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Genes and genomes

Chong Zhao, Jingyun Ding, Mingfang Yang, Dongtao Shi, Donghong Yin, Fangyuan Hu, Jiangnan Sun, Xiaomei Chi, Lingling Zhang, Yaqing Chang
Although the potential link exists between behavioral responses to UV-B radiation and the maximization of fitness, molecular mechanisms of these UV-B induced behaviors remain poorly understood. For the first time, we investigated the transcriptomes of covered (CB), sheltered (SB) and non-protected (NA) sea urchins Strongylocentrotus intermedius exposed to UV-B radiation. A total of 330 differentially expressed genes were revealed by transcriptome comparisons. By comparing with the group NA, we found 79 up-regulated and 118 down-regulated genes in SB group, as well as 26 up-regulated and 67 down-regulated genes in group CB...
October 17, 2018: Ecotoxicology and Environmental Safety
Katsuhiro Matsui, Takuya Tomatsu, Saeka Kinouchi, Tatsuro Suzuki, Takeshi Sato
Anthocyanins are a group of flavonoids found in buckwheat (Fagopyrum esculentum) and many other plant species; however; little is known about their mechanisms of synthesis and regulation in buckwheat. We previously reported a spontaneous mutant buckwheat line that shows the green stem phenotype; this line does not accumulate anthocyanins but synthesizes flavonol and proanthocyanidin in the stem. Here, we used this line and lines developed by this line to search for genes related to anthocyanin accumulation in buckwheat...
October 6, 2018: Journal of Plant Physiology
Jared M Andrews, Jacqueline E Payton
Normal B cell development, activation, and terminal differentiation depend on the intricate dynamics of cooperating epigenetic and non-coding components to control the level and timing of expression of thousands of genes. Recent genome-wide studies have integratively mapped changes in the chromatin landscape, DNA methylome, 3-dimensional interactome, and coding and non-coding transcriptomes of normal and malignant B cells. Genetic ablation in human cells and mouse models has begun to elucidate the coordinated roles of essential epigenetic modifiers, key transcription factors, and long non-coding RNAs in B cell biology...
October 17, 2018: Current Opinion in Immunology
Quan-You Lu, Lei Yang, Jinshan Huang, Luping Zheng, Xin Sun
Mulberry crinkle leaf virus (MCLV) is a novel geminivirus recently identified from the woody plant mulberry (Morus alba L.). Little is known about the functions of the proteins encoded by the MCLV genome. Here, all the MCLV-encoded proteins were examined for the ability to suppress gene silencing by an agroinfiltration assay in combination with northern blot analysis of green fluorescent protein (GFP) mRNA and western blot analysis. Of the six proteins, only one protein, V3, which has been predicted to play a role in viral movement, was found to suppress the gene silencing induced by a sense GFP gene in Nicotiana benthamiana 16c...
October 17, 2018: Virology
Chuanju Dong, Shengnan Kong, Xianhu Zheng, Jiangfan Zhang, Guoxing Nie, Xuejun Li, Peng Xu
Interleukin-17 (IL17) family cytokines are well known for having pro-inflammatory actions as important mediators of mucosal immune responses and are tightly regulated by various kinds of signals. However, most studies of IL17 genes have focused on mammals, and much less is known about IL17 genes in fish species. To better understand the scope and actions of the IL17 gene family in common carp, we characterized seven IL17 gene homologs from genomic and transcriptomic databases that could be classified into three subclasses according to different comparative genomic analyses...
October 17, 2018: Gene
Romina S Petrigh, María M Cafrune, Martín H Fugassa
Lamanema chavezi (Family Molineidae) is a parasitic nematode of South American camelids (SACs). A few studies have reported this parasite in SACs, mainly in domestic camelid species (llama and alpaca). Parasite identification by means of copro-parasitological methods is non-invasive and allows performing epidemiological studies. However, egg misidentification and difficulty to culture third-stage larvae do not allow identifying nematodes to species level. In contrast, molecular tools allow identifying eggs of gastrointestinal nematodes more accurately...
October 17, 2018: Parasitology International
Anna Aghajanyan, Aleksandra Fucic, Leila Tskhovrebova, Olga Gigani, Pasko Konjevoda
Ehlers-Danlos syndrome (EDS) is a heritable connective tissue disorder characterized by skin hyperextensibility, abnormal wound healing, and joint hypermobility with prevalence 1:20 000. Its incidence is probably underestimated due to unknown number of subjects having mild symptoms who may have never been diagnosed through entire life time. Classical EDS is characterized by pathogenic variants of genes encoding type V collagen. The biological effects and health risks of patients with EDS exposure to low doses of ionizing radiation is poorly understood...
October 17, 2018: European Journal of Medical Genetics
Chi Song, Yifei Liu, Aiping Song, Gangqiang Dong, Hongbo Zhao, Wei Sun, Shyam Ramakrishnan, Ying Wang, Shuaibin Wang, Tingzhao Li, Yan Niu, Jiafu Jiang, Bin Dong, Ye Xia, Sumei Chen, Zhigang Hu, Fadi Chen, Shilin Chen
The Asteraceae (Compositae), a large plant family of approximately 24,000-35,000 species that strongly contributes to plant diversity, accounts for ∼10% of all angiosperm species. Its most representative members are the economically important chrysanthemums (Chrysanthemum L.) that were diversified by reticulate evolution. Biodiversity is typically created by multiple evolutionary mechanisms such as whole-genome duplications (WGDs) or polyploidizations and locally repetitive genome expansion. However, the lack of genomic chrysanthemum data prevents an in-depth analysis of the evolutionary mechanisms involved in chrysanthemum diversification...
October 17, 2018: Molecular Plant
Weijie Zhang, Zhimeng Lv, Chenghua Li, Yahui Sun, Huijie Jiang, Manxi Zhao, Xuelin Zhao, Yina Shao, Yaqing Chang
Spotting disease is a common disease in the process of aquaculture and restocking of the sea urchin Strongylocentrotus intermedius and leads to mass mortality. To characterize the molecular processes and candidate genes related to spotting disease in S. intermedius, we conducted next-generation sequencing to assess the key genes/pathways in spotting diseased sea urchin (DUG) compared to healthy ones (HUG). A total of 321.1 million clean reads were obtained and assembled into 93,877 Unigenes with an N50 of 1185 bp, in which 86...
October 17, 2018: Fish & Shellfish Immunology
Benjamin L S Furman, Utkarsh J Dang, Ben J Evans, G Brian Golding
Whole genome duplication (WGD), the doubling of the nuclear DNA of a species, contributes to biological innovation by creating ge-netic redundancy. One mode of WGD is allopolyploidization, wherein each genome from two ancestral species becomes a 'subgenome' of a polyploid descendant species. The evolutionary trajectory of a dupli-cated gene that arises from WGD is influenced both by natural selec-tion, that may favour redundant, new, or partitioned functions, and by gene silencing (pseudogenization). Here, we explored how these two phenomena varied over time and within allopolyploid genomes in several allotetraploid clawed frog species (Xenopus)...
October 20, 2018: Journal of Evolutionary Biology
Lisa-Marie Niestroj, Juanjiangmeng Du, Michael Nothnagel, Patrick May, Aarno Palotie, Mark J Daly, Peter Nürnberg, Ingmar Blümcke, Dennis Lal
OBJECTIVE: Increasing availability of surgically resected brain tissue from patients with focal epilepsy and focal cortical dysplasia or low-grade glioneuronal tumors has fostered large-scale genetic examination. However, assessment of pathogenicity of germ line and somatic variants remains difficult. Here, we present a state-of-the-art evaluation of reported genes and variants associated with epileptic brain lesions. METHODS: We critically reevaluated the pathogenicity for all neuropathology-associated variants reported to date in the PubMed and ClinVar databases, including 101 neuropathology-associated missense variants encompassing 11 disease-related genes...
October 20, 2018: Epilepsia
Zhongju Shi, Guangzhi Ning, Bin Zhang, Shiyang Yuan, Hengxing Zhou, Bin Pan, Jiahe Li, Zhijian Wei, Fujiang Cao, Xiaohong Kong, Shiqing Feng
Spinal cord injury (SCI) is a highly severe disease and it can lead to the destruction of the motor and sensory function resulting in temporary or permanent disability. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt that play a critical role in central nervous system (CNS) injury. However, the exact roles of lncRNAs and messenger RNAs (mRNAs) in the early acute phase of SCI remain to be elucidated. We examined the expression of mRNAs and lncRNAs in a rat model at 2 days after SCI and identified the differentially expressed lncRNAs (DE lncRNAs) and differentially expressed mRNAs (DE mRNAs) using microarray analysis...
October 20, 2018: Journal of Cellular Physiology
Arash Salmaninejad, Mohammad Reza Zamani, Arezoo Gowhari Shabgah, Seyedmojtaba Hosseini, Fatemeh Mollaei, Nayyerehalsadat Hosseini, Amirhossein Sahebkar
Behçet's disease (BD) is a chronic and rare multisystemic disorder defined by autoimmunity and inflammatory characteristics, manifested by ocular lesions, recurrent genital and oral ulcers, skin symptoms and arthritis as well as neurological, intestinal, and vascular involvement. Despite the unknown cause of BD, there is some strong documentation for immunological, genetic, environmental, and infectious factors playing a role in the pathogenesis of BD. While the nature of the genetic variants remains unidentified, many genetic risk factors are considered to contribute to BD susceptibility...
October 20, 2018: Journal of Cellular Physiology
Juliana Arid, Daniela B Oliveira, Silvane S Evangelista, Katia R F Vasconcelos, André L T Dutra, Sara S de Oliveira, Alexandra M de Queiroz, Paulo Nelson-Filho, Alexandre R Vieira, Erika C Küchler
BACKGROUND: Oestrogen (ES) and growth hormone (GH) are hormones that may have a role in caries aetiology and developmental defects of enamel (DDE) since their receptors (ERs and GHR) are expressed during amelogenesis. AIM: To evaluate whether genetic polymorphisms in the genes that codify the ERα (ESR1) and GHR are associated with caries experience and DDE in children. DESIGN: Two hundred and sixteen children of both genders, aged 9-12 years, were examined and classified according to caries and DDE phenotype...
October 20, 2018: International Journal of Paediatric Dentistry
Ga Hun Boo, Jeffery R Hughey
Molecular surveys are leading to the discovery of many new cryptic species of marine algae. This is particularly true for red algal intertidal species, which exhibit a high degree of morphological convergence. DNA sequencing of recent collections of Gelidium along the coast of California, USA, identified two morphologically similar entities that differed in DNA sequence from existing species. To characterize the two new species of Gelidium and to determine their evolutionary relationships to other known taxa, phylogenomic, multigene analyses, and morphological observations were performed...
October 19, 2018: Journal of Phycology
Min Liu, Siying Zhou, Jinyan Wang, Qian Zhang, Sujin Yang, Jifeng Feng, Bin Xu, Shanliang Zhong
BACKGROUND: We aimed to investigate the potential of microRNA expression profiles to predict survival in breast cancer. METHODS: MicroRNA and mRNA expression data of breast cancer were downloaded from The Cancer Genome Atlas. LASSO regression was used to identify microRNAs signature predicting survival of breast cancer patients. Transfection experiment was conducted to explore the influence of microRNAs on their potential targets. RESULTS: We identified 56 differentially expressed microRNAs in breast cancer tissues compared to adjacent normal tissues...
October 19, 2018: Breast Cancer: the Journal of the Japanese Breast Cancer Society
Samantha LoRusso, Benjamin Weiner, W David Arnold
Myotonic dystrophy is an autosomal dominant muscular dystrophy not only associated with muscle weakness, atrophy, and myotonia but also prominent multisystem involvement. There are 2 similar, but distinct, forms of myotonic dystrophy; type 1 is caused by a CTG repeat expansion in the DMPK gene, and type 2 is caused by a CCTG repeat expansion in the CNBP gene. Type 1 is associated with distal limb, neck flexor, and bulbar weakness and results in different phenotypic subtypes with variable onset from congenital to very late-onset as well as variable signs and symptoms...
October 18, 2018: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
Jan Bettgenhaeuser, Simon G Krattinger
The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops. The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large resequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives...
October 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Wanlong Li, Qijun Zhang, Shuwen Wang, Marie A Langham, Dilkaran Singh, Robert L Bowden, Steven S Xu
Development of a complete wheat-Thinopyrum junceiforme amphiploid facilitated identification of resistance to multiple pests and abiotic stress derived from the wild species and shed new light on its genome composition. Wheat production is facing numerous challenges from biotic and abiotic stresses. Alien gene transfer has been an effective approach for wheat germplasm enhancement. Thinopyrum junceiforme, also known as sea wheatgrass (SWG), is a distant relative of wheat and a relatively untapped source for wheat improvement...
October 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Linhong Teng, Xiao Fan, David R Nelson, Wentao Han, Xiaowen Zhang, Dong Xu, Hugues Renault, Gabriel V Markov, Naihao Ye
Comparative genomic analysis of cytochromes P450 revealed high diversification and dynamic changes in stramenopiles, associated with transcriptional responsiveness to various environmental stimuli. Comparative genomic and molecular evolution approaches were used to characterize cytochromes P450 (P450) diversity in stramenopiles. Phylogenetic analysis pointed to a high diversity of P450 in stramenopiles and identified three major clans. The CYP51 and CYP97 clans were present in brown algae, diatoms and Nannochloropsis gaditana, whereas the CYP5014 clan mainly includes oomycetes...
October 19, 2018: Planta
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