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https://www.readbyqxmd.com/read/30551666/a-to-i-rna-editing-affects-lncrnas-expression-after-heat-shock
#1
Roni Haas, Nabeel S Ganem, Ayya Keshet, Angela Orlov, Alla Fishman, Ayelet T Lamm
Adenosine to inosine (A-to-I) RNA editing is a highly conserved regulatory process carried out by adenosine-deaminases (ADARs) on double-stranded RNA (dsRNAs). Although a considerable fraction of the transcriptome is edited, the function of most editing sites is unknown. Previous studies indicate changes in A-to-I RNA editing frequencies following exposure to several stress types. However, the overall effect of stress on the expression of ADAR targets is not fully understood. Here, we performed high-throughput RNA sequencing of wild-type and ADAR mutant Caenorhabditis elegans worms after heat-shock to analyze the effect of heat-shock stress on the expression pattern of genes...
December 13, 2018: Genes
https://www.readbyqxmd.com/read/30550887/lncrna-pms2l2-protects-atdc5-chondrocytes-against-lipopolysaccharide-induced-inflammatory-injury-by-sponging-mir-203
#2
Xiaoyan Li, Manqiu Yu, Lei Chen, Taitao Sun, Haibin Wang, Liang Zhao, Qiang Zhao
AIMS: PMS1 Homolog 2, Mismatch Repair System Component Pseudogene 2 (PMS2L2) has been reported as an up-regulated long non-coding RNA (lncRNA) in osteoarthritis (OA) tissues. The purpose of the present work is to explore whether the differently expressed PMS2L2 is associated with the pathogenesis of OA. MAIN METHODS: Chondrogenic ATDC5 cells were exposed to various doses of lipopolysaccharide (LPS). The expression of PMS2L2, miR-203, and MCL-1 in cell was altered by transfection...
December 11, 2018: Life Sciences
https://www.readbyqxmd.com/read/30544644/dna-damage-tolerance-mechanisms-revealed-from-the-analysis-of-immunoglobulin-v-gene-diversification-in-avian-dt40-cells
#3
REVIEW
Takuya Abe, Dana Branzei, Kouji Hirota
DNA replication is an essential biochemical reaction in dividing cells that frequently stalls at damaged sites. Homologous/homeologous recombination (HR)-mediated template switch and translesion DNA synthesis (TLS)-mediated bypass processes release arrested DNA replication forks. These mechanisms are pivotal for replication fork maintenance and play critical roles in DNA damage tolerance (DDT) and gap-filling. The avian DT40 B lymphocyte cell line provides an opportunity to examine HR-mediated template switch and TLS triggered by abasic sites by sequencing the constitutively diversifying immunoglobulin light-chain variable gene ( IgV )...
December 7, 2018: Genes
https://www.readbyqxmd.com/read/30537259/an-updated-gene-atlas-for-maize-reveals-organ-specific-and-stress-induced-genes
#4
Genevieve M Hoopes, John P Hamilton, Joshua C Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J Provart, C Robin Buell
Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36,207 expressed genes...
December 7, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/30537129/competing-endogenous-rna-cerna-cross-talk-and-language-in-cerna-regulatory-networks-a-new-look-at-hallmarks-of-breast-cancer
#5
REVIEW
Rasoul Abdollahzadeh, Abdolreza Daraei, Yaser Mansoori, Masoumeh Sepahvand, Mahsa M Amoli, Javad Tavakkoly-Bazzaz
Breast cancer (BC) is the most frequently occurring malignancy in women worldwide. Despite the substantial advancement in understanding the molecular mechanisms and management of BC, it remains the leading cause of cancer death in women. One of the main reasons for this obstacle is that we have not been able to find the Achilles heel for the BC as a highly heterogeneous disease. Accumulating evidence has revealed that noncoding RNAs (ncRNAs), play key roles in the development of BC; however, the involving of complex regulatory interactions between the different varieties of ncRNAs in the development of this cancer has been poorly understood...
December 10, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/30536583/accelerated-pseudogenization-of-trace-amine-associated-receptor-genes-in-primates
#6
S Eyun
Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine-associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus therian mammals have a high number of TAAR genes due to rapid species-specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals...
December 10, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/30532529/identification-of-novel-candidate-genes-involved-in-the-progression-of-emphysema-by-bioinformatic-methods
#7
Wei-Ping Hu, Ying-Ying Zeng, Yi-Hui Zuo, Jing Zhang
Purpose: By reanalyzing the gene expression profile GSE76925 in the Gene Expression Omnibus database using bioinformatic methods, we attempted to identify novel candidate genes promoting the development of emphysema in patients with COPD. Patients and methods: According to the Quantitative CT data in GSE76925, patients were divided into mild emphysema group (%LAA-950<20%, n=12) and severe emphysema group (%LAA-950>50%, n=11). Differentially expressed genes (DEGs) were identified using Agilent GeneSpring GX v11...
2018: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/30531937/ndufv2-pseudogene-ndufv2p1-contributes-to-mitochondrial-complex-i-deficits-in-schizophrenia
#8
Oded Bergman, Rachel Karry, Jumana Milhem, Dorit Ben-Shachar
Mitochondria together with other cellular components maintain a constant crosstalk, modulating transcriptional and posttranslational processes. We and others demonstrated mitochondrial multifaceted dysfunction in schizophrenia, with aberrant complex I (CoI) as a major cause. Here we show deficits in CoI activity and homeostasis in schizophrenia-derived cell lines. Focusing on a core CoI subunit, NDUFV2, one of the most severely affected subunits in schizophrenia, we observed reduced protein level and functioning, with no change in mRNA transcripts...
December 10, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/30512185/b7h6-is-a-functional-ligand-for-nkp30-in-rat-and-cattle-and-determines-nkp30-reactivity-towards-human-cancer-cell-lines
#9
Elisabeth G Bjørnsen, Lavanya Thiruchelvam-Kyle, Sigurd E Hoelsbrekken, Camilla Henden, Per C Saether, Preben Boysen, Michael R Daws, Erik Dissen
NK cells kill cancer cells and infected cells upon activation by cell surface receptors. Human NKp30 is an activating receptor expressed by all mature NK cells. The B7 family member B7H6 has been identified as one ligand for NKp30. Several alternative ligands have also been reported, and the field remains unsettled. To this end, we have identified full-length functional B7H6 orthologs in rat and cattle, demonstrated by phylogenetic analysis and transfection experiments. In cell-cell contact-dependent assays, chimeric NKp30 reporter cells responded strongly to B7H6 in rat and cattle...
December 4, 2018: European Journal of Immunology
https://www.readbyqxmd.com/read/30512036/-tripsacum-de-novo-transcriptome-assemblies-reveal-parallel-gene-evolution-with-maize-after-ancient-polyploidy
#10
Christine M Gault, Karl A Kremling, Edward S Buckler
Plant genomes reduce in size following a whole-genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize ( L.) and its sister genus, , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for exist, it is unknown whether grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high-quality de novo transcriptome assemblies for two species: (L...
November 2018: Plant Genome
https://www.readbyqxmd.com/read/30486770/genomic-insights-into-virulence-mechanisms-of-leishmania-donovani-evidence-from-an-atypical-strain
#11
Sumudu R Samarasinghe, Nilakshi Samaranayake, Udeshika L Kariyawasam, Yamuna D Siriwardana, Hideo Imamura, Nadira D Karunaweera
BACKGROUND: Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clinical phenotypes remains poorly understood. We present a genomic comparison of an atypical variant of Leishmania donovani from a South Asian focus, where it mostly causes cutaneous form of leishmaniasis...
November 28, 2018: BMC Genomics
https://www.readbyqxmd.com/read/30482145/pseudogenes-as-functionally-significant-elements-of-the-genome
#12
REVIEW
T F Kovalenko, L I Patrushev
Pseudogene is a gene copy that has lost its original function. For a long time, pseudogenes have been considered as "junk DNA" that inevitably arises as a result of ongoing evolutionary process. However, experimental data obtained during recent years indicate this understanding of the nature of pseudogenes is not entirely correct, and many pseudogenes perform important genetic functions. In the review, we have addressed classification of pseudogenes, methods of their detection in the genome, and the problem of their evolutionary conservatism and prevalence among species belonging to different taxonomic groups in the light of modern data...
November 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/30476305/lncactdb-2-0-an-updated-database-of-experimentally-supported-cerna-interactions-curated-from-low-and-high-throughput-experiments
#13
Peng Wang, Xin Li, Yue Gao, Qiuyan Guo, Yanxia Wang, Ying Fang, Xueyan Ma, Hui Zhi, Dianshuang Zhou, Weitao Shen, Weisha Liu, Lihua Wang, Yunpeng Zhang, Shangwei Ning, Xia Li
We describe LncACTdb 2.0 (http://www.bio-bigdata.net/LncACTdb/), an updated and significantly expanded database which provides comprehensive information of competing endogenous RNAs (ceRNAs) in different species and diseases. We have updated LncACTdb 2.0 with more data and several new features, including (i) manually curating 2663 experimentally supported ceRNA interactions from >5000 published literatures; (ii) expanding the scope of the database up to 23 species and 213 diseases/phenotypes; (iii) curating more ceRNA types such as circular RNAs and pseudogenes; (iv) identifying and scoring candidate lncRNA-associated ceRNA interactions across 33 cancer types from TCGA data; (v) providing illustration of survival, network and cancer hallmark information for ceRNAs...
November 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30476197/as-blind-as-a-bat-opsin-phylogenetics-illuminates-the-evolution-of-color-vision-in-bats
#14
Bruno F Simões, Nicole M Foley, Graham M Hughes, Huabin Zhao, Shuyi Zhang, Stephen J Rossiter, Emma C Teeling
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. While several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of colour vision in bats...
November 23, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30472000/pseudogenization-and-resurrection-of-a-speciation-gene
#15
Korinna Esfeld, Andrea E Berardi, Michel Moser, Eligio Bossolini, Loreta Freitas, Cris Kuhlemeier
A persistent question in evolutionary biology is how complex phenotypes evolve and whether phenotypic transitions are reversible. Multiple losses of floral pigmentation have been documented in the angiosperms, but color re-gain has not yet been described, supporting that re-gain is unlikely. Pollinator-mediated selection in Petunia has resulted in several color shifts comprised of both losses and gains of color. The R2R3-MYB transcription factor AN2 has been identified as a major locus responsible for shifts in pollinator preference...
November 9, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/30470980/approach-to-molecular-diagnosis-of-chronic-granulomatous-disease-cgd-an-experience-from-a-large-cohort-of-90-indian-patients
#16
Manasi Kulkarni, Gouri Hule, Martin de Boer, Karin van Leeuwen, Priyanka Kambli, Jahnavi Aluri, Maya Gupta, Aparna Dalvi, Snehal Mhatre, Prasad Taur, Mukesh Desai, Manisha Madkaikar
BACKGROUND: Chronic granulomatous disease (CGD) is characterized by mutation in any one of the five genes coding NADPH oxidase components that leads to functional abnormality preventing the killing of phagocytosed microbes by affecting the progression of a respiratory burst. CGD patients have an increased susceptibility to infections by opportunistic and pathogenic organisms. Though initial diagnosis of CGD using a nitroblue tetrazolium (NBT) test or dihydrorhodamine (DHR) test is relatively easy, molecular diagnosis is challenging due to involvement of multiple genes, presence of pseudogenes, large deletions, and GC-rich regions, among other factors...
November 23, 2018: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/30463509/towards-reducing-the-immunogenic-potential-of-wheat-flour-omega-gliadins-encoded-by-the-d-genome-of-hexaploid-wheat-may-also-harbor-epitopes-for-the-serious-food-allergy-wdeia
#17
Susan B Altenbach, Han-Chang Chang, Annamaria Simon-Buss, You-Ran Jang, Sandra Denery-Papini, Florence Pineau, Yong Q Gu, Naxin Huo, Sun-Hyung Lim, Chon-Sik Kang, Jong-Yeol Lee
BACKGROUND: Omega-5 gliadins are a group of highly repetitive gluten proteins in wheat flour encoded on the 1B chromosome of hexaploid wheat. These proteins are the major sensitizing allergens in a severe form of food allergy called wheat-dependent exercise-induced anaphylaxis (WDEIA). The elimination of omega-5 gliadins from wheat flour through biotechnology or breeding approaches could reduce the immunogenic potential and adverse health effects of the flour. RESULTS: A mutant line missing low-molecular weight glutenin subunits encoded at the Glu-B3 locus was selected previously from a doubled haploid population generated from two Korean wheat cultivars...
November 21, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/30462520/role-of-n-glycosylation-in-the-expression-of-human-slc26a2-and-a3-anion-transport-membrane-glycoproteins
#18
Chloe L Rapp, Jing Li, Katherine E Badior, David B Williams, Joseph R Casey, Reinhart A F Reithmeier
The human solute carrier 26 (SLC26) gene family of anion transporters consists of 10 members (SLC26A1-A11, A10 being a pseudogene) that encode membrane glycoproteins with 14 transmembrane (TM) segments and a C-terminal cytoplasmic sulfate transporter anti-sigma antagonist (STAS) domain. Thus far, mutations in eight members of the SLC26 family (A1 - A6, A8 and A9) have been linked to diseases in humans. Our goal is to characterize the role of N-glycosylation and the effect of mutations in SLC26A2 and A3 proteins on their functional expression in transfected HEK-293 cells...
November 21, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/30460733/new-member-of-gromochytriales-chytridiomycetes-apiochytrium-granulosporum-nov-gen-et-sp
#19
Sergey A Karpov, David Moreira, Maria A Mamkaeva, Olga V Popova, Vladimir V Aleoshin, Purificación López-García
Molecular phylogenetic analysis of 18S rRNA gene sequences of nearly any species of Chytridiomycota has typically challenged traditional classification and triggered taxonomic revision. This has often led to the establishment of new taxa which, normally, appear well supported by zoospore ultrastructure, which provides diagnostic characters. To construct a meaningful and comprehensive classification of Chytridiomycota, the combination of molecular phylogenies and morphological studies of traditionally defined chytrid species is needed...
November 20, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/30458858/mitochondrial-genomes-of-two-diplectanids-platyhelminthes-monogenea-expose-paraphyly-of-the-order-dactylogyridea-and-extensive-trna-gene-rearrangements
#20
Dong Zhang, Wen X Li, Hong Zou, Shan G Wu, Ming Li, Ivan Jakovlić, Jin Zhang, Rong Chen, Gui T Wang
BACKGROUND: Recent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae...
November 20, 2018: Parasites & Vectors
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