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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/27913887/transcriptomics-analysis-of-hulless-barley-during-grain-development-with-a-focus-on-starch-biosynthesis
#1
Yawei Tang, Xingquan Zeng, Yulin Wang, Lijun Bai, Qijun Xu, Zexiu Wei, Hongjun Yuan, Tashi Nyima
Hulless barley, with its unique nutritional value and potential health benefits, has increasingly attracted attentions in recent years. However, the transcription dynamics during hulless barley grain development is not well understood. In the present study, we investigated the transcriptome changes during barley grain development using Illumina paired-end RNA-sequencing. Two datasets of the developing grain transcriptomes from two barley landraces with the differential seed starch synthesis traits were generated, and comparative transcriptome approach in both genotypes was performed...
December 2, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27900504/a-large-scale-chromosome-specific-snp-discovery-guideline
#2
Bala Ani Akpinar, Stuart Lucas, Hikmet Budak
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae...
November 29, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27896456/dna-copy-number-profiling-in-microsatellite-stable-and-microsatellite-unstable-hereditary-non-polyposis-colorectal-cancers-by-targeted-cnv-array
#3
Weixiang Chen, Jun Ding, Long Jiang, Zebing Liu, Xiaoyan Zhou, Daren Shi
About half of hereditary non-polyposis colorectal cancers (HNPCCs) fulfilling the Amsterdam criteria (AC) do not display evidence of mismatch repair defects, and the difference between microsatellite-stable (MSS) and microsatellite-unstable HNPCC remains poorly understood. The study was to compare overall copy number variation (CNV) and loss of heterozygosity (LOH) of the entire genome in HNPCCs with MSS and microsatellite-instability (MSI) using the Cytoscan HD Array. This was a study carried out in samples from 20 patients with MSS HNPCC and four patients with MSI HNPCC from the Fudan University Shanghai Cancer Center (China)...
November 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27885507/erratum-to-genomic-and-functional-features-of-the-biosurfactant-producing-bacillus-sp-am13
#4
Shraddha Shaligram, Shreyas V Kumbhare, Dhiraj P Dhotre, Manohar G Muddeshwar, Atya Kapley, Neetha Joseph, Hemant J Purohit, Yogesh S Shouche, Shrikant P Pawar
No abstract text is available yet for this article.
November 25, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27866284/a-syntenic-locus-on-buffalo-chromosome-20-novel-genomic-hotspot-for-mirnas-involved-in-follicular-luteal-transition
#5
Vijay Simha Baddela, Suneel Kumar Onteru, Dheer Singh
The developmental reorganization of ovarian follicular granulosa cells (GC) during follicular maturation, ovulation, and luteinization require a well-controlled regulation of dynamic gene expression profiles. Recently, microRNAs (miRNAs) were found to be key players of ovarian follicular dynamics. The current study aimed to understand the miRNA regulatory role in follicular-luteal transition by characterizing the miRNA profile through miRNA-seq at different follicular (small, medium, and large) and luteal (early, mid, and late) stages in Indian water buffaloes, mono-ovulatory animals like humans...
November 19, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27858182/migration-of-endophytic-diazotroph-azorhizobium-caulinodans-ors571-inside-wheat-triticum-aestivum-l-and-its-effect-on-micrornas
#6
Li Qiu, Qiang Li, Junbiao Zhang, Yongchao Chen, Xiaojun Lin, Chao Sun, Weiling Wang, Huawei Liu, Baohong Zhang
Azorhizobium caulinodans ORS571, a novel rhizobium, forms endosymbionts with its nature host Sesbania rostrata, a semi-aquatic leguminous tree. Recent studies showed that A. caulinodans ORS571, as endophytic rhizobium, disseminated and colonized inside of cereal plants. However, how this rhizobium infects monocot plants and the regulatory mechanism remains unknown. MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression at the post-transcriptional levels. In this study, we employed laser scanning confocal microscope to monitor the pathway that rhizobium invade wheat; we also investigated the potential role of miRNAs during A...
November 18, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27848097/transcription-dynamics-of-saltol-qtl-localized-genes-encoding-transcription-factors-reveals-their-differential-regulation-in-contrasting-genotypes-of-rice
#7
Kamlesh K Nutan, Hemant R Kushwaha, Sneh L Singla-Pareek, Ashwani Pareek
Salinity is one of the major environmental factors affecting the growth and yield of rice crop. Salinity stress response is a multigenic trait and numerous approaches have been used to dissect out the key determinants of complex salt tolerance trait and their regulation in plant. In the current study, we have investigated expression dynamics of the genes encoding transcription factors (SalTFs) localized within a major salinity tolerance related QTL-'Saltol' in the contrasting cultivars of rice. SalTFs were found to be differentially regulated between the contrasting genotypes of rice, with higher constitutive expression in the salt tolerant landrace, Pokkali than the cultivar IR64...
November 15, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27819121/analysis-of-the-interplay-between-methylation-and-expression-reveals-its-potential-role-in-cancer-aetiology
#8
Bugra Ozer, Ugur Sezerman
With ongoing developments in technology, changes in DNA methylation levels have become prevalent to study cancer biology. Previous studies report that DNA methylation affects gene expression in a direct manner, most probably by blocking gene regulatory regions. In this study, we have studied the interplay between methylation and expression to improve our knowledge of cancer aetiology. For this purpose, we have investigated which genomic regions are of higher importance; hence, first exon, 5'UTR and 200 bp near the transcription start sites are proposed as being more crucial compared to other genomic regions...
November 7, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27778111/alr2954-of-anabaena-sp-pcc-7120-with-adp-ribose-pyrophosphatase-activity-bestows-abiotic-stress-tolerance-in-escherichia-coli
#9
Prashant Kumar Singh, Alok Kumar Shrivastava, Shilpi Singh, Ruchi Rai, Antra Chatterjee, L C Rai
In silico derived properties on experimental validation revealed that hypothetical protein Alr2954 of Anabaena sp. PCC7120 is ADP-ribose pyrophosphatase, which belongs to nudix hydrolase superfamily. Presence of ADP-ribose binding site was attested by ADP-ribose pyrophosphatase activity (K m 44.71 ± 8.043 mM, V max 7.128 ± 0.417 μmol min(-1) mg protein(-1), and K cat/K m 9.438 × 10(4) μM(-)1 min(-1)). Besides ADP-ribose, the enzyme efficiently hydrolyzed various nucleoside phosphatases such as 8-oxo-dGDP, 8-oxo-dADP, 8-oxo-dGTP, 8-oxo-dATP, GDP-mannose, ADP-glucose, and NADH...
October 24, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27778110/surface-proteome-mining-for-identification-of-potential-vaccine-candidates-against-campylobacter-jejuni-an-in-silico-approach
#10
Kusum Mehla, Jayashree Ramana
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task...
October 24, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27734229/micrornas-differentially-modulated-in-response-to-heat-and-drought-stress-in-durum-wheat-cultivars-with-contrasting-water-use-efficiency
#11
Lorenzo Giusti, Erica Mica, Edoardo Bertolini, Anna Maria De Leonardis, Primetta Faccioli, Luigi Cattivelli, Cristina Crosatti
Plant stress response is a complex molecular process based on transcriptional and posttranscriptional regulation of many stress-related genes. microRNAs are the best-studied class of small RNAs known to play key regulatory roles in plant response to stress, besides being involved in plant development and organogenesis. We analyzed the leaf miRNAome of two durum wheat cultivars (Cappelli and Ofanto) characterized by a contrasting water use efficiency, exposed to heat stress, and mild and severe drought stress...
October 12, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27730426/drought-inducible-expression-of-hv-mir827-enhances-drought-tolerance-in-transgenic-barley
#12
Jannatul Ferdous, Ryan Whitford, Martin Nguyen, Chris Brien, Peter Langridge, Penny J Tricker
Drought is one of the major abiotic stresses reducing crop yield. Since the discovery of plant microRNAs (miRNAs), considerable progress has been made in clarifying their role in plant responses to abiotic stresses, including drought. miR827 was previously reported to confer drought tolerance in transgenic Arabidopsis. We examined barley (Hordeum vulgare L. 'Golden Promise') plants over-expressing miR827 for plant performance under drought. Transgenic plants constitutively expressing CaMV-35S::Ath-miR827 and drought-inducible Zm-Rab17::Hv-miR827 were phenotyped by non-destructive imaging for growth and whole plant water use efficiency (WUEwp)...
October 11, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27709374/exploring-drought-stress-regulated-genes-in-senna-cassia-angustifolia-vahl-a-transcriptomic-approach
#13
Rucha Harishbhai Mehta, Manivel Ponnuchamy, Jitendra Kumar, Nagaraja Reddy Rama Reddy
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress...
October 5, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27709373/novel-snps-and-indels-discovered-in-two-promoter-regions-of-porcine-pregnancy-associated-glycoprotein-2-like-subfamily-ppag2-ls-in-crossbreed-pigs
#14
Martyna Bieniek-Kobuszewska, Grzegorz Panasiewicz, Aleksandra Lipka, Marta Majewska, Bozena Szafranska
This is a pioneer study of single nucleotide polymorphisms (SNPs) within the entire promoter region (1204 bp) of the dominant pPAG2-L subfamily in the pig. The pPAG2-L subfamily was sequenced/examined using genomic deoxyribonucleic acid (gDNA) templates of crossbreed pigs (Landrace x Large White), and compared to two bacterial artificial chromosome (BAC) clones containing gDNA of the Duroc breed (as the positive controls). Our analysis of the pPAG2-L promoter identified 31 SNPs and one InDel mutation in crossbreed pigs...
October 5, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27709372/genomic-analyses-identify-agents-regulating-somatotroph-and-lactotroph-functions
#15
Jun Fan, Cui Zhang, Qi Chen, Jin Zhou, Jean-Louis Franc, Qing Chen, Yunguang Tong
Isolated hormone deficiency might be caused by loss of a specific type of endocrine cells, and regenerating these missing cells may provide a new option for future treatment. It is known that POU1F1 lineage cells can differentiate into thyrotroph, somatotroph, and lactotroph. However, there is no effective way of controlling pituitary stem/progenitor cells to differentiate into a specific type of endocrine cell. We thereby analyzed multiple genomic publications related to POU1F1 and pituitary development in this study to identify genes and agents regulating POU1F1 lineage cell differentiation...
October 5, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27696076/characterization-of-mirnas-responsive-to-exogenous-ethylene-in-grapevine-berries-at-whole-genome-level
#16
Fanggui Zhao, Chen Wang, Jian Han, Xudong Zhu, Xiaopeng Li, Xicheng Wang, Jinggui Fang
MicroRNAs (miRNAs) are critical regulators of various biological and metabolic processes of plants. Numerous miRNAs and their functions have been identified and analyzed in many plants. However, till now, the involvement of miRNAs in the response of grapevine berries to ethylene has not been reported yet. Here, Solexa technology was employed to deeply sequence small RNA libraries constructed from grapevine berries treated with and without ethylene. A total of 124 known and 78 novel miRNAs were identified. Among these miRNAs, 162 miRNAs were clearly responsive to ethylene, with 55 downregulated, 59 upregulated, and 14 unchanged miRNAs detected only in the control...
September 30, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27681237/long-noncoding-rna-lincrna-a-new-paradigm-in-gene-expression-control
#17
Emre Deniz, Batu Erman
Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome...
September 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27665284/abiotic-stress-mirnomes-in-the-triticeae
#18
Burcu Alptekin, Peter Langridge, Hikmet Budak
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage...
September 24, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27647143/integrative-analysis-of-signaling-pathways-and-diseases-associated-with-the-mir-106b-25-cluster-and-their-function-study-in%C3%A2-berb%C3%AF-erine-induced-multiple-myeloma-cells
#19
Chunming Gu, Tianfu Li, Zhao Yin, Shengting Chen, Jia Fei, Jianping Shen, Yuan Zhang
Berberine (BBR), a traditional Chinese herbal medicine compound, has emerged as a novel class of anti-tumor agent. Our previous microRNA (miRNA) microarray demonstrated that miR-106b/25 was significantly down-regulated in BBR-treated multiple myeloma (MM) cells. Here, systematic integration showed that miR-106b/25 cluster is involved in multiple cancer-related signaling pathways and tumorigenesis. MiREnvironment database revealed that multiple environmental factors (drug, ionizing radiation, hypoxia) affected the miR-106b/25 cluster expression...
September 19, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27638632/regulatory-network-analysis-of-micrornas-and-genes-in-imatinib-resistant-chronic-myeloid-leukemia
#20
Ismael Soltani, Hanen Gharbi, Islem Ben Hassine, Ghada Bouguerra, Kais Douzi, Mouheb Teber, Salem Abbes, Samia Menif
Targeted therapy in the form of selective breakpoint cluster region-abelson (BCR/ABL) tyrosine kinase inhibitor (imatinib mesylate) has successfully been introduced in the treatment of the chronic myeloid leukemia (CML). However, acquired resistance against imatinib mesylate (IM) has been reported in nearly half of patients and has been recognized as major issue in clinical practice. Multiple resistance genes and microRNAs (miRNAs) are thought to be involved in the IM resistance process. These resistance genes and miRNAs tend to interact with each other through a regulatory network...
September 16, 2016: Functional & Integrative Genomics
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