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https://www.readbyqxmd.com/read/28812997/distribution-of-fmr1-and-fmr2-repeats-in-argentinean-patients-with-primary-ovarian-insufficiency
#1
Lucía Daniela Espeche, Violeta Chiauzzi, Ianina Ferder, Mehrnoosh Arrar, Andrea Paula Solari, Carlos David Bruque, Marisol Delea, Susana Belli, Cecilia Soledad Fernández, Noemí Delia Buzzalino, Eduardo Hernán Charreau, Liliana Beatriz Dain
The premutation state of FMR1 (Fragile X Mental Retardation 1) has been associated with primary ovarian insufficiency (POI), and is the most common known genetic cause for 46,XX patients. Nevertheless, very few studies have analyzed its frequency in Latin American populations. Additionally, a relationship between alleles carrying a cryptic microdeletion in the 5'UTR of FMR2 and the onset of POI has only been studied in one population. Our aim was to analyze the incidence of FMR1 premutations and putative microdeletions in exon 1 of FMR2 in a cohort of Argentinean women with POI...
August 16, 2017: Genes
https://www.readbyqxmd.com/read/28809811/mutation-clusters-from-cancer-exome
#2
Zura Kakushadze, Willie Yu
We apply our statistically deterministic machine learning/clustering algorithm *K-means (recently developed in https://ssrn.com/abstract=2908286) to 10,656 published exome samples for 32 cancer types. A majority of cancer types exhibit a mutation clustering structure. Our results are in-sample stable. They are also out-of-sample stable when applied to 1389 published genome samples across 14 cancer types. In contrast, we find in- and out-of-sample instabilities in cancer signatures extracted from exome samples via nonnegative matrix factorization (NMF), a computationally-costly and non-deterministic method...
August 15, 2017: Genes
https://www.readbyqxmd.com/read/28800125/large-introns-of-5-to-10-kilo-base-pairs-can-be-spliced-out-in-arabidopsis
#3
Ning Chang, Qingqing Sun, Jinglei Hu, Chuanjing An, And Hongbo Gao
Most of the eukaryotic genes contain introns, which are removed from the pre-RNA during RNA processing. In contrast to the introns in animals, which are usually several kilo base pairs (kb), those in plants generally are very small, which are mostly from dozens of base pairs (bp) to a few hundred bp. According to annotation version 10.0 of the genome of Arabidopsis thaliana, there are 127,854 introns in the nuclear genes; 99.23% of them are less than 1 kb, and only 16 introns are annotated to be larger than 5 kb, which are extremely large introns (ELI) in Arabidopsis...
August 11, 2017: Genes
https://www.readbyqxmd.com/read/28796196/two-c3h-type-zinc-finger-protein-genes-cpczf1-and-cpczf2-from-chimonanthus-praecox-affect-stamen-development-in-arabidopsis
#4
Huamin Liu, Renwei Huang, Jing Ma, Shunzhao Sui, Yulong Guo, Daofeng Liu, Zhineng Li, Yechun Lin, Mingyang Li
Wintersweet (Chimonanthus praecox) is a popular garden plant because of its flowering time, sweet fragrance, and ornamental value. However, research into the molecular mechanism that regulates flower development in wintersweet is still limited. In this study, we sought to investigate the molecular characteristics, expression patterns, and potential functions of two C3H-type zinc finger (CZF) protein genes, CpCZF1 and CpCZF2, which were isolated from the wintersweet flowers based on the flower developmental transcriptome database...
August 10, 2017: Genes
https://www.readbyqxmd.com/read/28783137/acetylation-and-methylation-related-epigenetic-proteins-in-the-context-of-their-targets
#5
REVIEW
Nasir Javaid, Sangdun Choi
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed "epigenetics". These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28783101/analysis-of-argonaute-4-associated-long-non-coding-rna-in-arabidopsis-thaliana-sheds-novel-insights-into-gene-regulation-through-rna-directed-dna-methylation
#6
Phil Chi Khang Au, Elizabeth S Dennis, Ming-Bo Wang
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28783096/c-di-amp-an-essential-molecule-in-the-signaling-pathways-that-regulate-the-viability-and-virulence-of-gram-positive-bacteria
#7
REVIEW
Tazin Fahmi, Gary C Port, Kyu Hong Cho
Signal transduction pathways enable organisms to monitor their external environment and adjust gene regulation to appropriately modify their cellular processes. Second messenger nucleotides including cyclic adenosine monophosphate (c-AMP), cyclic guanosine monophosphate (c-GMP), cyclic di-guanosine monophosphate (c-di-GMP), and cyclic di-adenosine monophosphate (c-di-AMP) play key roles in many signal transduction pathways used by prokaryotes and/or eukaryotes. Among the various second messenger nucleotides molecules, c-di-AMP was discovered recently and has since been shown to be involved in cell growth, survival, and regulation of virulence, primarily within Gram-positive bacteria...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28771200/dissecting-tissue-specific-transcriptomic-responses-from-leaf-and-roots-under-salt-stress-in-petunia-hybrida-mitchell
#8
Gonzalo H Villarino, Qiwen Hu, Michael J Scanlon, Lukas Mueller, Aureliano Bombarely, Neil S Mattson
One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affecting normal plant growth and causing agricultural losses worldwide. The advent of state-of-the-art technologies such as high throughput mRNA sequencing (RNA-seq) has revolutionized whole-transcriptome analysis by allowing, with high precision, to measure changes in gene expression...
August 3, 2017: Genes
https://www.readbyqxmd.com/read/28763026/genome-wide-analysis-reveals-extensive-changes-in-lncrnas-during-skeletal-muscle-development-in-hu-sheep
#9
Caifang Ren, Mingtian Deng, Yixuan Fan, Hua Yang, Guomin Zhang, Xu Feng, Fengzhe Li, Dan Wang, Feng Wang, Yanli Zhang
As an important type of noncoding RNA molecules, long non-coding RNAs (lncRNAs) act as versatile players in various biological processes. However, little is known about lncRNA regulators during sheep muscle growth. To explore functional lncRNAs during sheep muscle growth, we systematically investigated lncRNAs using strand-specific Ribo-Zero RNA sequencing at three key developmental stages in Hu sheep. A total of 6924 lncRNAs were obtained, and the differentially expressed lncRNAs and genes were screened from (control vs...
August 1, 2017: Genes
https://www.readbyqxmd.com/read/28763022/characterization-and-expression-profiling-of-camellia-sinensis-cinnamate-4-hydroxylase-genes-in-phenylpropanoid-pathways
#10
Jinxin Xia, Yajun Liu, Shengbo Yao, Ming Li, Mengqing Zhu, Keyi Huang, Liping Gao, Tao Xia
Cinnamate 4-hydroxylase (C4H), a cytochrome P450-dependent monooxygenase, participates in the synthesis of numerous polyphenoid compounds, such as flavonoids and lignins. However, the C4H gene number and function in tea plants are not clear. We screened all available transcriptome and genome databases of tea plants and three C4H genes were identified and named CsC4Ha, CsC4Hb, and CsC4Hc, respectively. Both CsC4Ha and CsC4Hb have 1518-bp open reading frames that encode 505-amino acid proteins. CsC4Hc has a 1635-bp open reading frame that encodes a 544-amino acid protein...
August 1, 2017: Genes
https://www.readbyqxmd.com/read/28763006/proteins-recognizing-dna-structural-uniqueness-and-versatility-of-dna-binding-domains-in-stem-cell-transcription-factors
#11
REVIEW
Dhanusha Yesudhas, Maria Batool, Muhammad Ayaz Anwar, Suresh Panneerselvam, Sangdun Choi
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation...
August 1, 2017: Genes
https://www.readbyqxmd.com/read/28737709/regulation-and-modulation-of-human-dna-polymerase-%C3%AE-activity-and-function
#12
REVIEW
Marietta Y W T Lee, Xiaoxiao Wang, Sufang Zhang, Zhongtao Zhang, Ernest Y C Lee
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair...
July 24, 2017: Genes
https://www.readbyqxmd.com/read/28754007/developmental-expression-of-hsp60-and-hsp10-in-the-coilia-nasus-testis-during-upstream-spawning-migration
#13
Di-An Fang, Yan-Feng Zhou, Min-Ying Zhang, Dong-Po Xu, Kai Liu, Jin-Rong Duan
Heat shock protein 60 (HSP60) and heat shock protein 10 (HSP10) are important chaperones, which have been proven to have essential roles in mediating the correct folding of nuclear encoded proteins imported to mitochondria. Mitochondria are known as the power house of the cell, with which it produces energy and respires aerobically. In this regard, the obtained HSP60 and HSP10 have typical characteristics of the HSP60/10 family signature. Their mRNA transcripts detected were highest during the developmental phase (in April), while the lowest levels were found in the resting phase (after spawning in late July)...
July 21, 2017: Genes
https://www.readbyqxmd.com/read/28753996/boron-tolerance-in-aspergillus-nidulans-is-sustained-by-the-slta-pathway-through-the-slc-family-transporters-sbta-and-sbtb
#14
María Villarino, Oier Etxebeste, Gorka Mendizabal, Aitor Garzia, Unai Ugalde, Eduardo A Espeso
Microbial cells interact with the environment by adapting to external changes. Signal transduction pathways participate in both sensing and responding in the form of modification of gene expression patterns, enabling cell survival. The filamentous fungal-specific SltA pathway regulates tolerance to alkalinity, elevated cation concentrations and, as shown in this work, also stress conditions induced by borates. Growth of sltA(-) mutants is inhibited by increasing millimolar concentrations of boric acid or borax (sodium tetraborate)...
July 21, 2017: Genes
https://www.readbyqxmd.com/read/28753988/evolutionary-significance-of-wolbachia-to-animal-horizontal-gene-transfer-female-sex-determination-and-the-f-element-in-the-isopod-armadillidium-vulgare
#15
REVIEW
Richard Cordaux, Clément Gilbert
An increasing number of horizontal gene transfer (HGT) events from bacteria to animals have been reported in the past years, many of which involve Wolbachia bacterial endosymbionts and their invertebrate hosts. Most transferred Wolbachia genes are neutrally-evolving fossils embedded in host genomes. A remarkable case of Wolbachia HGT for which a clear evolutionary significance has been demonstrated is the "f element", a nuclear Wolbachia insert involved in female sex determination in the terrestrial isopod Armadillidium vulgare...
July 21, 2017: Genes
https://www.readbyqxmd.com/read/28753983/outcome-of-full-thickness-macular-hole-surgery-in-choroideremia
#16
Mays Talib, Leonoor S Koetsier, Robert E MacLaren, Camiel J F Boon
The development of a macular hole is relatively common in retinal dystrophies eligible for gene therapy such as choroideremia. However, the subretinal delivery of gene therapy requires an uninterrupted retina to allow dispersion of the viral vector. A macular hole may thus hinder effective gene therapy. Little is known about the outcome of macular hole surgery and its possible beneficial and/or adverse effects on retinal function in patients with choroideremia. We describe a case of a unilateral full-thickness macular hole (FTMH) in a 45year-old choroideremia patient (c...
July 21, 2017: Genes
https://www.readbyqxmd.com/read/28726763/cloning-and-characterization-of-thshrs-and-thscr-transcription-factors-in-taxodium-hybrid-zhongshanshan-406
#17
Zhiquan Wang, Yunlong Yin, Jianfeng Hua, Wencai Fan, Chaoguang Yu, Lei Xuan, Fangyuan Yu
Among the GRAS family of transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR) are key regulators of the formation of root tissues. In this study, we isolated and characterized two genes encoding SHR proteins and one gene encoding an SCR protein: ThSHR1 (Accession Number MF045148), ThSHR2 (Accession Number MF045149) and ThSCR (Accession Number MF045152) in the adventitious roots of Taxodium hybrid 'Zhongshanshan'. Gene structure analysis indicated that ThSHR1, ThSHR2 and ThSCR are all intron free. Multiple protein sequence alignments showed that each of the corresponding proteins, ThSHR1, ThSHR2 and ThSCR, contained five well-conserved domains: leucine heptad repeat I (LHRI), the VHIID motif, leucine heptad repeat II (LHR II), the PFYRE motif, and the SAW motif...
July 20, 2017: Genes
https://www.readbyqxmd.com/read/28726715/overexpression-of-the-osimp-gene-increases-the-accumulation-of-inositol-and-confers-enhanced-cold-tolerance-in-tobacco-through-modulation-of-the-antioxidant-enzymes-activities
#18
Rong-Xiang Zhang, Li-Jun Qin, De-Gang Zhao
Inositol is a cyclic polyol that is involved in various physiological processes, including signal transduction and stress adaptation in plants. l-myo-inositol monophosphatase (IMPase) is one of the metal-dependent phosphatase family members and catalyzes the last reaction step of biosynthesis of inositol. Although increased IMPase activity induced by abiotic stress has been reported in chickpea plants, the role and regulation of the IMP gene in rice (Oryza sativa L.) remains poorly understood. In the present work, we obtained a full-length cDNA sequence coding IMPase in the cold tolerant rice landraces in Gaogonggui, which is named as OsIMP...
July 20, 2017: Genes
https://www.readbyqxmd.com/read/28718817/time-to-spread-your-wings-a-review-of-the-avian-ancient-dna-field
#19
REVIEW
Alicia Grealy, Nicolas J Rawlence, Michael Bunce
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of "avian ancient DNA" by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions...
July 18, 2017: Genes
https://www.readbyqxmd.com/read/28714907/genetic-contribution-to-alcohol-dependence-investigation-of-a-heterogeneous-german-sample-of-individuals-with-alcohol-dependence-chronic-alcoholic-pancreatitis-and-alcohol-related-cirrhosis
#20
Jens Treutlein, Josef Frank, Fabian Streit, Céline S Reinbold, Dilafruz Juraeva, Franziska Degenhardt, Liz Rietschel, Stephanie H Witt, Andreas J Forstner, Monika Ridinger, Jana Strohmaier, Norbert Wodarz, Helene Dukal, Jerome C Foo, Per Hoffmann, Stefan Herms, Stefanie Heilmann-Heimbach, Michael Soyka, Wolfgang Maier, Wolfgang Gaebel, Norbert Dahmen, Norbert Scherbaum, Bertram Müller-Myhsok, Susanne Lucae, Marcus Ising, Felix Stickel, Thomas Berg, Ulla Roggenbuck, Karl-Heinz Jöckel, Henrike Scholz, Ulrich S Zimmermann, Stephan Buch, Wolfgang H Sommer, Rainer Spanagel, Benedikt Brors, Sven Cichon, Karl Mann, Falk Kiefer, Jochen Hampe, Jonas Rosendahl, Markus M Nöthen, Marcella Rietschel
The present study investigated the genetic contribution to alcohol dependence (AD) using genome-wide association data from three German samples. These comprised patients with: (i) AD; (ii) chronic alcoholic pancreatitis (ACP); and (iii) alcohol-related liver cirrhosis (ALC). Single marker, gene-based, and pathway analyses were conducted. A significant association was detected for the ADH1B locus in a gene-based approach (puncorrected = 1.2 × 10(-6); pcorrected = 0.020). This was driven by the AD subsample...
July 17, 2017: Genes
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