scholarly journals CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2805
Author(s):  
Jing Yu ◽  
Sook Jung ◽  
Chun-Huai Cheng ◽  
Taein Lee ◽  
Ping Zheng ◽  
...  
Keyword(s):  
Online Community ◽  
Crop Improvement ◽  
Fold Increase ◽  
Information Management System ◽  
Data Types ◽  
Online Tools ◽  
A Genome ◽  
Phenotype Data ◽  
Breeding Research ◽  
Communication And Coordination

Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.

Overproduction of yeast viruslike particles by strains deficient in a mitochondrial nuclease

1989 ◽  
Vol 9 (8) ◽  
pp. 3323-3331
Author(s):  
Y X Liu ◽  
C L Dieckmann
Keyword(s):  
Coat Protein ◽  
Killer Toxin ◽  
Nuclear Gene ◽  
Fold Increase ◽  
Mitochondrial Outer Membrane ◽  
Gene Encoding ◽  
Recessive Mutations ◽  
A Genome ◽  
Nonfermentable Carbon Source ◽  
Viruslike Particles

Saccharomyces cerevisiae strains are often host to several types of cytoplasmic double-stranded RNA (dsRNA) genomes, some of which are encapsidated by the L-A dsRNA product, an 86,000-dalton coat protein. Here we present the finding that nuclear recessive mutations in the NUC1 gene, which encodes the major nonspecific nuclease of yeast mitochondria, resulted in at least a 10-fold increase in amounts of the L-A dsRNA and its encoded coat protein. The effect of nuc1 mutations on L-A abundance was completely suppressed in strains that also hosted the killer-toxin-encoding M dsRNA. Both NUC1 and nuc1 strains containing the L-A genome exhibited an increase in coat protein abundance and a concomitant increase in L-A dsRNA when the cells were grown on a nonfermentable carbon source rather than on glucose, an effect independent of the increase in coat protein due to nuc1 mutations or to the absence of M. The increase in L-A expression in nuc1 strains was similar to that observed in strains with mutations in the nuclear gene encoding the most abundant outer mitochondrial membrane protein, porin. nuc1 mutations did not affect the level of porin in the mitochondrial outer membrane. Since the effect of mutations in nuc1 was to alter the copy number of the L-A coat protein genome rather than to change the level of the M toxin genome (as do mak and ski mutations), these mutations define a new class of nuclear genes affecting yeast dsRNA abundance.

scholarly journals Genome-wide polygenic score to identify a monogenic risk-equivalent for coronary disease

2017 ◽  
Author(s):  
Amit V. Khera ◽  
Mark Chaffin ◽  
Krishna G. Aragam ◽  
Connor A. Emdin ◽  
Derek Klarin ◽  
...  
Keyword(s):  
Coronary Disease ◽  
Fold Increase ◽  
Predictive Capacity ◽  
Cumulative Impact ◽  
Polygenic Score ◽  
Genome Wide ◽  
A Genome ◽  
Increased Risk ◽  
Polygenic Scores ◽  
Artery Disease

AbstractIdentification of individuals at increased genetic risk for a complex disorder such as coronary disease can facilitate treatments or enhanced screening strategies. A rare monogenic mutation associated with increased cholesterol is present in ~1:250 carriers and confers an up to 4-fold increase in coronary risk when compared with non-carriers. Although individual common polymorphisms have modest predictive capacity, their cumulative impact can be aggregated into a polygenic score. Here, we develop a new, genome-wide polygenic score that aggregates information from 6.6 million common polymorphisms and show that this score can similarly identify individuals with a 4-fold increased risk for coronary disease. In >400,000 participants from UK Biobank, the score conforms to a normal distribution and those in the top 2.5% of the distribution are at 4-fold increased risk compared to the remaining 97.5%. Similar patterns are observed with genome-wide polygenic scores for two additional diseases – breast cancer and severe obesity.One Sentence SummaryA genome-wide polygenic score identifies 2.5% of the population born with a 4-fold increased risk for coronary artery disease.

Online Communities of Practice and Web 2.0

2016 ◽  
pp. 265-292
Author(s):  
Amir Manzoor
Keyword(s):  
Communities Of Practice ◽  
Web 2.0 ◽  
Community Of Practice ◽  
Online Communities ◽  
Online Community ◽  
Management Communication ◽  
Organizational Goals ◽  
The People ◽  
Online Tools ◽  
Online Communities Of Practice

In contemporary Knowledge Management, communication and collaboration play very significant role. Knowledge exists within the stakeholders of an organization. Such knowledge, when extracted and harnessed effectively, can become an extremely valuable asset to achieve organizational goals and objectives. This knowledge, embedded in the people, must be properly released through an appropriate channel to make it usable. Through dialogue and discussions, using online tools, this release and reuses of knowledge can be made possible. The Community of Practice (CoP) is a useful organizing concept for enhancing collaboration, sharing knowledge, and disseminating best practices among researchers and practitioners. This chapter explores the concept of Communities of Practice and how Web 2.0 technologies can facilitate the transformation from a conventional community of practice to online community of practice for better and effective online communities of practices.

scholarly journals Bioconversion of Non Edible Vegetables from Market into Biofertilizer for Crop Improvement

2016 ◽  
Vol 8 (6) ◽  
pp. 71
Author(s):  
Geetha Karuppasamy ◽  
Michael Antony D'Couto ◽  
Anant Achary
Keyword(s):  
Plant Growth ◽  
Root Length ◽  
Growth Parameters ◽  
Crop Improvement ◽  
C:N Ratio ◽  
Value Added ◽  
Fold Increase ◽  
Shoot Length ◽  
Germination Index ◽  
Vigour Index

<p>The fruits and vegetables lost due to spoilage in the market can be converted to nutrient rich organic biofertilizer, vermicompost and worm tea. In this study, non-edible vegetables from market [French beans (S1), Lady’s fingers (S2) and Brinjal (S3)] were used for production of vermicompost and worm tea using <em>Eisenia fetida</em> for environmental friendly management and recycling, as value added product for crop production. Vermicomposting was carried out in four bins. Three bins (S1, S2 &amp; S3) consisted of individual pre-digested vegetables and the fourth bin (S4) was set up with a mixture of all three pre-digested vegetables in equal proportions. Physico-chemical properties and essential nutrients like pH, temperature, moisture content, total organic carbon (C), total nitrogen (N), available phosphorus (P) and exchangeable potassium (K) of the pre-digested vegetables and/or compost were analysed at regular time intervals. There was around 6-10 fold increase in earthworm count at the end of vermicomposting. During vermicomposting, the N and P content of the compost showed 2 to 4 fold increase whereas 10 to 15 fold increase in K content was noticed. Low C:N ratio (4 to 9) was obtained for vermicompost VS4. The worm tea (vermi wash) and vermicompost collected were used for plant growth studies on <em>Vigna radiata</em> (Green gram). Growth parameters like germination percentage, vigour index, germination index (GI), shoot length (cm), root length (cm) and leaf length (cm) were studied. There was noticeable improvement in germination % (1.7 fold), vigour index (2.7 fold) and germination index. A 20 fold increase in shoot length was also seen in test plants when compared to control (2 fold). Statistical analysis of various growth parameters like root length and plant height indicated that vermicompost made with waste brinjal has a significant response with p ≤ 0.05. Based on the results obtained, waste brinjal, which is abundantly available locally can be economically converted to organic biofertilizers and used for soil and crop improvement. Through this study, a cost effective and environment friendly method for efficient utilization of market waste vegetables has been proposed for promoting plant growth and development.</p>

scholarly journals Probing the rice Rubisco–Rubisco activase interaction via subunit heterooligomerization

2019 ◽  
Vol 116 (48) ◽  
pp. 24041-24048 ◽  
Author(s):  
Devendra Shivhare ◽  
Jediael Ng ◽  
Yi-Chin Candace Tsai ◽  
Oliver Mueller-Cajar
Keyword(s):  
Active Sites ◽  
Crop Improvement ◽  
Fold Increase ◽  
Rubisco Activase ◽  
Growth And Yield ◽  
Higher Plant ◽  
Bisphosphate Carboxylase ◽  
Functional Understanding ◽  
Sugar Phosphates ◽  
Aaa Protein

During photosynthesis the AAA+ protein and essential molecular chaperone Rubisco activase (Rca) constantly remodels inhibited active sites of the CO2-fixing enzyme Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) to release tightly bound sugar phosphates. Higher plant Rca is a crop improvement target, but its mechanism remains poorly understood. Here we used structure-guided mutagenesis to probe the Rubisco-interacting surface of rice Rca. Mutations in Ser-23, Lys-148, and Arg-321 uncoupled adenosine triphosphatase and Rca activity, implicating them in the Rubisco interaction. Mutant doping experiments were used to evaluate a suite of known Rubisco-interacting residues for relative importance in the context of the functional hexamer. Hexamers containing some subunits that lack the Rubisco-interacting N-terminal domain displayed a ∼2-fold increase in Rca function. Overall Rubisco-interacting residues located toward the rim of the hexamer were found to be less critical to Rca function than those positioned toward the axial pore. Rca is a key regulator of the rate-limiting CO2-fixing reactions of photosynthesis. A detailed functional understanding will assist the ongoing endeavors to enhance crop CO2 assimilation rate, growth, and yield.

scholarly journals Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1479
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Dhiman Biswas ◽  
Jennifer Ann Harikrishna ◽  
Yuxuan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Comparative Mapping ◽  
In Silico ◽  
Large Scale ◽  
Crop Improvement ◽  
Musa Spp ◽  
Population Structure Analysis ◽  
A Genome ◽  
Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

scholarly journals Pregnancy Up-Regulates Intestinal Calcium Absorption and Skeletal Mineralization Independently of the Vitamin D Receptor

Endocrinology ◽  
2010 ◽  
Vol 151 (3) ◽  
pp. 886-895 ◽  
Author(s):  
Neva J. Fudge ◽  
Christopher S. Kovacs
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Calcium Absorption ◽  
Fold Increase ◽  
Normal Diet ◽  
Intestinal Calcium Absorption ◽  
A Genome ◽  
Pregnancy And Lactation ◽  
Turnover Markers ◽  
Calbindin D

Without the vitamin D receptor (VDR), adult mammals develop reduced intestinal calcium absorption, rickets, and osteomalacia. Intestinal calcium absorption normally increases during pregnancy so that the mother can supply sufficient calcium to her fetuses. The maternal skeleton is rapidly resorbed during lactation to provide calcium needed for milk; that lost bone mineral content (BMC) is completely restored after weaning. We studied Vdr null mice to determine whether these adaptations during pregnancy and lactation require the VDR. Vdr nulls were severely rachitic at 10 wk of age on a normal diet. Pregnancy induced a 158% increase in Vdr null BMC to equal the pregnant wild-type (WT) value. Lactation caused BMC losses that were equal in Vdr nulls and WT. Vdr nulls recovered after weaning to a BMC 50% higher than before pregnancy and equal to WT. Additional analyses showed that during pregnancy, duodenal 45Ca absorption increased in Vdr nulls, secondary hyperparathyroidism lessened, bone turnover markers decreased, and osteoid became fully mineralized. A genome-wide microarray analysis of duodenal RNA found marked reduction of Trpv6 in Vdr nulls at baseline but a 13.5-fold increase during pregnancy. Calbindin D-9K (S100g) and Ca2+-ATPase (Pmca1) were not altered by pregnancy. Several other solute transporters increased during pregnancy in Vdr nulls. In summary, Vdr nulls adapt to pregnancy by up-regulating duodenal Trpv6 and intestinal 45Ca absorption, thereby enabling rapid normalization of BMC during pregnancy. These mice lactate normally and fully restore BMC after weaning. Therefore, VDR is not required for the skeletal adaptations during pregnancy, lactation, and after weaning.

scholarly journals Applicability of chromosome-specific SSR wheat markers for the introgression of Triticum urartu in durum wheat breeding programmes

2011 ◽  
Vol 9 (3) ◽  
pp. 439-444 ◽  
Author(s):  
C. Rodríguez-Suárez ◽  
M. C. Ramírez ◽  
A. Martín ◽  
S. G. Atienza
Keyword(s):  
Durum Wheat ◽  
Triticum Turgidum ◽  
Crop Improvement ◽  
Wheat Chromosome ◽  
Wheat Breeding ◽  
Triticum Urartu ◽  
Founder Line ◽  
A Genome ◽  
Breeding Programmes ◽  
Novel Alleles

Triticum urartu, the A-genome donor of tetraploid and hexaploid wheats, is a potential source of novel alleles for crop improvement. A fertile amphiploid between T. urartu (2n = 2x = 14; AuAu) and durum wheat cv ‘Yavaros’ (Triticum turgidum ssp. durum; 2n = 4x = 28, AABB) was obtained as a first step to making the genetic variability of the wild ancestor available to durum wheat breeding. The amphiploid was backcrossed with ‘Yavaros’ and the offspring from this cross was selfed. A plant from this progeny (founder line) with 28 chromosomes and active x and y subunits of the Glu-A1 locus of T. urartu was selfed, which resulted in the obtaining of 98 pre-introgression lines (pre-ILs). In this work, a set of 78 wheat chromosome-specific microsatellite markers (simple sequence repeats, SSR), uniformly distributed over the A genome, was used for marker-assisted selection of T. urartu in a durum wheat background. A total of 57 SSRs allowed a clear discrimination between T. urartu and ‘Yavaros’. This set of markers was further used for characterizing the pre-ILs, identifying and defining the T. urartu introgressed regions. The applicability of these markers is discussed.

scholarly journals FILER: a framework for harmonizing and querying large-scale functional genomics knowledge

2022 ◽  
Vol 4 (1) ◽  
Author(s):  
Pavel P Kuksa ◽  
Yuk Yee Leung ◽  
Prabhakaran Gangadharan ◽  
Zivadin Katanic ◽  
Lauren Kleidermacher ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Large Scale ◽  
Fold Increase ◽  
Cell Types ◽  
Data Sources ◽  
Reproducible Research ◽  
Functional Genomic ◽  
Data Types ◽  
Annotation Data ◽  
Data Collections

ABSTRACT Querying massive functional genomic and annotation data collections, linking and summarizing the query results across data sources/data types are important steps in high-throughput genomic and genetic analytical workflows. However, these steps are made difficult by the heterogeneity and breadth of data sources, experimental assays, biological conditions/tissues/cell types and file formats. FILER (FunctIonaL gEnomics Repository) is a framework for querying large-scale genomics knowledge with a large, curated integrated catalog of harmonized functional genomic and annotation data coupled with a scalable genomic search and querying interface. FILER uniquely provides: (i) streamlined access to &gt;50 000 harmonized, annotated genomic datasets across &gt;20 integrated data sources, &gt;1100 tissues/cell types and &gt;20 experimental assays; (ii) a scalable genomic querying interface; and (iii) ability to analyze and annotate user’s experimental data. This rich resource spans &gt;17 billion GRCh37/hg19 and GRCh38/hg38 genomic records. Our benchmark querying 7 × 109 hg19 FILER records shows FILER is highly scalable, with a sub-linear 32-fold increase in querying time when increasing the number of queries 1000-fold from 1000 to 1 000 000 intervals. Together, these features facilitate reproducible research and streamline integrating/querying large-scale genomic data within analyses/workflows. FILER can be deployed on cloud or local servers (https://bitbucket.org/wanglab-upenn/FILER) for integration with custom pipelines and is freely available (https://lisanwanglab.org/FILER).

scholarly journals A supervised learning framework for chromatin loop detection in genome-wide contact maps

2019 ◽  
Author(s):  
Tarik J. Salameh ◽  
Xiaotao Wang ◽  
Fan Song ◽  
Bo Zhang ◽  
Sage M. Wright ◽  
...  
Keyword(s):  
Supervised Learning ◽  
Data Types ◽  
Random Forest Classification ◽  
Chromatin Loops ◽  
3D Genome ◽  
Contact Maps ◽  
Genome Wide ◽  
A Genome ◽  
Loop Detection ◽  
Wide Contact

ABSTRACTAccurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepen our understanding of proper gene regulation events. Current approaches are mainly focused on searching for statistically enriched dots on a genome-wide map. However, given the availability of a wide variety of orthogonal data types such as ChIA-PET, GAM, SPRITE, and high-throughput imaging, a supervised learning approach could facilitate the discovery of a comprehensive set of chromatin interactions. Here we present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps. Compared with current enrichment-based approaches, Peakachu identified more meaningful short-range interactions. We show that our models perform well in different platforms such as Hi-C, Micro-C, and DNA SPRITE, across different sequencing depths, and across different species. We applied this framework to systematically predict chromatin loops in 56 Hi-C datasets, and the results are available at the 3D Genome Browser (www.3dgenome.org).

Sign in / Sign up

Export Citation Format

Share Document