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https://read.qxmd.com/read/30781727/genome-wide-identification-and-analysis-of-high-copy-number-ltr-retrotransposons-in-asian-pears
#1
Shuang Jiang, Xiaoqing Wang, Chunhui Shi, Jun Luo
A large proportion of the genome of 'Suli' pear ( Pyrus pyrifolia ) contains long terminal repeat retrotransposons (LTR-RTs), which suggests that LTR-RTs have played important roles in the evolution of Pyrus . Further analysis of retrotransposons, particularly of high-copy-number LTR-RTs in different species, will provide new insights into the evolutionary history of Pyrus . A total of 4912 putative LTR-RTs classified into 198 subfamilies were identified in the 'Suli' pear genome. Six Asian pear accessions, including cultivars and wild species, were resequenced...
February 18, 2019: Genes
https://read.qxmd.com/read/30781725/pituitary-transcriptomic-study-reveals-the-differential-regulation-of-lncrnas-and-mrnas-related-to-prolificacy-in-different-fecb-genotyping-sheep
#2
Jian Zheng, Zhibo Wang, Hua Yang, Xiaolei Yao, Pengcheng Yang, CaiFang Ren, Feng Wang, YanLi Zhang
Long non-coding RNA (LncRNA) have been identified as important regulators in the hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, their expression pattern and potential roles in the pituitary are yet unclear. To explore the potential mRNAs and lncRNAs that regulate the expression of the genes involved in sheep prolificacy, we used stranded specific RNA-seq to profile the pituitary transcriptome (lncRNA and mRNA) in high prolificacy (genotype FecB BB, litter size = 3; H) and low prolificacy sheep (genotype FecB B+; litter size = 1; L)...
February 18, 2019: Genes
https://read.qxmd.com/read/30781724/identification-of-differentially-expressed-genes-and-pathways-for-abdominal-fat-deposition-in-ovariectomized-and-sham-operated-chickens
#3
Xiaopeng Mu, Xiaoyan Cui, Ranran Liu, Qinghe Li, Maiqing Zheng, Guiping Zhao, Changrong Ge, Jie Wen, Yaodong Hu, Huanxian Cui
Ovariectomy results in improved meat quality (growth rate, tenderness, and flavor) of broilers. However, some negative effects increased (abdominal fat (AF) deposition, low feed conversion, etc.) have also been reported. In this study, the gene expression profiles of AF tissue in ovariectomized and sham-operated chickens were determined to identify differentially expressed genes (DEGs) and pathways to explore the molecular mechanisms underlying AF accumulation. Comparing the ovariectomized group and the sham-operated group, the abdominal fat weight (AFW) and abdominal fat percentage (AFP) were increased significantly ( p < 0...
February 18, 2019: Genes
https://read.qxmd.com/read/30781719/phewas-based-systems-genetics-methods-for-anti-breast-cancer-drug-discovery
#4
LETTER
Min Gao, Yuan Quan, Xiong-Hui Zhou, Hong-Yu Zhang
Breast cancer is a high-risk disease worldwide. For such complex diseases that are induced by multiple pathogenic genes, determining how to establish an effective drug discovery strategy is a challenge. In recent years, a large amount of genetic data has accumulated, particularly in the genome-wide identification of disorder genes. However, understanding how to use these data efficiently for pathogenesis elucidation and drug discovery is still a problem because the gene⁻disease links that are identified by high-throughput techniques such as phenome-wide association studies (PheWASs) are usually too weak to have biological significance...
February 18, 2019: Genes
https://read.qxmd.com/read/30781715/genetic-epidemiology-of-breast-cancer-in-latin-america
#5
REVIEW
Valentina A Zavala, Silvia J Serrano-Gomez, Julie Dutil, Laura Fejerman
The last 10 years witnessed an acceleration of our understanding of what genetic factors underpin the risk of breast cancer. Rare high- and moderate-penetrance variants such as those in the BRCA genes account for a small proportion of the familial risk of breast cancer. Low-penetrance alleles are expected to underlie the remaining heritability. By now, there are about 180 genetic polymorphisms that are associated with risk, most of them of modest effect. In combination, they can be used to identify women at the lowest or highest ends of the risk spectrum, which might lead to more efficient cancer prevention strategies...
February 18, 2019: Genes
https://read.qxmd.com/read/30781667/origin-behaviour-and-transmission-of-b-chromosome-with-special-reference-to-plantago-lagopus
#6
REVIEW
Manoj K Dhar, Jasmeet Kour, Sanjana Kaul
B chromosomes have been reported in many eukaryotic organisms. These chromosomes occur in addition to the standard complement of a species. Bs do not pair with any of the A chromosomes and they have generally been considered to be non-essential and genetically inert. However, due to tremendous advancements in the technologies, the molecular composition of B chromosomes has been determined. The sequencing data has revealed that B chromosomes have originated from A chromosomes and they are rich in repetitive elements...
February 18, 2019: Genes
https://read.qxmd.com/read/30781664/novel-missense-mutations-in-best1-are-associated-with-bestrophinopathies-in-lebanese-patients
#7
Lama Jaffal, Wissam H Joumaa, Alexandre Assi, Charles Helou, Christel Condroyer, Maya El Dor, Georges Cherfan, Christina Zeitz, Isabelle Audo, Kazem Zibara, Said El Shamieh
To identify Bestrophin 1 ( BEST1 ) causative mutations in six Lebanese patients from three families, of whom four had a presumed clinical diagnosis of autosomal recessive bestrophinopathy (ARB) and two showed a phenotype with a single vitelliform lesion, patients were subjected to standard ophthalmic examinations. In addition, BEST1 exons and their flanking regions were amplified and sequenced by Sanger sequencing. Co-segregation and detailed bio-informatic analyses were performed. Clinical examination results were consistent with ARB diagnosis for all index patients showing multifocal vitelliform lesions and a markedly reduced light peak in the electrooculogram, including the two patients with a single vitelliform lesion...
February 18, 2019: Genes
https://read.qxmd.com/read/30781443/human-genetic-adaptation-to-high-altitude-evidence-from-the-andes
#8
REVIEW
Colleen G Julian, Lorna G Moore
Whether Andean populations are genetically adapted to high altitudes has long been of interest. Initial studies focused on physiological changes in the O₂ transport system that occur with acclimatization in newcomers and their comparison with those of long-resident Andeans. These as well as more recent studies indicate that Andeans have somewhat larger lung volumes, narrower alveolar to arterial O₂ gradients, slightly less hypoxic pulmonary vasoconstrictor response, greater uterine artery blood flow during pregnancy, and increased cardiac O2 utilization, which overall suggests greater efficiency of O₂ transfer and utilization...
February 15, 2019: Genes
https://read.qxmd.com/read/30781432/investigating-the-dna-binding-site-for-virb-a-key-transcriptional-regulator-of-shigella-virulence-genes-using-an-in-vivo-binding-tool
#9
Monika Ma Karney, Joy A McKenna, Natasha Weatherspoon-Griffin, Alexander D Karabachev, Makensie E Millar, Eliese A Potocek, Helen J Wing
The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB . Our previous in vivo studies at a different VirB-dependent promoter, icsP , found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer...
February 15, 2019: Genes
https://read.qxmd.com/read/30781418/the-role-of-the-late-embryogenesis-abundant-lea-protein-family-in-development-and-the-abiotic-stress-response-a-comprehensive-expression-analysis-of-potato-solanum-tuberosum
#10
Yongkun Chen, Canhui Li, Bo Zhang, Jing Yi, Yu Yang, Chunyan Kong, Chunxia Lei, Ming Gong
Late embryogenesis-abundant (LEA) proteins are a large and highly diverse family believed to function in normal plant growth and development, and in protecting cells from abiotic stress. This study presents a characterisation of 74 Solanum tuberosum LEA (StLEA) proteins belonging to nine groups. StLEA genes have few introns (≤2) and are distributed on all chromosomes, occurring as gene clusters on chromosomes 1, 2, and 10. All four StASR ( StLEA7 group) genes were concentrated on chromosome 4, suggesting their evolutionary conservation on one chromosome...
February 15, 2019: Genes
https://read.qxmd.com/read/30769915/population-genetic-and-functional-analysis-of-a-cis-regulatory-polymorphism-in-the-drosophila-melanogaster-metallothionein-a-gene
#11
Timothy J S Ramnarine, Amanda Glaser-Schmitt, Ana Catalán, John Parsch
Although gene expression can vary extensively within and among populations, the genetic basis of this variation and the evolutionary forces that maintain it are largely unknown. In Drosophila melanogaster , a 49-bp insertion/deletion (indel) polymorphism in the Metallothionein A ( MtnA ) gene is associated with variation in MtnA expression and oxidative stress tolerance. To better understand the functional and evolutionary significance of this polymorphism, we investigated it in several worldwide populations...
February 14, 2019: Genes
https://read.qxmd.com/read/30769913/-scdreb10-an-a-5c-type-of-dreb-gene-of-the-desert-moss-syntrichia-caninervis-confers-osmotic-and-salt-tolerances-to-arabidopsis
#12
Xiaoshuang Li, Yuqing Liang, Bei Gao, Meiheriguli Mijiti, Tohir A Bozorov, Honglan Yang, Daoyuan Zhang, Andrew J Wood
Drought and salinity are major factors limiting crop productivity worldwide. DREB (dehydration-responsive element-binding) transcription factors play important roles in plant stress response and have been identified in a wide variety of plants. Studies on DREB are focused on the A-1 ( DREB1 ) and A-2 ( DREB2 ) groups. Studies on A-5 group DREBs, which represent a large proportion of the DREB subfamily, is limited. In this study, we characterized and analyzed the stress tolerance function of ScDREB10, an A-5c type DREB gene from the desert moss Syntrichia caninervis ...
February 14, 2019: Genes
https://read.qxmd.com/read/30769908/dynamic-expression-of-interferon-lambda-regulated-genes-in-primary-fibroblasts-and-immune-organs-of-the-chicken
#13
Mehboob Arslan, Xin Yang, Diwakar Santhakumar, Xingjian Liu, Xiaoyuan Hu, Muhammad Munir, Yinü Li, Zhifang Zhang
Interferons (IFNs) are pleiotropic cytokines that establish a first line of defense against viral infections in vertebrates. Several types of IFN have been identified; however, limited information is available in poultry, especially using live animal experimental models. IFN-lambda (IFN-λ) has recently been shown to exert a significant antiviral impact against viral pathogens in mammals. In order to investigate the in vivo potential of chicken IFN-λ (chIFN-λ) as a regulator of innate immunity, and potential antiviral therapeutics, we profiled the transcriptome of chIFN-λ-stimulated chicken immune organs (in vivo) and compared it with primary chicken embryo fibroblasts (in vitro)...
February 14, 2019: Genes
https://read.qxmd.com/read/30769903/molecular-evolution-of-the-vacuolar-iron-transporter-vit-family-genes-in-14-plant-species
#14
Jun Cao
The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family...
February 14, 2019: Genes
https://read.qxmd.com/read/30769902/analysis-of-topological-parameters-of-complex-disease-genes-reveals-the-importance-of-location-in-a-biomolecular-network
#15
Xiaohui Zhao, Zhi-Ping Liu
Network biology and medicine provide unprecedented opportunities and challenges for deciphering disease mechanisms from integrative viewpoints. The disease genes and their products perform their dysfunctions via physical and biochemical interactions in the form of a molecular network. The topological parameters of these disease genes in the interactome are of prominent interest to the understanding of their functionality from a systematic perspective. In this work, we provide a systems biology analysis of the topological features of complex disease genes in an integrated biomolecular network...
February 14, 2019: Genes
https://read.qxmd.com/read/30769841/overexpression-of-stdreb2-transcription-factor-enhances-drought-stress-tolerance-in-cotton-gossypium-barbadense-l
#16
Mohamed A El-Esawi, Aisha A Alayafi
Drought stress significantly restricts plant growth and crop productivity. Cotton is the most important textile fiber and oilseed crop worldwide, and its cultivation is affected by drought stress, particularly in dry regions. Improving cotton tolerance to drought stress using the advanced genetic engineering technologies is a promising strategy to maintain crop production and fiber quality and meet the increasing worldwide fiber and oil demand. Dehydration-responsive element binding (DREB) transcription factors play a main role in regulating stresses-tolerance pathways in plant...
February 14, 2019: Genes
https://read.qxmd.com/read/30781903/n%C3%A2-methyladenosine-landscape-of-glioma-stem-like-cells-mettl3-is-essential-for-the-expression-of-actively-transcribed-genes-and-sustenance-of-the-oncogenic-signaling
#17
Abhirami Visvanathan, Vikas Patil, Shibla Abdulla, Jörg D Hoheisel, Kumaravel Somasundaram
Despite recent advances in N ⁶-methyladenosine (m⁶A) biology, the regulation of crucial RNA processing steps by the RNA methyltransferase-like 3 (METTL3) in glioma stem-like cells (GSCs) remains obscure. An integrated analysis of m⁶A-RIP (RNA immunoprecipitation) and total RNA-Seq of METTL3-silenced GSCs identified that m⁶A modification in GSCs is principally carried out by METTL3. The m⁶A-modified transcripts showed higher abundance compared to non-modified transcripts. Further, we showed that the METTL3 is essential for the expression of GSC-specific actively transcribed genes...
February 13, 2019: Genes
https://read.qxmd.com/read/30781888/a-review-of-epigenetics-of-ptsd-in-comorbid-psychiatric-conditions
#18
REVIEW
Caren J Blacker, Mark A Frye, Eva Morava, Tamas Kozicz, Marin Veldic
Post-traumatic stress disorder (PTSD) is an acquired psychiatric disorder with functionally impairing physiological and psychological symptoms following a traumatic exposure. Genetic, epigenetic, and environmental factors act together to determine both an individual's susceptibility to PTSD and its clinical phenotype. In this literature review, we briefly review the candidate genes that have been implicated in the development and severity of the PTSD phenotype. We discuss the importance of the epigenetic regulation of these candidate genes...
February 13, 2019: Genes
https://read.qxmd.com/read/30781872/an-integrative-systems-perspective-on-plant-phosphate-research
#19
REVIEW
Ishan Ajmera, T Charlie Hodgman, Chungui Lu
The case for improving crop phosphorus-use-efficiency is widely recognized. Although much is known about the molecular and regulatory mechanisms, improvements have been hampered by the extreme complexity of phosphorus (P) dynamics, which involves soil chemistry; plant-soil interactions; uptake, transport, utilization and remobilization within plants; and agricultural practices. The urgency and direction of phosphate research is also dependent upon the finite sources of P, availability of stocks to farmers and reducing environmental hazards...
February 13, 2019: Genes
https://read.qxmd.com/read/30781862/spatio-temporal-transcriptional-dynamics-of-maize-long-non-coding-rnas-responsive-to-drought-stress
#20
Junling Pang, Xia Zhang, Xuhui Ma, Jun Zhao
Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons...
February 13, 2019: Genes
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