated as the overall effect index by inverse variance models. Results: Seven studies were included in this meta-analysis. Overall quality of these included studies was moderate. As for the primary outcome, saffron showed more improvements in depression symptoms when compared with placebo, with an SMD of -1.22 (95% CI -1.94, -0.49, P=0.001. Meanwhile, saffron was as effective as synthetic antidepressants, with an SMD of 0.16 (95% CI -0.25, 0.57, P=0.44. Moderate heterogeneity existed in our analysis. Through subgroup analyses, we found that treatment dosage and duration, types of synthetic antidepressants administered in the comparison group, and outcome measures could explain most of the variance. No differences were found in remission rate, response

iSyTE 2.0: a database for expression-based gene discovery in the eye

Science.gov (United States)

Kakrana, Atul; Yang, Andrian; Anand, Deepti; Djordjevic, Djordje; Ramachandruni, Deepti; Singh, Abhyudai; Huang, Hongzhan

2018-01-01

Abstract Although successful in identifying new cataract-linked genes, the previous version of the database iSyTE (integrated Systems Tool for Eye gene discovery) was based on expression information on just three mouse lens stages and was functionally limited to visualization by only UCSC-Genome Browser tracks. To increase its efficacy, here we provide an enhanced iSyTE version 2.0 (URL: http://research.bioinformatics.udel.edu/iSyTE) based on well-curated, comprehensive genome-level lens expression data as a one-stop portal for the effective visualization and analysis of candidate genes in lens development and disease. iSyTE 2.0 includes all publicly available lens Affymetrix and Illumina microarray datasets representing a broad range of embryonic and postnatal stages from wild-type and specific gene-perturbation mouse mutants with eye defects. Further, we developed a new user-friendly web interface for direct access and cogent visualization of the curated expression data, which supports convenient searches and a range of downstream analyses. The utility of these new iSyTE 2.0 features is illustrated through examples of established genes associated with lens development and pathobiology, which serve as tutorials for its application by the end-user. iSyTE 2.0 will facilitate the prioritization of eye development and disease-linked candidate genes in studies involving transcriptomics or next-generation sequencing data, linkage analysis and GWAS approaches. PMID:29036527

PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

Directory of Open Access Journals (Sweden)

Lalucat Jorge

2010-04-01

Full Text Available Abstract Background The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. Description The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI. Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. Conclusions The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://www.uib.es/microbiologiaBD/Welcome.html. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer

Quantitative expression of regulatory and differentiation-related genes in the key steps of human hematopoiesis: The LeukoStage Database.

Science.gov (United States)

Polgárová, K; Vášková, M; Froňková, E; Slámová, L; Kalina, T; Mejstříková, E; Dobiášová, A; Fišer, K; Hrušák, O

2016-01-01

Differentiation during hematopoiesis leads to the generation of many cell types with specific functions. At various stages of maturation, the cells may change pathologically, leading to diseases including acute leukemias (ALs). Expression levels of regulatory molecules (such as the IKZF, GATA, HOX, FOX, NOTCH and CEBP families, as well as SPI-1/PU1 and PAX5) and lineage-specific molecules (including CD2, CD14, CD79A, and BLNK) may be compared between pathological and physiological cells. Although the key steps of differentiation are known, the available databases focus mainly on fully differentiated cells as a reference. Precursor cells may be a more appropriate reference point for diseases that evolve at immature stages. Therefore, we developed a quantitative real-time polymerase chain reaction (qPCR) array to investigate 90 genes that are characteristic of the lymphoid or myeloid lineages and/or are thought to be involved in their regulation. Using this array, sorted cells of granulocytic, monocytic, T and B lineages were analyzed. For each of these lineages, 3-5 differentiation stages were selected (17 stages total), and cells were sorted from 3 different donors per stage. The qPCR results were compared to similarly processed AL cells of lymphoblastic (n=18) or myeloid (n=6) origins and biphenotypic AL cells of B cell origin with myeloid involvement (n=5). Molecules characteristic of each lineage were found. In addition, cells of a newly discovered switching lymphoblastic AL (swALL) were sorted at various phases during the supposed transdifferentiation from an immature B cell to a monocytic phenotype. As demonstrated previously, gene expression changed along with the immunophenotype. The qPCR data are publicly available in the LeukoStage Database in which gene expression in malignant and non-malignant cells of different lineages can be explored graphically and differentially expressed genes can be identified. In addition, the LeukoStage Database can aid the

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

Science.gov (United States)

Huang, Weiliang; Brewer, Luke K; Jones, Jace W; Nguyen, Angela T; Marcu, Ana; Wishart, David S; Oglesby-Sherrouse, Amanda G; Kane, Maureen A; Wilks, Angela

2018-01-04

The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The NCBI BioSystems database.

Science.gov (United States)

Geer, Lewis Y; Marchler-Bauer, Aron; Geer, Renata C; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

SoyDB: a knowledge database of soybean transcription factors

Directory of Open Access Journals (Sweden)

Valliyodan Babu

2010-01-01

Full Text Available Abstract Background Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. Description The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB, protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models. Conclusions A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.

Tissue repair genes: the TiRe database and its implication for skin wound healing.

Science.gov (United States)

Yanai, Hagai; Budovsky, Arie; Tacutu, Robi; Barzilay, Thomer; Abramovich, Amir; Ziesche, Rolf; Fraifeld, Vadim E

2016-04-19

Wound healing is an inherent feature of any multicellular organism and recent years have brought about a huge amount of data regarding regular and abnormal tissue repair. Despite the accumulated knowledge, modulation of wound healing is still a major biomedical challenge, especially in advanced ages. In order to collect and systematically organize what we know about the key players in wound healing, we created the TiRe (Tissue Repair) database, an online collection of genes and proteins that were shown to directly affect skin wound healing. To date, TiRe contains 397 entries for four organisms: Mus musculus, Rattus norvegicus, Sus domesticus, and Homo sapiens. Analysis of the TiRe dataset of skin wound healing-associated genes showed that skin wound healing genes are (i) over-conserved among vertebrates, but are under-conserved in invertebrates; (ii) enriched in extracellular and immuno-inflammatory genes; and display (iii) high interconnectivity and connectivity to other proteins. The latter may provide potential therapeutic targets. In addition, a slower or faster skin wound healing is indicative of an aging or longevity phenotype only when assessed in advanced ages, but not in the young. In the long run, we aim for TiRe to be a one-station resource that provides researchers and clinicians with the essential data needed for a better understanding of the mechanisms of wound healing, designing new experiments, and the development of new therapeutic strategies. TiRe is freely available online at http://www.tiredb.org.

Databases in the Area of Pharmacogenetics

Science.gov (United States)

Sim, Sarah C.; Altman, Russ B.; Ingelman-Sundberg, Magnus

2012-01-01

In the area of pharmacogenetics and personalized health care it is obvious that databases, providing important information of the occurrence and consequences of variant genes encoding drug metabolizing enzymes, drug transporters, drug targets, and other proteins of importance for drug response or toxicity, are of critical value for scientists, physicians, and industry. The primary outcome of the pharmacogenomic field is the identification of biomarkers that can predict drug toxicity and drug response, thereby individualizing and improving drug treatment of patients. The drug in question and the polymorphic gene exerting the impact are the main issues to be searched for in the databases. Here, we review the databases that provide useful information in this respect, of benefit for the development of the pharmacogenomic field. PMID:21309040

GMDD: a database of GMO detection methods.

Science.gov (United States)

Dong, Wei; Yang, Litao; Shen, Kailin; Kim, Banghyun; Kleter, Gijs A; Marvin, Hans J P; Guo, Rong; Liang, Wanqi; Zhang, Dabing

2008-06-04

Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of GMO labelling regulations. Protein and nucleic acid-based detection techniques have been developed and utilized for GMOs identification and quantification. However, the information for harmonization and standardization of GMO analysis methods at global level is needed. GMO Detection method Database (GMDD) has collected almost all the previous developed and reported GMOs detection methods, which have been grouped by different strategies (screen-, gene-, construct-, and event-specific), and also provide a user-friendly search service of the detection methods by GMO event name, exogenous gene, or protein information, etc. In this database, users can obtain the sequences of exogenous integration, which will facilitate PCR primers and probes design. Also the information on endogenous genes, certified reference materials, reference molecules, and the validation status of developed methods is included in this database. Furthermore, registered users can also submit new detection methods and sequences to this database, and the newly submitted information will be released soon after being checked. GMDD contains comprehensive information of GMO detection methods. The database will make the GMOs analysis much easier.

An Open Access Database of Genome-wide Association Results

Directory of Open Access Journals (Sweden)

Johnson Andrew D

2009-01-01

Full Text Available Abstract Background The number of genome-wide association studies (GWAS is growing rapidly leading to the discovery and replication of many new disease loci. Combining results from multiple GWAS datasets may potentially strengthen previous conclusions and suggest new disease loci, pathways or pleiotropic genes. However, no database or centralized resource currently exists that contains anywhere near the full scope of GWAS results. Methods We collected available results from 118 GWAS articles into a database of 56,411 significant SNP-phenotype associations and accompanying information, making this database freely available here. In doing so, we met and describe here a number of challenges to creating an open access database of GWAS results. Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS. Results Using a genomic bin-based density analysis to search for highly associated regions of the genome, positive control loci (e.g., MHC loci were detected with high sensitivity. Likewise, an analysis of highly repeated SNPs across GWAS identified replicated loci (e.g., APOE, LPL. At the same time we identified novel, highly suggestive loci for a variety of traits that did not meet genome-wide significant thresholds in prior analyses, in some cases with strong support from the primary medical genetics literature (SLC16A7, CSMD1, OAS1, suggesting these genes merit further study. Additional adjustment for linkage disequilibrium within most regions with a high density of GWAS associations did not materially alter our findings. Having a centralized database with standardized gene annotation also allowed us to examine the representation of functional gene categories (gene ontologies containing one or more associations among top GWAS results. Genes relating to cell adhesion functions were highly over-represented among significant associations (p -14, a finding

HOLLYWOOD: a comparative relational database of alternative splicing.

Science.gov (United States)

Holste, Dirk; Huo, George; Tung, Vivian; Burge, Christopher B

2006-01-01

RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the Hollywood system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu.

An Integrated Molecular Database on Indian Insects.

Science.gov (United States)

Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

2018-01-01

MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(DJ recombinations

Directory of Open Access Journals (Sweden)

Jouvin-Marche Evelyne

2006-04-01

Full Text Available Abstract Background Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V, diversity (D and joining (J genes in the immunoglobulin (IG loci of B lymphocytes and in the T cell receptor (TR loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS. Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files and are difficult to extract. Description IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the αβ and γδ TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the αβ TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(DJ genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/GeneInfo. Conclusion IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(DJ gene rearrangements and their applications in immune response analysis.

Effect of cinnamon, cardamom, saffron and ginger consumption on blood pressure and a marker of endothelial function in patients with type 2 diabetes mellitus: A randomized controlled clinical trial.

Science.gov (United States)

Azimi, Paria; Ghiasvand, Reza; Feizi, Awat; Hosseinzadeh, Javad; Bahreynian, Maryam; Hariri, Mitra; Khosravi-Boroujeni, Hossein

2016-06-01

Herbal medicines with high amounts of phytochemicals have been shown to have beneficial effects on blood pressure (BP), endothelial function and anthropometric measures. This study aimed to determine the effect of herbal treatment on BP, endothelial function and anthropometric measures in patients with type 2 diabetes mellitus (T2DM). This clinical trial included 204 T2DM patients randomly assigned to four intervention groups receiving 3 g cinnamon, 3 g cardamom, 1 g saffron or 3 g ginger with three glasses of black tea, and one control group consuming only three glasses of tea without any herbals, for 8 weeks. Intercellular adhesion molecule-1 (ICAM-1), systolic and diastolic BP and anthropometric measures were collected at baseline and after 8 weeks. No significant difference was found between various medicinal plants in terms of influencing BP, serum soluble (s)ICAM-1 concentrations and anthropometric measures. However, in within-group comparison saffron and ginger intakes significantly reduced sICAM-1 concentrations (340.9 ± 14.4 vs 339.69 ± 14.4 ng/ml, p = 0.01, and 391.78 ± 16.0 vs 390.97 ± 15.8 ng/ml, p = 0.009, respectively) and ginger intake affected systolic BP (143.06 ± 0.2 vs 142.07 ± 0.2 mmHg, p = 0.02). Although administration of these herbal medicines as supplementary remedies could affect BP and sICAM-1 concentrations, there was no significant difference between the plants in terms of influencing anthropometric measures, BP and endothelial function.

IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations

Science.gov (United States)

Baum, Thierry-Pascal; Hierle, Vivien; Pasqual, Nicolas; Bellahcene, Fatena; Chaume, Denys; Lefranc, Marie-Paule; Jouvin-Marche, Evelyne; Marche, Patrice Noël; Demongeot, Jacques

2006-01-01

Background Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. Description IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the αβ and γδ TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the αβ TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at . Conclusion IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis. PMID:16640788

UniGene Tabulator: a full parser for the UniGene format.

Science.gov (United States)

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Effects of Crocin on The Pituitary-Gonadal Axis and Hypothalamic Kiss-1 Gene Expression in Female Wistar Rats

Directory of Open Access Journals (Sweden)

Dina Zohrabi

2018-01-01

Full Text Available Background Saffron (Crocus sativus L. has been traditionally used as a spice for coloring and flavoring in some countries cuisine. One of the main components of saffron is Crocin. Recent research have shown that crocin has various pharmacological effects. The aim of this study was to assess the effects of crocin on the Pituitary-Gonadal axis and Kiss-1 gene expression in hypothalamus and ovarian tissue organization in female Wistar rats. Materials and Methods In this experimental study, 18 adult female Wistar rats were randomly divided into three groups. Control group received normal saline and experimental groups received two different doses of crocin (100 and 200 mg/kg every two days for 30 days. After the treatment period, blood samples were obtained from the heart and centrifuged. Next, the serum levels of follicle-stimulating hormone (FSH and luteinizing hormone (LH, estrogen and progesterone hormones were measured by ELISA assay. The ovarian tissues were removed and fixed for histological investigation. The hypothalamic Kiss-1 gene expression was measured using real-time polymerase chain reaction (PCR. All data were analyzed using one-way ANOVA. Results A significant reduction (P=0.038 in the number of atretic graafian follicles (0.5 ± 0.31 was observed in rats treated with 200 mg/kg crocin. In addition, estrogen concentration in experimental groups (35.04 ± 0.85 and 36.18 ± 0.69 in crocin 100 and 200 mg/kg groups, respectively compared to control group (38.35 ± 0.64 and progesterone concentration in rats treated with crocin 200 mg/kg (2.06 ± 0.07 compared to control group (2.16 ± 0.04, significantly decreased. Interestingly, relative expressions of Kiss-1 mRNA significantly decreased in experimental groups (0.00053 ± 0.00051 and 0.0011 ± 0.00066 in crocin 100 and 200 mg/kg groups, respectively (P=0.000 compared to control group (1 ± 0. Conclusion Crocin, at hypothalamic level, reduces Kiss-1 gene expression and it can prevent

BioWarehouse: a bioinformatics database warehouse toolkit.

Science.gov (United States)

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

TrSDB: a proteome database of transcription factors

Science.gov (United States)

Hermoso, Antoni; Aguilar, Daniel; Aviles, Francesc X.; Querol, Enrique

2004-01-01

TrSDB—TranScout Database—(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation. Nine eukaryotic proteomes are included in the current version. Extensive and diverse information for each database entry, different analyses considering TranScout classification and similarity relationships are offered for research on transcription factors or gene expression. PMID:14681387

CyanoBase: the cyanobacteria genome database update 2010

OpenAIRE

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2009-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in var...

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

Directory of Open Access Journals (Sweden)

Wincker Patrick

2010-06-01

Full Text Available Abstract Background The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. Results A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center, the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR and to the Gene Ontology (GO protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes.

Science.gov (United States)

Macagno, Eduardo R; Gaasterland, Terry; Edsall, Lee; Bafna, Vineet; Soares, Marcelo B; Scheetz, Todd; Casavant, Thomas; Da Silva, Corinne; Wincker, Patrick; Tasiemski, Aurélie; Salzet, Michel

2010-06-25

The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. A total of approximately 133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences

Follicle Online: an integrated database of follicle assembly, development and ovulation.

Science.gov (United States)

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Cooke, Howard J; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43,000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php © The Author(s) 2015. Published by Oxford University Press.

Potential translational targets revealed by linking mouse grooming behavioral phenotypes to gene expression using public databases.

Science.gov (United States)

Roth, Andrew; Kyzar, Evan J; Cachat, Jonathan; Stewart, Adam Michael; Green, Jeremy; Gaikwad, Siddharth; O'Leary, Timothy P; Tabakoff, Boris; Brown, Richard E; Kalueff, Allan V

2013-01-10

Rodent self-grooming is an important, evolutionarily conserved behavior, highly sensitive to pharmacological and genetic manipulations. Mice with aberrant grooming phenotypes are currently used to model various human disorders. Therefore, it is critical to understand the biology of grooming behavior, and to assess its translational validity to humans. The present in-silico study used publicly available gene expression and behavioral data obtained from several inbred mouse strains in the open-field, light-dark box, elevated plus- and elevated zero-maze tests. As grooming duration differed between strains, our analysis revealed several candidate genes with significant correlations between gene expression in the brain and grooming duration. The Allen Brain Atlas, STRING, GoMiner and Mouse Genome Informatics databases were used to functionally map and analyze these candidate mouse genes against their human orthologs, assessing the strain ranking of their expression and the regional distribution of expression in the mouse brain. This allowed us to identify an interconnected network of candidate genes (which have expression levels that correlate with grooming behavior), display altered patterns of expression in key brain areas related to grooming, and underlie important functions in the brain. Collectively, our results demonstrate the utility of large-scale, high-throughput data-mining and in-silico modeling for linking genomic and behavioral data, as well as their potential to identify novel neural targets for complex neurobehavioral phenotypes, including grooming. Copyright © 2012 Elsevier Inc. All rights reserved.

Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1.

Science.gov (United States)

Park, Jeongbin; Bae, Sangsu

2018-03-15

Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time. Free access at http://www.rgenome.net/cpf1-database/. sangsubae@hanyang.ac.kr.

NABIC marker database: A molecular markers information network of agricultural crops.

Science.gov (United States)

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Benchmarking database performance for genomic data.

Science.gov (United States)

Khushi, Matloob

2015-06-01

Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a novel region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).Inc. © 2015 Wiley Periodicals, Inc.

Effect of Tribulus terrestris, ginger, saffron, and Cinnamomum on menopausal symptoms: a randomised, placebo-controlled clinical trial.

Science.gov (United States)

Taavoni, Simin; Ekbatani, Neda Nazem; Haghani, Hamid

2017-03-01

Menopausal symptoms experienced by women vary widely, and while many women transition through menopause with manageable symptoms, others experience severe symptoms, which may impair their quality of life. The purpose of this study was to determine the effect of Tribulus terrestris , ginger, saffron, and Cinnamomum on menopausal symptoms. A randomised, triple-blind, controlled trial design was used for this study. The participants were 80 postmenopausal women aged 50-60 years. A demographic data form and the Menopause Rating Scale were used to collect data. The women were randomly divided into two groups, each of which received either an Aphrodit capsule or a placebo twice a day for four weeks. The two bottles looked exactly the same, so that the investigator and the participants were not aware of the contents of the bottles. Each Aphrodit capsule contained 40 mg of Tribulus terrestris , 12.27 mg of Zingiber officinale , 3 mg of Crocus sativus extract, and 11 mg of Cinnamomum zeylanicum , while the placebo capsules contained 50 mg of starch. Descriptive and inferential statistics were used to analyse the data. A statistically significant change was reported in the menopausal symptoms of the intervention group compared with the placebo group. The results of the study demonstrate that the Aphrodit capsule was effective in reducing menopausal symptoms.

VariVis: a visualisation toolkit for variation databases

Directory of Open Access Journals (Sweden)

Smith Timothy D

2008-04-01

Full Text Available Abstract Background With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in online variation databases and provide important clues to the cause of diseases and potential side effects or resistance to drugs. However, the data presentation techniques employed by most of these databases make them difficult to use and understand. Results Here we present a visualisation toolkit that can be employed by online variation databases to generate graphical models of gene sequence with corresponding variations and their consequences. The VariVis software package can run on any web server capable of executing Perl CGI scripts and can interface with numerous Database Management Systems and "flat-file" data files. VariVis produces two easily understandable graphical depictions of any gene sequence and matches these with variant data. While developed with the goal of improving the utility of human variation databases, the VariVis package can be used in any variation database to enhance utilisation of, and access to, critical information.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

Science.gov (United States)

Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

2017-08-10

Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or

CyanoBase: the cyanobacteria genome database update 2010.

Science.gov (United States)

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2010-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

BGD: a database of bat genomes.

Science.gov (United States)

Fang, Jianfei; Wang, Xuan; Mu, Shuo; Zhang, Shuyi; Dong, Dong

2015-01-01

Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

BGD: a database of bat genomes.

Directory of Open Access Journals (Sweden)

Jianfei Fang

Full Text Available Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD. BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

The UCSC Genome Browser Database: update 2006

DEFF Research Database (Denmark)

Hinrichs, A S; Karolchik, D; Baertsch, R

2006-01-01

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

HCVpro: Hepatitis C virus protein interaction database

KAUST Repository

Kwofie, Samuel K.

2011-12-01

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

BioWarehouse: a bioinformatics database warehouse toolkit

Directory of Open Access Journals (Sweden)

Stringer-Calvert David WJ

2006-03-01

Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database.

Directory of Open Access Journals (Sweden)

Allan Peter Davis

Full Text Available Strategies for discovering common molecular events among disparate diseases hold promise for improving understanding of disease etiology and expanding treatment options. One technique is to leverage curated datasets found in the public domain. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/ manually curates chemical-gene, chemical-disease, and gene-disease interactions from the scientific literature. The use of official gene symbols in CTD interactions enables this information to be combined with the Gene Ontology (GO file from NCBI Gene. By integrating these GO-gene annotations with CTD's gene-disease dataset, we produce 753,000 inferences between 15,700 GO terms and 4,200 diseases, providing opportunities to explore presumptive molecular underpinnings of diseases and identify biological similarities. Through a variety of applications, we demonstrate the utility of this novel resource. As a proof-of-concept, we first analyze known repositioned drugs (e.g., raloxifene and sildenafil and see that their target diseases have a greater degree of similarity when comparing GO terms vs. genes. Next, a computational analysis predicts seemingly non-intuitive diseases (e.g., stomach ulcers and atherosclerosis as being similar to bipolar disorder, and these are validated in the literature as reported co-diseases. Additionally, we leverage other CTD content to develop testable hypotheses about thalidomide-gene networks to treat seemingly disparate diseases. Finally, we illustrate how CTD tools can rank a series of drugs as potential candidates for repositioning against B-cell chronic lymphocytic leukemia and predict cisplatin and the small molecule inhibitor JQ1 as lead compounds. The CTD dataset is freely available for users to navigate pathologies within the context of extensive biological processes, molecular functions, and cellular components conferred by GO. This inference set should aid researchers, bioinformaticists, and

Lung cancer gene expression database analysis incorporating prior knowledge with support vector machine-based classification method

Directory of Open Access Journals (Sweden)

Huang Desheng

2009-07-01

Full Text Available Abstract Background A reliable and precise classification is essential for successful diagnosis and treatment of cancer. Gene expression microarrays have provided the high-throughput platform to discover genomic biomarkers for cancer diagnosis and prognosis. Rational use of the available bioinformation can not only effectively remove or suppress noise in gene chips, but also avoid one-sided results of separate experiment. However, only some studies have been aware of the importance of prior information in cancer classification. Methods Together with the application of support vector machine as the discriminant approach, we proposed one modified method that incorporated prior knowledge into cancer classification based on gene expression data to improve accuracy. A public well-known dataset, Malignant pleural mesothelioma and lung adenocarcinoma gene expression database, was used in this study. Prior knowledge is viewed here as a means of directing the classifier using known lung adenocarcinoma related genes. The procedures were performed by software R 2.80. Results The modified method performed better after incorporating prior knowledge. Accuracy of the modified method improved from 98.86% to 100% in training set and from 98.51% to 99.06% in test set. The standard deviations of the modified method decreased from 0.26% to 0 in training set and from 3.04% to 2.10% in test set. Conclusion The method that incorporates prior knowledge into discriminant analysis could effectively improve the capacity and reduce the impact of noise. This idea may have good future not only in practice but also in methodology.

Molecular signatures database (MSigDB) 3.0.

Science.gov (United States)

Liberzon, Arthur; Subramanian, Aravind; Pinchback, Reid; Thorvaldsdóttir, Helga; Tamayo, Pablo; Mesirov, Jill P

2011-06-15

Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.

CardioTF, a database of deconstructing transcriptional circuits in the heart system.

Science.gov (United States)

Zhen, Yisong

2016-01-01

Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Database URL: http://www.cardiosignal.org/database/cardiotf.html.

FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events.

Science.gov (United States)

Korla, Praveen Kumar; Cheng, Jack; Huang, Chien-Hung; Tsai, Jeffrey J P; Liu, Yu-Hsuan; Kurubanjerdjit, Nilubon; Hsieh, Wen-Tsong; Chen, Huey-Yi; Ng, Ka-Lok

2015-01-01

Chromosomal translocation (CT) is of enormous clinical interest because this disorder is associated with various major solid tumors and leukemia. A tumor-specific fusion gene event may occur when a translocation joins two separate genes. Currently, various CT databases provide information about fusion genes and their genomic elements. However, no database of the roles of fusion genes, in terms of essential functional and regulatory elements in oncogenesis, is available. FARE-CAFE is a unique combination of CTs, fusion proteins, protein domains, domain-domain interactions, protein-protein interactions, transcription factors and microRNAs, with subsequent experimental information, which cannot be found in any other CT database. Genomic DNA information including, for example, manually collected exact locations of the first and second break points, sequences and karyotypes of fusion genes are included. FARE-CAFE will substantially facilitate the cancer biologist's mission of elucidating the pathogenesis of various types of cancer. This database will ultimately help to develop 'novel' therapeutic approaches. Database URL: http://ppi.bioinfo.asia.edu.tw/FARE-CAFE. © The Author(s) 2015. Published by Oxford University Press.

HIVsirDB: a database of HIV inhibiting siRNAs.

Directory of Open Access Journals (Sweden)

Atul Tyagi

Full Text Available Human immunodeficiency virus (HIV is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes.HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i siRNAmap for mapping siRNAs on target sequence, ii HIVsirblast for BLAST search against database, iii siRNAalign for aligning siRNAs.HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire.

Science.gov (United States)

Park, Hae-Min; Park, Ju-Hyeong; Kim, Yoon-Woo; Kim, Kyoung-Jin; Jeong, Hee-Jin; Jang, Kyoung-Soon; Kim, Byung-Gee; Kim, Yun-Gon

2013-11-15

In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells/organs in xenotransplantation and might eventually provide new targets in the α1,3-galactosyltransferase gene-knock out pigs era. The database can be accessed on the web at http://bioinformatics.snu.ac.kr/xdb.

Databases for rRNA gene profiling of microbial communities

Energy Technology Data Exchange (ETDEWEB)

Ashby, Matthew

2013-07-02

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

DBGC: A Database of Human Gastric Cancer

Science.gov (United States)

Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

2015-01-01

The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

Effect of Tribulus terrestris, ginger, saffron, and Cinnamomum on menopausal symptoms: a randomised, placebo-controlled clinical trial

Science.gov (United States)

Taavoni, Simin; Haghani, Hamid

2017-01-01

Menopausal symptoms experienced by women vary widely, and while many women transition through menopause with manageable symptoms, others experience severe symptoms, which may impair their quality of life. The purpose of this study was to determine the effect of Tribulus terrestris, ginger, saffron, and Cinnamomum on menopausal symptoms. A randomised, triple-blind, controlled trial design was used for this study. The participants were 80 postmenopausal women aged 50–60 years. A demographic data form and the Menopause Rating Scale were used to collect data. The women were randomly divided into two groups, each of which received either an Aphrodit capsule or a placebo twice a day for four weeks. The two bottles looked exactly the same, so that the investigator and the participants were not aware of the contents of the bottles. Each Aphrodit capsule contained 40 mg of Tribulus terrestris, 12.27 mg of Zingiber officinale, 3 mg of Crocus sativus extract, and 11 mg of Cinnamomum zeylanicum, while the placebo capsules contained 50 mg of starch. Descriptive and inferential statistics were used to analyse the data. A statistically significant change was reported in the menopausal symptoms of the intervention group compared with the placebo group. The results of the study demonstrate that the Aphrodit capsule was effective in reducing menopausal symptoms. PMID:28546803

Effect of Tribulus terrestris , ginger, saffron, and Cinnamomum on menopausal symptoms: a randomised, placebo-controlled clinical trial

Directory of Open Access Journals (Sweden)

Simin Taavoni

2017-04-01

Full Text Available Menopausal symptoms experienced by women vary widely, and while many women transition through menopause with manageable symptoms, others experience severe symptoms, which may impair their quality of life. The purpose of this study was to determine the effect of Tribulus terrestris , ginger, saffron, and Cinnamomum on menopausal symptoms. A randomised, triple-blind, controlled trial design was used for this study. The participants were 80 postmenopausal women aged 50–60 years. A demographic data form and the Menopause Rating Scale were used to collect data. The women were randomly divided into two groups, each of which received either an Aphrodit capsule or a placebo twice a day for four weeks. The two bottles looked exactly the same, so that the investigator and the participants were not aware of the contents of the bottles. Each Aphrodit capsule contained 40 mg of Tribulus terrestris , 12.27 mg of Zingiber officinale, 3 mg of Crocus sativus extract, and 11 mg of Cinnamomum zeylanicum, while the placebo capsules contained 50 mg of starch. Descriptive and inferential statistics were used to analyse the data. A statistically significant change was reported in the menopausal symptoms of the intervention group compared with the placebo group. The results of the study demonstrate that the Aphrodit capsule was effective in reducing menopausal symptoms.

CGPD: Cancer Genetics and Proteomics Database - A Dataset for Computational Analysis and Online Cancer Diagnostic Centre

Directory of Open Access Journals (Sweden)

Muhammad Rizwan Riaz

2014-06-01

Full Text Available Cancer Genetics and Proteomics Database (CGPD is a repository for genetics and proteomics data of those Homo sapiens genes which are involved in Cancer. These genes are categorized in the database on the basis of cancer type. 72 genes of 13 types of cancers are considered in this database yet. Primers, promoters and peptides of these genes are also made available. Primers provided for each gene, with their features and conditions given to facilitate the researchers, are useful in PCR amplification, especially in cloning experiments. CGPD also contains Online Cancer Diagnostic Center (OCDC. It also contains transcription and translation tools to assist research work in progressive manner. The database is publicly available at http://www.cgpd.comyr.com.

Saffron Aqueous Extract Inhibits the Chemically-induced Gastric Cancer Progression in the Wistar Albino Rat

Directory of Open Access Journals (Sweden)

S. Zahra Bathaie

2013-01-01

Full Text Available Objective(s: Gastric cancer is the first and second leading cause of cancer related death in Iranian men and women, respectively. Gastric cancer management is based on the surgery, radiotherapy and chemotherapy. In the present study, for the first time, the beneficial effect of saffron (Crocus sativus L. aqueous extract (SAE on the 1-Methyl-3-nitro-1-nitrosoguanidine (MNNG-induced gastric cancer in rat was investigated. Materials and Methods: MNNG was used to induce gastric cancer and then, different concentrations of SAE were administered to rats. After sacrificing, the stomach tissue was investigated by both pathologist and flow cytometry, and several biochemical parameters was determined in the plasma (or serum and stomach of rats. Results: Pathologic data indicated the induction of cancer at different stages from hyperplasia to adenoma in rats; and the inhibition of cancer progression in the gastric tissue by SAE administration; so that, 20% of cancerous rats treated with higher doses of SAE was completely normal at the end of experiment and there was no rat with adenoma in the SAE treated groups. In addition, the results of the flow cytometry/ propidium iodide staining showed that the apoptosis/proliferation ratio was increased due to the SAE treatment of cancerous rats. Moreover, the significantly increased serum LDH and decreased plasma antioxidant activity due to cancer induction fell backwards after treatment of rats with SAE. But changes in the other parameters (Ca2+, tyrosine kinase activity and carcino-embryonic antigen were not significant. Conclusion: SAE inhibits the progression of gastric cancer in rats, in a dose dependent manner.

PlantCARE, a plant cis-acting regulatory element database

OpenAIRE

Rombauts, Stephane; Déhais, Patrice; Van Montagu, Marc; Rouzé, Pierre

1999-01-01

PlantCARE is a database of plant cis- acting regulatory elements, enhancers and repressors. Besides the transcription motifs found on a sequence, it also offers a link to the EMBL entry that contains the full gene sequence as well as a description of the conditions in which a motif becomes functional. The information on these sites is given by matrices, consensus and individual site sequences on particular genes, depending on the available information. PlantCARE is a relational database avail...

SinEx DB: a database for single exon coding sequences in mammalian genomes.

Science.gov (United States)

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

Bioinformatics Database Tools in Analysis of Genetics of Neurodevelopmental Disorders

Directory of Open Access Journals (Sweden)

Dibyashree Mallik

2017-10-01

Full Text Available Bioinformatics tools are recently used in various sectors of biology. Many questions regarding Neurodevelopmental disorder which arises as a major health issue recently can be solved by using various bioinformatics databases. Schizophrenia is such a mental disorder which is now arises as a major threat in young age people because it is mostly seen in case of people during their late adolescence or early adulthood period. Databases like DISGENET, GWAS, PHARMGKB, and DRUGBANK have huge repository of genes associated with schizophrenia. We found a lot of genes are being associated with schizophrenia, but approximately 200 genes are found to be present in any of these databases. After further screening out process 20 genes are found to be highly associated with each other and are also a common genes in many other diseases also. It is also found that they all are serves as a common targeting gene in many antipsychotic drugs. After analysis of various biological properties, molecular function it is found that these 20 genes are mostly involved in biological regulation process and are having receptor activity. They are belonging mainly to receptor protein class. Among these 20 genes CYP2C9, CYP3A4, DRD2, HTR1A, HTR2A are shown to be a main targeting genes of most of the antipsychotic drugs and are associated with  more than 40% diseases. The basic findings of the present study enumerated that a suitable combined drug can be design by targeting these genes which can be used for the better treatment of schizophrenia.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

Science.gov (United States)

Decelle, Johan; Romac, Sarah; Stern, Rowena F; Bendif, El Mahdi; Zingone, Adriana; Audic, Stéphane; Guiry, Michael D; Guillou, Laure; Tessier, Désiré; Le Gall, Florence; Gourvil, Priscillia; Dos Santos, Adriana L; Probert, Ian; Vaulot, Daniel; de Vargas, Colomban; Christen, Richard

2015-11-01

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing. © 2015 John Wiley & Sons Ltd.

A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining

Directory of Open Access Journals (Sweden)

Lan Chung-Yu

2008-09-01

Full Text Available Abstract Background Inflammation is a hallmark of many human diseases. Elucidating the mechanisms underlying systemic inflammation has long been an important topic in basic and clinical research. When primary pathogenetic events remains unclear due to its immense complexity, construction and analysis of the gene regulatory network of inflammation at times becomes the best way to understand the detrimental effects of disease. However, it is difficult to recognize and evaluate relevant biological processes from the huge quantities of experimental data. It is hence appealing to find an algorithm which can generate a gene regulatory network of systemic inflammation from high-throughput genomic studies of human diseases. Such network will be essential for us to extract valuable information from the complex and chaotic network under diseased conditions. Results In this study, we construct a gene regulatory network of inflammation using data extracted from the Ensembl and JASPAR databases. We also integrate and apply a number of systematic algorithms like cross correlation threshold, maximum likelihood estimation method and Akaike Information Criterion (AIC on time-lapsed microarray data to refine the genome-wide transcriptional regulatory network in response to bacterial endotoxins in the context of dynamic activated genes, which are regulated by transcription factors (TFs such as NF-κB. This systematic approach is used to investigate the stochastic interaction represented by the dynamic leukocyte gene expression profiles of human subject exposed to an inflammatory stimulus (bacterial endotoxin. Based on the kinetic parameters of the dynamic gene regulatory network, we identify important properties (such as susceptibility to infection of the immune system, which may be useful for translational research. Finally, robustness of the inflammatory gene network is also inferred by analyzing the hubs and "weak ties" structures of the gene network

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function.

Science.gov (United States)

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-02-01

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named 'RiceFOX'. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/.

PlantTribes: a gene and gene family resource for comparative genomics in plants

OpenAIRE

Wall, P. Kerr; Leebens-Mack, Jim; Müller, Kai F.; Field, Dawn; Altman, Naomi S.; dePamphilis, Claude W.

2007-01-01

The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575–1584)] to classify all of these species’ protein-coding genes into putative gene families, ca...

Genetic and bibliographic information - GenLibi | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available n Data acquisition method Articles related to genes were obtained from the bibliography database (JDream II)...provided from the JST bibliographic information system (JDream II) About This Database Database Description

Elucidation and functional characterization of CsPSY and CsUGT promoters in Crocus sativus L.

Science.gov (United States)

Bhat, Archana; Mishra, Sonal; Kaul, Sanjana; Dhar, Manoj K

2018-01-01

The dried stigmas of Crocus sativus constitute the saffron, which is considered to be the costliest spice of the world. Saffron is valuable for its constituents, which are mainly apocarotenoids. In order to enhance the production of apocarotenoids, it is imperative to understand the regulation of apocarotenoid biosynthetic pathway. In C. sativus, although the pathway has been elucidated, the information regarding the regulation of the pathwaygenes is scanty. During the present investigation, the characterization of promoters regulating the expression of two important genes i.e. CsPSY and CsUGT was performed. We successfully cloned the promoters of both the genes, which were functionally characterized in Crocus sativus and Nicotiana tabaccum. In silico analysis of the promoters demonstrated the presence of several important cis regulatory elements responding tolight, hormonesand interaction with transcription factors (TFs). Further analysis suggested the regulation of CsPSY promoter by Abscisic acid (ABA) and that of CsUGT by Gibberellic acid (GA). In addition, we also observed ABA and GA mediated modulation in the expression of significant TFs and CsPSY and CsUGT transcripts. Overall, the study addresses issues related to regulation of key genes of apocarotenoid pathway in C.sativus.

pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

Science.gov (United States)

Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.

2015-01-01

Background Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. Methods In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. Results We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/). PMID:26258475

AgdbNet – antigen sequence database software for bacterial typing

Directory of Open Access Journals (Sweden)

Maiden Martin CJ

2006-06-01

Full Text Available Abstract Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated.

PairWise Neighbours database: overlaps and spacers among prokaryote genomes

Directory of Open Access Journals (Sweden)

Garcia-Vallvé Santiago

2009-06-01

Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

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

Directory of Open Access Journals (Sweden)

Mohit Verma

Full Text Available Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB, which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database features many tools for similarity search, functional annotation (putative function, PFAM domain and gene ontology search and comparative gene expression analysis. The current release of CTDB (v2.0 hosts transcriptome datasets with high quality functional annotation from cultivated (desi and kabuli types and wild chickpea. A catalog of transcription factor families and their expression profiles in chickpea are available in the database. The gene expression data have been integrated to study the expression profiles of chickpea transcripts in major tissues/organs and various stages of flower development. The utilities, such as similarity search, ortholog identification and comparative gene expression have also been implemented in the database to facilitate comparative genomic studies among different legumes and Arabidopsis. Furthermore, the CTDB represents a resource for the discovery of functional molecular markers (microsatellites and single nucleotide polymorphisms between different chickpea types. We anticipate that integrated information content of this database will accelerate the functional and applied genomic research for improvement of chickpea. The CTDB web service is freely available at http://nipgr.res.in/ctdb.html.

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

NARCIS (Netherlands)

Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D'Elia, D.; Montalvo, A.; Pinto, B.; de Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H.; Sloof, P.; Saccone, C.

2000-01-01

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces

Effects of crocin and safranal, saffron constituents, on the formalin-induced orofacial pain in rats

Directory of Open Access Journals (Sweden)

Amir Erfanparast

2015-08-01

Full Text Available Objective: Crocin and safranal are the main components of saffron, and have many biological functions such as anti-inflammatory and antioxidant activities. In the present study, we investigated the effects of crocin, safranal, morphine, diclofenac and naloxone in combined and separately on formalin-induced orofacial pain in rats. Materials and Methods: Subcutaneous injection of a diluted formalin solution (50 µl, 1.5% into the upper lip region produced a biphasic pattern of pain response (a neurogenic phase: 0-3 min and an inflammatory phase: 15-33 min. The time each animal spent face rubbing with ipsilateral forepaw was recorded and considered as an index of nociception Results: Intraperitoneal injections of crocin (12.5 and 25 mg/kg, safranal (0.25 and 0.5 mg/kg, diclofenac (5 and 10 mg/kg and morphine (1 and 2 mg/kg suppressed the second phase of pain. The second phase of pain was also reduced when low (ineffective doses of crocin (6.25 mg/kg and safranal (0.125 mg/kg were co-administered with low doses of diclofenac (2.5 mg/kg and morphine (0.5 mg/kg. The more antinociceptive effects were observed when the medium doses of the above-mentioned chemicals used together. Naloxone prevented morphine-induced antinociception, but did not inhibit the suppressive effects of crocin and safranal. Safranal at a high dose (0.5 mg/kg suppressed locomotor activity. Conclusion: The present results showed antinociceptive effects for crocin and safranal in inflammatory pain. Opioid receptors may not be involved in the antinociceptive effect of crocin and safranal. Crocin and safranal increased diclofenac-induced antinociception.

FINDbase: A worldwide database for genetic variation allele frequencies updated

NARCIS (Netherlands)

M. Georgitsi (Marianthi); E. Viennas (Emmanouil); D.I. Antoniou (Dimitris I.); V. Gkantouna (Vassiliki); S. van Baal (Sjozef); E.F. Petricoin (Emanuel F.); K. Poulas (Konstantinos); G. Tzimas (Giannis); G.P. Patrinos (George)

2011-01-01

textabstractFrequency of INherited Disorders database (FIND base; http://www.findbase. org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to

Comparative study of the sol-gel based solid phase microextraction fibers in extraction of naphthalene, fluorene, anthracene and phenanthrene from saffron samples extractants

International Nuclear Information System (INIS)

Sarafraz-Yazdi, A.; Ghaemi, F.; Amiri, A.

2012-01-01

We are introducing a method for the determination of some polycyclic aromatic hydrocarbons in aqueous saffron sample by direct immersion solid phase microextraction (SPME) and gas chromatography. A sol-gel technique is used for the preparation of the SPME fibers. Three kinds of sol-gel coatings on the fibers were tested and compared. They are composed of poly(dimethyl siloxane) (PDMS), poly(ethylene glycol) (PEG), and a poly(ethylene glycol) modified with multi-walled carbon nanotubes (PEG/CNTs). The effects of fiber coating, desorption time, desorption temperature, extraction time, stirring speed and salting effect were optimized. Under the optimal conditions, the detection limits (at S/N = 3) are 7-50, 5-50, and 1-10 pg mL -1 , respectively, for SPME fibers made from PDMS, PEG and PEG/CNTs. The relative standard deviations for one type of fiber are from 2.1% to 9.6% for all fibers (at n = 5), and in the range from 1.9% to 9.8% from batch to batch (for n = 3). (author)

Gene annotation from scientific literature using mappings between keyword systems.

Science.gov (United States)

Pérez, Antonio J; Perez-Iratxeta, Carolina; Bork, Peer; Thode, Guillermo; Andrade, Miguel A

2004-09-01

The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene. To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%). The algorithm can be publicly accessed and used for the annotation of sequences through a web server at http://www.bork.embl.de/kat

GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.

Science.gov (United States)

Ben-Ari Fuchs, Shani; Lieder, Iris; Stelzer, Gil; Mazor, Yaron; Buzhor, Ella; Kaplan, Sergey; Bogoch, Yoel; Plaschkes, Inbar; Shitrit, Alina; Rappaport, Noa; Kohn, Asher; Edgar, Ron; Shenhav, Liraz; Safran, Marilyn; Lancet, Doron; Guan-Golan, Yaron; Warshawsky, David; Shtrichman, Ronit

2016-03-01

Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from "data-to-knowledge-to-innovation," a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ ( geneanalytics.genecards.org ), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®--the human gene database; the MalaCards-the human diseases database; and the PathCards--the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®--the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene-tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell "cards" in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

Science.gov (United States)

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma.

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

Science.gov (United States)

Portales-Casamar, Elodie; Arenillas, David; Lim, Jonathan; Swanson, Magdalena I.; Jiang, Steven; McCallum, Anthony; Kirov, Stefan; Wasserman, Wyeth W.

2009-01-01

The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk. PMID:18971253

The breeding biology, nest success, habitat and behavior of the endangered Saffron-cowled Blackbird, Xanthopsar flavus (Aves: Icteridae, at an Important Bird Area (IBA in Rio Grande do Sul, Brazil

Directory of Open Access Journals (Sweden)

Luciane R. da Silva Mohr

2017-10-01

Full Text Available ABSTRACT The Saffron-cowled Blackbird, Xanthopsar flavus (Gmelin, 1788, is a globally vulnerable icterid endemic to grasslands and open areas, and a priority species for research and conservation programs. This contribution provides information on the population size, habitat, behavior, breeding biology and nest success of X. flavus in two conservation units (CUs in Viamão, state of Rio Grande do Sul, Brazil: the Environmental Protection Area Banhado Grande, and the Wildlife Refuge Banhado dos Pachecos, classified as an “Important Bird Area”. Searches for X. flavus were carried out mainly in open areas, the type of habitat favored by the species. Outside the breeding season individual behavior was recorded by the ad libitum method; during the breeding season, selected X. flavus pairs were observed following the sequence sampling method. The research areas were visited once a month, totaling approximately 530 hours of observations (September 2014 to June 2016 over 84 days, which included two breeding seasons. The species was observed across all months (not necessarily within the same year and several X. flavus flocks were encountered, some with more than one hundred individuals (range = 2-137. Additionally, the behavior and feeding aspects, habitat use and breeding information on X. flavus were recorded. Two breeding colonies were found, and eleven nests were monitored. The estimated nesting success was 10% in Colony 1, but zero in Colony 2, where all eggs and nestlings were predated. Saffron-cowled Blackbirds were recorded in mixed flocks, mostly with Pseudoleistes guirahuro (Vieillot, 1819, P. virescens (Vieillot, 1819 and Xolmis dominicanus (Vieillot, 1823, the last also a globally endangered species. The collected information highlights the importance of CUs for the maintenance of X. flavus populations in the region. Maintenance of proper areas for feeding and breeding is necessary and urgent. Information from current research is being

Biomine: predicting links between biological entities using network models of heterogeneous databases

Directory of Open Access Journals (Sweden)

Eronen Lauri

2012-06-01

Full Text Available Abstract Background Biological databases contain large amounts of data concerning the functions and associations of genes and proteins. Integration of data from several such databases into a single repository can aid the discovery of previously unknown connections spanning multiple types of relationships and databases. Results Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. We present Biomine and evaluate its performance in link prediction, where the goal is to predict pairs of nodes that will be connected in the future, based on current data. In particular, we formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. We consider and experiment with several such measures, and perform a parameter optimization procedure where different edge types are weighted to optimize link prediction accuracy. We also propose a novel method for disease-gene prioritization, defined as finding a subset of candidate genes that cluster together in the graph. We experimentally evaluate Biomine by predicting future annotations in the source databases and prioritizing lists of putative disease genes. Conclusions The experimental results show that Biomine has strong potential for predicting links when a set of selected candidate links is available. The predictions obtained using the entire Biomine dataset are shown to clearly outperform ones obtained using any single source of data alone, when different types of links are suitably weighted. In the gene prioritization task, an established reference set of disease-associated genes is useful, but the results show that under favorable

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

A literature search tool for intelligent extraction of disease-associated genes.

Science.gov (United States)

Jung, Jae-Yoon; DeLuca, Todd F; Nelson, Tristan H; Wall, Dennis P

2014-01-01

To extract disorder-associated genes from the scientific literature in PubMed with greater sensitivity for literature-based support than existing methods. We developed a PubMed query to retrieve disorder-related, original research articles. Then we applied a rule-based text-mining algorithm with keyword matching to extract target disorders, genes with significant results, and the type of study described by the article. We compared our resulting candidate disorder genes and supporting references with existing databases. We demonstrated that our candidate gene set covers nearly all genes in manually curated databases, and that the references supporting the disorder-gene link are more extensive and accurate than other general purpose gene-to-disorder association databases. We implemented a novel publication search tool to find target articles, specifically focused on links between disorders and genotypes. Through comparison against gold-standard manually updated gene-disorder databases and comparison with automated databases of similar functionality we show that our tool can search through the entirety of PubMed to extract the main gene findings for human diseases rapidly and accurately.

The FH mutation database: an online database of fumarate hydratase mutations involved in the MCUL (HLRCC tumor syndrome and congenital fumarase deficiency

Directory of Open Access Journals (Sweden)

Tomlinson Ian PM

2008-03-01

Full Text Available Abstract Background Fumarate hydratase (HGNC approved gene symbol – FH, also known as fumarase, is an enzyme of the tricarboxylic acid (TCA cycle, involved in fundamental cellular energy production. First described by Zinn et al in 1986, deficiency of FH results in early onset, severe encephalopathy. In 2002, the Multiple Leiomyoma Consortium identified heterozygous germline mutations of FH in patients with multiple cutaneous and uterine leiomyomas, (MCUL: OMIM 150800. In some families renal cell cancer also forms a component of the complex and as such has been described as hereditary leiomyomatosis and renal cell cancer (HLRCC: OMIM 605839. The identification of FH as a tumor suppressor was an unexpected finding and following the identification of subunits of succinate dehydrogenase in 2000 and 2001, was only the second description of the involvement of an enzyme of intermediary metabolism in tumorigenesis. Description The FH mutation database is a part of the TCA cycle gene mutation database (formerly the succinate dehydrogenase gene mutation database and is based on the Leiden Open (source Variation Database (LOVD system. The variants included in the database were derived from the published literature and annotated to conform to current mutation nomenclature. The FH database applies HGVS nomenclature guidelines, and will assist researchers in applying these guidelines when directly submitting new sequence variants online. Since the first molecular characterization of an FH mutation by Bourgeron et al in 1994, a series of reports of both FH deficiency patients and patients with MCUL/HLRRC have described 107 variants, of which 93 are thought to be pathogenic. The most common type of mutation is missense (57%, followed by frameshifts & nonsense (27%, and diverse deletions, insertions and duplications. Here we introduce an online database detailing all reported FH sequence variants. Conclusion The FH mutation database strives to systematically

IMGT/GeneInfo: enhancing V(D)J recombination database accessibility

Science.gov (United States)

Baum, Thierry-Pascal; Pasqual, Nicolas; Thuderoz, Florence; Hierle, Vivien; Chaume, Denys; Lefranc, Marie-Paule; Jouvin-Marche, Evelyne; Marche, Patrice-Noël; Demongeot, Jacques

2004-01-01

IMGT/GeneInfo is a user-friendly online information system that provides information on data resulting from the complex mechanisms of immunoglobulin (IG) and T cell receptor (TR) V(D)J recombinations. For the first time, it is possible to visualize all the rearrangement parameters on a single page. IMGT/GeneInfo is part of the international ImMunoGeneTics information system® (IMGT), a high-quality integrated knowledge resource specializing in IG, TR, major histocompatibility complex (MHC), and related proteins of the immune system of human and other vertebrate species. The IMGT/GeneInfo system was developed by the TIMC and ICH laboratories (with the collaboration of LIGM), and is the first example of an external system being incorporated into IMGT. In this paper, we report the first part of this work. IMGT/GeneInfo_TR deals with the human and mouse TRA/TRD and TRB loci of the TR. Data handling and visualization are complementary to the current data and tools in IMGT, and will subsequently allow the modelling of V(D)J gene use, and thus, to predict non-standard recombination profiles which may eventually be found in conditions such as leukaemias or lymphomas. Access to IMGT/GeneInfo is free and can be found at http://imgt.cines.fr/GeneInfo. PMID:14681357

TabSQL: a MySQL tool to facilitate mapping user data to public databases.

Science.gov (United States)

Xia, Xiao-Qin; McClelland, Michael; Wang, Yipeng

2010-06-23

With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.

HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

DEFF Research Database (Denmark)

Bagger, Frederik Otzen; Rapin, Nicolas; Theilgaard-Mönch, Kim

2013-01-01

lead to full integrity of the data in the database. The HemaExplorer has comprehensive visualization interface that can make it useful as a daily tool for biologists and cancer researchers to assess the expression patterns of genes encountered in research or literature. HemaExplorer is relevant for all......The HemaExplorer (http://servers.binf.ku.dk/hemaexplorer) is a curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells. HemaExplorer contains GEPs derived from mouse/human haematopoietic stem and progenitor cells...... as well as from more differentiated cell types. Moreover, data from distinct subtypes of human acute myeloid leukemia is included in the database allowing researchers to directly compare gene expression of leukemic cells with those of their closest normal counterpart. Normalization and batch correction...

CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks

DEFF Research Database (Denmark)

Abreu, Vinicius A C; Almeida, Sintia; Tiwari, Sandeep

2015-01-01

gene regulatory network can lead to various practical applications, creating a greater understanding of how organisms control their cellular behavior. DESCRIPTION: In this work, we present a new database, CMRegNet for the gene regulatory networks of Corynebacterium glutamicum ATCC 13032......Net to date the most comprehensive database of regulatory interactions of CMNR bacteria. The content of CMRegNet is publicly available online via a web interface found at http://lgcm.icb.ufmg.br/cmregnet ....

ProCarDB: a database of bacterial carotenoids.

Science.gov (United States)

Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

2016-05-26

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

Specialized microbial databases for inductive exploration of microbial genome sequences

Directory of Open Access Journals (Sweden)

Cabau Cédric

2005-02-01

Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

The Importance of Biological Databases in Biological Discovery.

Science.gov (United States)

Baxevanis, Andreas D; Bateman, Alex

2015-06-19

Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. Copyright © 2015 John Wiley & Sons, Inc.

Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

Science.gov (United States)

Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

2015-03-01

The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (≈ 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database.

Analysis of gene and protein name synonyms in Entrez Gene and UniProtKB resources

KAUST Repository

Arkasosy, Basil

2013-05-11

Ambiguity in texts is a well-known problem: words can carry several meanings, and hence, can be read and interpreted differently. This is also true in the biological literature; names of biological concepts, such as genes and proteins, might be ambiguous, referring in some cases to more than one gene or one protein, or in others, to both genes and proteins at the same time. Public biological databases give a very useful insight about genes and proteins information, including their names. In this study, we made a thorough analysis of the nomenclatures of genes and proteins in two data sources and for six different species. We developed an automated process that parses, extracts, processes and stores information available in two major biological databases: Entrez Gene and UniProtKB. We analysed gene and protein synonyms, their types, frequencies, and the ambiguities within a species, in between data sources and cross-species. We found that at least 40% of the cross-species ambiguities are caused by names that are already ambiguous within the species. Our study shows that from the six species we analysed (Homo Sapiens, Mus Musculus, Arabidopsis Thaliana, Oryza Sativa, Bacillus Subtilis and Pseudomonas Fluorescens), rice (Oriza Sativa) has the best naming model in Entrez Gene database, with low ambiguities between data sources and cross-species.

Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database

Directory of Open Access Journals (Sweden)

Nicolas Aurélie

2012-07-01

Full Text Available Abstract Background Dystrophin is a large essential protein of skeletal and heart muscle. It is a filamentous scaffolding protein with numerous binding domains. Mutations in the DMD gene, which encodes dystrophin, mostly result in the deletion of one or several exons and cause Duchenne (DMD and Becker (BMD muscular dystrophies. The most common DMD mutations are frameshift mutations resulting in an absence of dystrophin from tissues. In-frame DMD mutations are less frequent and result in a protein with partial wild-type dystrophin function. The aim of this study was to highlight structural and functional modifications of dystrophin caused by in-frame mutations. Methods and results We developed a dedicated database for dystrophin, the eDystrophin database. It contains 209 different non frame-shifting mutations found in 945 patients from a French cohort and previous studies. Bioinformatics tools provide models of the three-dimensional structure of the protein at deletion sites, making it possible to determine whether the mutated protein retains the typical filamentous structure of dystrophin. An analysis of the structure of mutated dystrophin molecules showed that hybrid repeats were reconstituted at the deletion site in some cases. These hybrid repeats harbored the typical triple coiled-coil structure of native repeats, which may be correlated with better function in muscle cells. Conclusion This new database focuses on the dystrophin protein and its modification due to in-frame deletions in BMD patients. The observation of hybrid repeat reconstitution in some cases provides insight into phenotype-genotype correlations in dystrophin diseases and possible strategies for gene therapy. The eDystrophin database is freely available: http://edystrophin.genouest.org/.

Databases for neurogenetics: introduction, overview, and challenges.

Science.gov (United States)

Sobrido, María-Jesús; Cacheiro, Pilar; Carracedo, Angel; Bertram, Lars

2012-09-01

The importance for research and clinical utility of mutation databases, as well as the issues and difficulties entailed in their construction, is discussed within the Human Variome Project. While general principles and standards can apply to most human diseases, some specific questions arise when dealing with the nature of genetic neurological disorders. So far, publically accessible mutation databases exist for only about half of the genes causing neurogenetic disorders; and a considerable work is clearly still needed to optimize their content. The current landscape, main challenges, some potential solutions, and future perspectives on genetic databases for disorders of the nervous system are reviewed in this special issue of Human Mutation on neurogenetics. © 2012 Wiley Periodicals, Inc.

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA

Directory of Open Access Journals (Sweden)

Jyotsna Choubey

2017-01-01

Results and Conclusions: RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria.

Directory of Open Access Journals (Sweden)

Mario Fruzangohar

Full Text Available The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO, which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria from different sources simultaneously. Comparing GO protein distribution among up- or down-regulated genes from different samples can improve understanding of biological pathways, and mechanism(s of infection. It can also aid in the discovery of genes associated with specific function(s for investigation as a novel vaccine or therapeutic targets.http://turing.ersa.edu.au/BacteriaGO.

Effect of drought stress, corm size and corm tunic on morphoecophysiological characteristics of saffron (Crocus sativus L. in greenhouse conditions

Directory of Open Access Journals (Sweden)

M. Sabet Teimouri

2016-04-01

Full Text Available In order to investigate the effects of corm tunic, corm weight and drought stress on saffron (Crocus sativus L., an experiment was conducted at the greenhouse of Ferdowsi University of Mashhad, Iran. Treatment were combination of four corm weights range (2-4, 4-6, 6-8 and 8-10 g, two levels of water availability (100% field capacity and drought and two levels of corm tunic (natural corm with tunic and without tunic as factorial arrangement based on completely randomized block design with three replications. The corms were divided to four groups based on their weights and removed tunics of corm in tunic free treatment. Results indicated that the highest biomass produced in irrigation, corms with tunic with maximum weight. Both chlorophyll a and b contents decreased significantly under drought stress and chlorophyll b content was 50% of chlorophyll a content. Effect of corm size and corm tunic and interaction of these treatments imposed a significant effect on the leaf number per plant, leaf weight and chlorophyll content. Effect of corm tunic in 8-10 g corm size increased ch (a/ch (b ratio and leaf number. The relative water content was decreased in drought treatment in both tunic and tunicless treatments and the best corm weight in all treatment was 6-8g and could be useful to tolerate drought stress.

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database

Science.gov (United States)

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful user interface in the for...

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database.

Science.gov (United States)

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful AOP-DB user interface in...

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

Directory of Open Access Journals (Sweden)

Miao Zhenyan

2012-02-01

Full Text Available Abstract Background Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula. Description The M. truncatula transporter database (MTDB contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG V3.5 V3 and the M. truncatula Gene Index (MTGI V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments. Conclusions In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/.

Analysis of gene and protein name synonyms in Entrez Gene and UniProtKB resources

KAUST Repository

Arkasosy, Basil

2013-01-01

be ambiguous, referring in some cases to more than one gene or one protein, or in others, to both genes and proteins at the same time. Public biological databases give a very useful insight about genes and proteins information, including their names

IMGT/GeneInfo: enhancing V(D)J recombination database accessibility

OpenAIRE

Baum, Thierry-Pascal; Pasqual, Nicolas; Thuderoz, Florence; Hierle, Vivien; Chaume, Denys; Lefranc, Marie-Paule; Jouvin-Marche, Evelyne; Marche, Patrice-Noël; Demongeot, Jacques

2004-01-01

IMGT/GeneInfo is a user-friendly online information system that provides information on data resulting from the complex mechanisms of immunoglobulin (IG) and T cell receptor (TR) V(D)J recombinations. For the first time, it is possible to visualize all the rearrangement parameters on a single page. IMGT/GeneInfo is part of the international ImMunoGeneTics information system® (IMGT), a high-quality integrated knowledge resource specializing in IG, TR, major histocompatibility complex (MHC), an...

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

Directory of Open Access Journals (Sweden)

Jordi Vilaplana

2014-01-01

Full Text Available Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (reannotation of proteomes, to properly identify both the individual proteins involved in the process(es of interest and their function. It also enables the sets of proteins involved in the process(es in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Database constraints applied to metabolic pathway reconstruction tools.

Science.gov (United States)

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Comparison of gene coverage of mouse oligonucleotide microarray platforms

Directory of Open Access Journals (Sweden)

Medrano Juan F

2006-03-01

Full Text Available Abstract Background The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. Results A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis: Affymetrix430 2.0 (75.6%, ABI Genome Survey (81.24%, Agilent (79.33%, Codelink (78.09%, Sentrix (90.47%; and four array-ready oligosets: Sigma (47.95%, Operon v.3 (69.89%, Operon v.4 (84.03%, and MEEBO (84.03%. The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. Conclusion The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here

Database Description - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Trypanosomes Database Database Description General information of database Database name Trypanosomes Database...stitute of Genetics Research Organization of Information and Systems Yata 1111, Mishima, Shizuoka 411-8540, JAPAN E mail: Database...y Name: Trypanosoma Taxonomy ID: 5690 Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database description The... Article title: Author name(s): Journal: External Links: Original website information Database maintenance s...DB (Protein Data Bank) KEGG PATHWAY Database DrugPort Entry list Available Query search Available Web servic

The database on transgenic luminescent microorganisms as an instrument of studying a microbial component of closed ecosystems

Science.gov (United States)

Boyandin, A. N.; Lankin, Y. P.; Kargatova, T. V.; Popova, L. Y.; Pechurkin, N. S.

Luminescent transgenic microorganisms are widely used for study of microbial communities' functioning including closed ones. Bioluminescence is of high sensitive to effects of different environmental factors. Integration of lux-genes into different metabolic ways allows studying many aspects of microorganisms' life permitting to carry out measurements in situ. There is much information about applications of bioluminescent bacteria in different researches. But for effective using these data their summarizing and accumulation in common source is required. Therefore an information system on characteristics of transgenic microorganisms with cloned lux-genes was created. The database and client software related were developed. A database structure includes information on common characteristics of cloned lux-genes, their sources and properties, on regulation of gene expression in bacterial cells, on dependence of bioluminescence manifestation on biotic, abiotic and anthropogenic environmental factors. The database also can store description of changes in bacterial populations depending on environmental changes. The database created allows storing and using bibliographic information and also links to web sites of world collections of microorganisms. Internet publishing software permitting to open access to the database through the Internet is developed.

MIRNA-DISTILLER: a stand-alone application to compile microRNA data from databases

Directory of Open Access Journals (Sweden)

Jessica K. Rieger

2011-07-01

Full Text Available MicroRNAs (miRNA are small non-coding RNA molecules of ~22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3’-UTR of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp

MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases.

Science.gov (United States)

Rieger, Jessica K; Bodan, Denis A; Zanger, Ulrich M

2011-01-01

MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3'-untranslated region of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp.

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets

Directory of Open Access Journals (Sweden)

Lemoine Nicholas R

2007-11-01

Full Text Available Abstract Background Pancreatic cancer is the 5th leading cause of cancer death in both males and females. In recent years, a wealth of gene and protein expression studies have been published broadening our understanding of pancreatic cancer biology. Due to the explosive growth in publicly available data from multiple different sources it is becoming increasingly difficult for individual researchers to integrate these into their current research programmes. The Pancreatic Expression database, a generic web-based system, is aiming to close this gap by providing the research community with an open access tool, not only to mine currently available pancreatic cancer data sets but also to include their own data in the database. Description Currently, the database holds 32 datasets comprising 7636 gene expression measurements extracted from 20 different published gene or protein expression studies from various pancreatic cancer types, pancreatic precursor lesions (PanINs and chronic pancreatitis. The pancreatic data are stored in a data management system based on the BioMart technology alongside the human genome gene and protein annotations, sequence, homologue, SNP and antibody data. Interrogation of the database can be achieved through both a web-based query interface and through web services using combined criteria from pancreatic (disease stages, regulation, differential expression, expression, platform technology, publication and/or public data (antibodies, genomic region, gene-related accessions, ontology, expression patterns, multi-species comparisons, protein data, SNPs. Thus, our database enables connections between otherwise disparate data sources and allows relatively simple navigation between all data types and annotations. Conclusion The database structure and content provides a powerful and high-speed data-mining tool for cancer research. It can be used for target discovery i.e. of biomarkers from body fluids, identification and analysis

Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

2006-06-08

With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

KBERG: KnowledgeBase for Estrogen Responsive Genes

DEFF Research Database (Denmark)

Tang, Suisheng; Zhang, Zhuo; Tan, Sin Lam

2007-01-01

Estrogen has a profound impact on human physiology affecting transcription of numerous genes. To decipher functional characteristics of estrogen responsive genes, we developed KnowledgeBase for Estrogen Responsive Genes (KBERG). Genes in KBERG were derived from Estrogen Responsive Gene Database...... (ERGDB) and were analyzed from multiple aspects. We explored the possible transcription regulation mechanism by capturing highly conserved promoter motifs across orthologous genes, using promoter regions that cover the range of [-1200, +500] relative to the transcription start sites. The motif detection...... is based on ab initio discovery of common cis-elements from the orthologous gene cluster from human, mouse and rat, thus reflecting a degree of promoter sequence preservation during evolution. The identified motifs are linked to transcription factor binding sites based on the TRANSFAC database. In addition...

Database Description - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Arabidopsis Phenome Database Database Description General information of database Database n... BioResource Center Hiroshi Masuya Database classification Plant databases - Arabidopsis thaliana Organism T...axonomy Name: Arabidopsis thaliana Taxonomy ID: 3702 Database description The Arabidopsis thaliana phenome i...heir effective application. We developed the new Arabidopsis Phenome Database integrating two novel database...seful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing

LeishCyc: a biochemical pathways database for Leishmania major

Directory of Open Access Journals (Sweden)

Doyle Maria A

2009-06-01

Full Text Available Abstract Background Leishmania spp. are sandfly transmitted protozoan parasites that cause a spectrum of diseases in more than 12 million people worldwide. Much research is now focusing on how these parasites adapt to the distinct nutrient environments they encounter in the digestive tract of the sandfly vector and the phagolysosome compartment of mammalian macrophages. While data mining and annotation of the genomes of three Leishmania species has provided an initial inventory of predicted metabolic components and associated pathways, resources for integrating this information into metabolic networks and incorporating data from transcript, protein, and metabolite profiling studies is currently lacking. The development of a reliable, expertly curated, and widely available model of Leishmania metabolic networks is required to facilitate systems analysis, as well as discovery and prioritization of new drug targets for this important human pathogen. Description The LeishCyc database was initially built from the genome sequence of Leishmania major (v5.2, based on the annotation published by the Wellcome Trust Sanger Institute. LeishCyc was manually curated to remove errors, correct automated predictions, and add information from the literature. The ongoing curation is based on public sources, literature searches, and our own experimental and bioinformatics studies. In a number of instances we have improved on the original genome annotation, and, in some ambiguous cases, collected relevant information from the literature in order to help clarify gene or protein annotation in the future. All genes in LeishCyc are linked to the corresponding entry in GeneDB (Wellcome Trust Sanger Institute. Conclusion The LeishCyc database describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the evolving information about Leishmania

DRUMS: a human disease related unique gene mutation search engine.

Science.gov (United States)

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

Brassica ASTRA: an integrated database for Brassica genomic research.

Science.gov (United States)

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

Dictionary-driven prokaryotic gene finding

Science.gov (United States)

Shibuya, Tetsuo; Rigoutsos, Isidore

2002-01-01

Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified in a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm’s implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method’s generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed in detail. PMID:12060689

HEROD: a human ethnic and regional specific omics database.

Science.gov (United States)

Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

2017-10-15

Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

Directory of Open Access Journals (Sweden)

Rita eSharma

2013-08-01

Full Text Available Glycoside hydrolases (GH catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/. This database integrates multiple data types including the structural features, orthologous relationships, mutant availability and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum transcriptome

Directory of Open Access Journals (Sweden)

Kim Woo Taek

2008-10-01

Full Text Available Abstract Background There is no dedicated database available for Expressed Sequence Tags (EST of the chili pepper (Capsicum annuum, although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses. Results We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO, and MIPS Functional Catalogue (FunCat. The Pepper EST database is designed to provide a workbench for (i identifying unigenes in pepper plants, (ii analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/. Conclusion The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.

TransAtlasDB: an integrated database connecting expression data, metadata and variants

Science.gov (United States)

Adetunji, Modupeore O; Lamont, Susan J; Schmidt, Carl J

2018-01-01

Abstract High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful functionalities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis. Database URL: https://modupeore.github.io/TransAtlasDB/ PMID:29688361

Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

Directory of Open Access Journals (Sweden)

Weis Patrick

2010-01-01

Full Text Available Abstract Background The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration. Results A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish. Conclusion We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

Gene2Function: An Integrated Online Resource for Gene Function Discovery

Directory of Open Access Journals (Sweden)

Yanhui Hu

2017-08-01

Full Text Available One of the most powerful ways to develop hypotheses regarding the biological functions of conserved genes in a given species, such as humans, is to first look at what is known about their function in another species. Model organism databases and other resources are rich with functional information but difficult to mine. Gene2Function addresses a broad need by integrating information about conserved genes in a single online resource.

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

Directory of Open Access Journals (Sweden)

Zhu Liucun

2010-02-01

Full Text Available Abstract Background Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop. Description Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I and 6,029 DNA transposons (Class II with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95% of these elements (particularly a few hundred low-copy-number families are first described in this study. Conclusion SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually

MiRNA-TF-gene network analysis through ranking of biomolecules for multi-informative uterine leiomyoma dataset.

Science.gov (United States)

Mallik, Saurav; Maulik, Ujjwal

2015-10-01

Gene ranking is an important problem in bioinformatics. Here, we propose a new framework for ranking biomolecules (viz., miRNAs, transcription-factors/TFs and genes) in a multi-informative uterine leiomyoma dataset having both gene expression and methylation data using (statistical) eigenvector centrality based approach. At first, genes that are both differentially expressed and methylated, are identified using Limma statistical test. A network, comprising these genes, corresponding TFs from TRANSFAC and ITFP databases, and targeter miRNAs from miRWalk database, is then built. The biomolecules are then ranked based on eigenvector centrality. Our proposed method provides better average accuracy in hub gene and non-hub gene classifications than other methods. Furthermore, pre-ranked Gene set enrichment analysis is applied on the pathway database as well as GO-term databases of Molecular Signatures Database with providing a pre-ranked gene-list based on different centrality values for comparing among the ranking methods. Finally, top novel potential gene-markers for the uterine leiomyoma are provided. Copyright © 2015 Elsevier Inc. All rights reserved.

Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

Directory of Open Access Journals (Sweden)

Allan Peter Davis

Full Text Available The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/ is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS, wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel. Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency.

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

Science.gov (United States)

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

Gene coexpression network analysis as a source of functional annotation for rice genes.

Directory of Open Access Journals (Sweden)

Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

Recode-2: new design, new search tools, and many more genes.

LENUS (Irish Health Repository)

Bekaert, Michaël

2010-01-01

\\'Recoding\\' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of \\'recoded\\' genes lags far behind annotation of \\'standard\\' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression--a factor of approximately three increase over the previous version of the database. Recode-2 is available at http:\\/\\/recode.ucc.ie.

A comprehensive review of the pharmacological potential of Crocus sativus and its bioactive apocarotenoids.

Science.gov (United States)

Bukhari, Syed Imran; Manzoor, Mahreen; Dhar, M K

2018-02-01

Crocus sativus is an herbaceous plant that belongs to family Iridaceae. It is commonly known as saffron and has been used for medicinal purposes since many centuries in India and other parts of the world. Saffron of commercial importance comprises of dried stigmas of the plant and is rich in flavonoids, vitamins, and carotenoids. Carotenoids represent the main components of saffron and their cleavage results in the formation of apocarotenoids such as crocin, picrocrocin, and safranal. Studies conducted during the past two decades have revealed the immense therapeutic potential of saffron. Most of the therapeutic properties are due to the presence of unique apocarotenoids having strong free radical scavenging activity. The mode of action of these apocarotenoids could be: modulatory effects on detoxifying enzymes involved in combating oxidative stress, decreasing telomerase activity, increased the proapoptotic effect, inhibition of DNA, RNA and protein synthesis, and by a strong binding capacity of crocetin with tRNA. The present review focuses on the therapeutic role of saffron and its bio oxidative cleavage products and also highlights the possible molecular mechanism of action. The findings reported in this review describes the wide range of applications of saffron and attributes its free radical scavenging nature the main property which makes this spice a potent chemotherapeutic agent for the treatment of various diseases. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

MIPS: curated databases and comprehensive secondary data resources in 2010.

Science.gov (United States)

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

Petals of Crocus sativus L. as a potential source of the antioxidants crocin and kaempferol.

Science.gov (United States)

Zeka, Keti; Ruparelia, Ketan C; Continenza, Maria A; Stagos, Dimitrios; Vegliò, Francesco; Arroo, Randolph R J

2015-12-01

Saffron from the province of L'Aquila, in the Abruzzo region of Italy, is highly prized and has been awarded a formal recognition by the European Union with EU Protected Designation of Origin (PDO) status. Despite this, the saffron regions are abandoned by the younger generations because the traditional cultivation of saffron (Crocus sativus L.) is labour intensive and yields only one crop of valuable saffron stamens per year. Petals of the saffron Crocus have had additional uses in traditional medicine and may add value to the crops for local farmers. This is especially important because the plant only flowers between October and November, and farmers will need to make the best use of the flowers harvested in this period. Recently, the petals of C. sativus L., which are considered a waste material in the production of saffron spice, were identified as a potential source of natural antioxidants. The antioxidants crocin and kaempferol were purified by flash column chromatography, and identified by thin layer chromatography (TLC), HPLC-DAD, infrared (IR), and nuclear magnetic resonance ((1)H &(13)C NMR) spectroscopy. The antioxidant activity was determined with the ABTS and DPPH tests. The antioxidant activities are mainly attributed to carotenoid and flavonoid compounds, notably glycosides of crocin and kaempferol. We found in dried petals 0.6% (w/w) and 12.6 (w/w) of crocin and kaempferol, respectively. Petals of C. sativus L. have commercial potential as a source for kaempferol and crocetin glycosides, natural compounds with antioxidant activity that are considered to be the active ingredients in saffron-based herbal medicine. Copyright © 2015 Elsevier B.V. All rights reserved.

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

Directory of Open Access Journals (Sweden)

Rodríguez-Valera Francisco

2005-09-01

Full Text Available Abstract Background The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes. Description The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information. Conclusion The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at http://egg.umh.es/micromar/.

EcoGene 3.0.

Science.gov (United States)

Zhou, Jindan; Rudd, Kenneth E

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.

EcoGene 3.0

Science.gov (United States)

Zhou, Jindan; Rudd, Kenneth E.

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection. PMID:23197660

Human synthetic lethal inference as potential anti-cancer target gene detection

Directory of Open Access Journals (Sweden)

Solé Ricard V

2009-12-01

Full Text Available Abstract Background Two genes are called synthetic lethal (SL if mutation of either alone is not lethal, but mutation of both leads to death or a significant decrease in organism's fitness. The detection of SL gene pairs constitutes a promising alternative for anti-cancer therapy. As cancer cells exhibit a large number of mutations, the identification of these mutated genes' SL partners may provide specific anti-cancer drug candidates, with minor perturbations to the healthy cells. Since existent SL data is mainly restricted to yeast screenings, the road towards human SL candidates is limited to inference methods. Results In the present work, we use phylogenetic analysis and database manipulation (BioGRID for interactions, Ensembl and NCBI for homology, Gene Ontology for GO attributes in order to reconstruct the phylogenetically-inferred SL gene network for human. In addition, available data on cancer mutated genes (COSMIC and Cancer Gene Census databases as well as on existent approved drugs (DrugBank database supports our selection of cancer-therapy candidates. Conclusions Our work provides a complementary alternative to the current methods for drug discovering and gene target identification in anti-cancer research. Novel SL screening analysis and the use of highly curated databases would contribute to improve the results of this methodology.

Visualizing information across multidimensional post-genomic structured and textual databases.

Science.gov (United States)

Tao, Ying; Friedman, Carol; Lussier, Yves A

2005-04-15

Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface. We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research. PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ Lussier@dbmi.columbia.edu.