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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/30406402/intensive-targeting-of-regulatory-competence-genes-by-transposable-elements-in-streptococci
#1
Maud Fléchard, Céline Lucchetti-Miganeh, Bernard Hallet, Pascal Hols, Philippe Gilot
Competence for natural transformation is a widespread developmental process of streptococci. By allowing the uptake and recombination of exogenous naked DNA into the genome, natural transformation, as transposable elements, plays a key role in the plasticity of bacterial genomes. We previously analysed the insertion sites of IS1548, an insertion sequence present in Streptococcus agalactiae and S. pyogenes, and showed that some targeted loci are involved in competence induction. In this work, we investigated on a large scale if loci coding for early competence factors (ComX and the two pheromone-dependent signalling systems ComCDE and ComRS) of streptococci are especially targeted by transposable elements...
November 7, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30382349/evidence-of-the-functional-role-of-the-ethylene-receptor-genes-sletr4-and-sletr5-in-ethylene-signal-transduction-in-tomato
#2
Syariful Mubarok, Ken Hoshikawa, Yoshihiro Okabe, Ryoichi Yano, Matthew Duc Tri, Tohru Ariizumi, Hiroshi Ezura
Ethylene receptors are key factors for ethylene signal transduction. In tomato, six ethylene receptor genes (SlETR1-SlETR6) have been identified. Mutations in different ethylene receptor genes result in different phenotypes that are useful for elucidating the roles of each gene. In this study, we screened mutants of two ethylene receptor genes, SLETR4 and SLETR5, from a Micro-Tom mutant library generated by TILLING. We identified two ethylene receptor mutants with altered phenotypes and named them Sletr4-1 and Sletr5-1...
October 31, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30377773/identification-of-critical-sex-biased-genes-in-andrias-davidianus-by-de-novo-transcriptome
#3
Qiaomu Hu, Haifeng Tian, Wei Li, Yan Meng, Quanhe Wang, Hanbing Xiao
The Chinese giant salamander Andrias davidianus is a protected amphibian with high nutritional and economic value. Understanding its sex determination mechanism is important for improving culture techniques and sex control in breeding. However, little information on the characterization of critical genes involved in sex is available. Herein, sequencing of ovary and test produced 40,783,222 and 46,128,902 raw reads, respectively, which were jointly assembled into 80,497 unigenes. Of these, 36,609 unigenes were annotated, of which 8907 were female-biased and 10,385 were male-biased...
October 30, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30374564/construction-of-boolean-logic-gates-based-on-dual-vector-circuits-of-multiple-gene-regulatory-elements
#4
Zhao Wei, Wenliang Fu, Qing Liu, Haoran Jing, Chen Jin, Yao Chen, Wenrong Xia, Xiaoming Zhu, Donggang Xu
Gene circuits are constructed to run complex logical operations for the precise regulation of biological metabolic processes. At present, the implementation of most genetic circuits is based on the regulatory mechanism of various circuit components, but we hope to realize complex logic gates through biological metabolic pathways of organisms. In this study, we matched the regulatory elements of different functional mechanisms to build a Boolean logic gate model by means of a dual-vector circuit. In Escherichia coli, we made 12 circuit logic gate modules and validated the functions of four of the logic gates, including "AND", "NAND", "OR" and "NOR" by the expression and analysis of a reporter gene...
October 29, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30374563/divergence-of-vrn-b3-alleles-during-the-evolution-of-domesticated-wheat
#5
Alexandr Muterko, Elena Salina
Genetic changes accrued during the domestication of wheat have been crucial in improving the cultivation and yield of this strategic crop. Allelic variation at the VRN3 gene makes a significant contribution to the adaptability of wheat to a wide range of environmental conditions. In the present study, the origin and distribution of the Vrn-B3a and Vrn-B3b alleles during the evolution of wheat were investigated. Analysis of 214 accessions of 11 polyploid wheat species from different eco-geographical areas found the Vrn-B3a and Vrn-B3b alleles in accessions of tetraploid wheat T...
October 29, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30357478/investigation-of-direct-repeats-spacers-and-proteins-associated-with-clustered-regularly-interspaced-short-palindromic-repeat-crispr-system-of-vibrio-parahaemolyticus
#6
Pallavi Baliga, Malathi Shekar, Moleyur Nagarajappa Venugopal
Vibrio parahaemolyticus, a ubiquitous bacterium of the marine environment is an important food-borne pathogen responsible for gastroenteritis worldwide. In this study, we aimed to investigate the occurrence and diversity of the CRISPR-Cas system in V. parahaemolyticus genomes using a bioinformatics approach. The CRISPR-Cas system functions as an adaptive immune system in prokaryotes that provides immunity against foreign genetic elements. In total, 570 genomes V. parahaemolyticus genomes were analyzed of which 200 confirmed for the presence of CRISPR-Cas system...
October 24, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30315370/a-longitudinal-quantitative-trait-locus-mapping-of-chicken-growth-traits
#7
Tatsuhiko Goto, Akira Ishikawa, Masahide Nishibori, Masaoki Tsudzuki
Since the growth traits of chickens are largely related to the production of meat and eggs, it is definitely important to understand genetic basis of growth traits. Although many quantitative trait loci (QTLs) that affect growth traits have recently been reported in chickens, little is known about genetic architecture of growth traits across all growth stages. Therefore, we conducted a longitudinal QTL study of growth traits measured from 0 to 64 weeks of age using 134 microsatellite DNA markers on 26 autosomes from 406 F2 females, which resulted from an intercross of Oh-Shamo and White Leghorn chicken breeds...
October 12, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30298213/h3k4-k9-acetylation-and-lr28-mediated-expression-of-six-leaf-rust-responsive-genes-in-wheat-triticum-aestivum
#8
Chanchal Sharma, Santosh Kumar, Gautam Saripalli, Neelu Jain, Saurabh Raghuvanshi, J B Sharma, K V Prabhu, P K Sharma, H S Balyan, P K Gupta
Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose...
October 8, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30293092/the-bear-giant-skipper-genome-suggests-genetic-adaptations-to-living-inside-yucca-roots
#9
Qian Cong, Wenlin Li, Dominika Borek, Zbyszek Otwinowski, Nick V Grishin
Giant-Skippers (Megathymini) are unusual thick-bodied, moth-like butterflies whose caterpillars feed inside Yucca roots and Agave leaves. Giant-Skippers are attributed to the subfamily Hesperiinae and they are endemic to southern and mostly desert regions of the North American continent. To shed light on the genotypic determinants of their unusual phenotypic traits, we sequenced and annotated a draft genome of the largest Giant-Skipper species, the Bear (Megathymus ursus violae). The Bear skipper genome is the least heterozygous among sequenced Lepidoptera genomes, possibly due to much smaller population size and extensive inbreeding...
October 6, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30291426/inuc-ext-psetnc-an-efficient-ensemble-model-for-identification-of-nucleosome-positioning-by-extending-the-concept-of-chou-s-pseaac-to-pseudo-tri-nucleotide-composition
#10
Muhammad Tahir, Maqsood Hayat, Sher Afzal Khan
Nucleosome is a central element of eukaryotic chromatin, which composes of histone proteins and DNA molecules. It performs vital roles in many eukaryotic intra-nuclear processes, for instance, chromatin structure and transcriptional regulation formation. Identification of nucleosome positioning via wet lab is difficult; so, the attention is diverted towards the accurate intelligent automated prediction. In this regard, a novel intelligent automated model "iNuc-ext-PseTNC" is developed to identify the nucleosome positioning in genomes accurately...
October 5, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30288581/a-gene-graveyard-in-the-genome-of-the-fungus-podospora-comata
#11
Philippe Silar, Jean-Marc Dauget, Valérie Gautier, Pierre Grognet, Michelle Chablat, Sylvie Hermann-Le Denmat, Arnaud Couloux, Patrick Wincker, Robert Debuchy
Mechanisms involved in fine adaptation of fungi to their environment include differential gene regulation associated with single nucleotide polymorphisms and indels (including transposons), horizontal gene transfer, gene copy amplification, as well as pseudogenization and gene loss. The two Podospora genome sequences examined here emphasize the role of pseudogenization and gene loss, which have rarely been documented in fungi. Podospora comata is a species closely related to Podospora anserina, a fungus used as model in several laboratories...
October 4, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30284619/glyphosate-induces-the-synthesis-of-ppgpp
#12
Gabriela Torres Cruvinel, Henrique Iglesias Neves, Beny Spira
Glyphosate, the most widely used herbicide in both agricultural and urban areas is toxic for plants and for many bacterial species. The mechanism of action of glyphosate is through the inhibition of the EPSP synthase, a key enzyme in the biosynthetic pathway of aromatic amino acids. Here we show that glyphosate induces the stringent response in Escherichia coli. Bacteria treated with glyphosate stop growing and accumulate ppGpp. Both growth arrest and ppGpp accumulation are restored to normal levels upon addition of aromatic amino acids...
October 4, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30267144/tissue-specific-transcriptomic-profiling-of-plantago-major-provides-insights-for-the-involvement-of-vasculature-in-phosphate-deficiency-responses
#13
Jing Huang, Zhiqiang Huang, Xiangjun Zhou, Chao Xia, Muhammad Imran, Shujuan Wang, Congshan Xu, Manrong Zha, Yan Liu, Cankui Zhang
The vasculature of higher plants is important with transport of both nutrient and information molecules. To understand the correspondence of this tissue in molecular responses under phosphate (Pi) deficiency, Plantago major, a model plant for vasculature biology study, was chosen in our analysis. After RNA-Seq and de novo transcriptome assembly of 24 libraries prepared from the vasculature of P. major, 37,309 unigenes with a mean length of 1571 base pairs were obtained. Upon 24 h of Pi deficiency, 237 genes were shown to be differentially expressed in the vasculature of P...
September 28, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30264192/proliferation-of-aneuploid-cells-induced-by-cenp-e-depletion-is-counteracted-by-the-p14-arf-tumor-suppressor
#14
Lorena Veneziano, Viviana Barra, Danilo Cilluffo, Aldo Di Leonardo
The spindle assembly checkpoint (SAC) is a cellular surveillance mechanism that ensures the fidelity of chromosomes segregation. Reduced expression of some of its components weakens the SAC and induces chromosome instability and aneuploidy, which are both well-known hallmarks of cancer cells. Centromere protein-E (CENP-E) is a crucial component of the SAC and its function is to facilitate kinetochore microtubule attachment required to achieve and maintain chromosome alignment. The present study investigates the possible role of p14ARF as a controller of aneuploid cells proliferation...
September 27, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30255205/development-of-est-ssr-markers-and-their-application-in-an-analysis-of-the-genetic-diversity-of-the-endangered-species-magnolia-sinostellata
#15
Xingli Wang, Wenchong Chen, Jia Luo, Zhangxiu Yao, Qin Yu, Yaling Wang, Shouzhou Zhang, Zhigao Liu, Mingru Zhang, Yamei Shen
Magnolia sinostellata is an endemic species of Magnoliaceae that is narrowly distributed in the south of Zhejiang Province, China. To explore the genetic diversity and population structure of this endangered species, this study developed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data of M. sinostellata. In total, 25472 SSRs were identified among 110644 unique assembled sequences with a total of 90.83 Mb and an average frequency of 23.02%. The mononucleotide (33.53%) and dinucleotide (42...
September 25, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30238319/birth-and-death-of-mx-genes-and-the-presence-absence-of-genes-regulating-mx-transcription-are-correlated-with-the-diversity-of-anti-pathogenicity-in-vertebrate-species
#16
Furong Qi, Airong Yang, Sadaf Ambreen, Xue Bai, Yali Hou, Xuemei Lu
Gene duplication and amino acid substitution are two types of genetic innovations of antiviral genes in inhibiting the emerging pathogens in different species. Mx proteins are well known for inhibiting negative-stranded RNA viruses and have evolved a number of paralogs or orthologs, showing distinct antiviral activities or capacities within or between species. The presence of upstream genes in the signaling pathway(s) that activates Mx genes (upstream regulators of Mx gene) also exhibits variety across species...
September 20, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30229293/the-influence-of-paternal-diet-on-sncrna-mediated-epigenetic-inheritance
#17
REVIEW
Line Katrine Klastrup, Stine Thorhauge Bak, Anders Lade Nielsen
The risk of developing metabolic diseases is conferred by genetic predisposition from risk genes and by environmental exposures that can manifest in epigenetic changes. The global rise in obesity and type II diabetes has motivated a search for the epigenetic factors underlying these diseases. The possibility of transgenerational inheritance of epigenetic changes raises questions regarding how spermatozoa transmit acquired epigenetic changes that affect the metabolic health of the next generation. The purpose of this review is to describe current key literature concerning small non-coding RNA (sncRNA), specifically (1) the effects of high-fat or low-protein diets on sncRNA presence in spermatozoa; (2) sncRNA transmission from father to offspring; and (3) the functional effects of inherited sncRNA on offspring metabolic phenotype...
September 18, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30229292/an-efficient-method-for-multigene-co-interference-by-recombinant-bombyx-mori-nucleopolyhedrovirus
#18
Hao Zheng, Feifei Ren, Qiuyuan Lu, Zhenming Cao, Jichen Song, Min Feng, Jisheng Liu, Jingchen Sun
Bombyx mori Nucleopolyhedrovirus (BmNPV), which is a member of the Baculoviridae family, is a significant pathogen of the silkworm. The infection of BmNPV is often lethal and causes about 20% loss of cocoon in the silk industry annually. To explore the effects of different gene inhibition strategies on the replication cycle of baculovirus, we constructed the mutant virus to infect BmN cells directly and further identified ie0, ie1, and gp64 as the essential viral genes of BmNPV. To elucidate the significance of the inhibition effect of different interference strategies, we characterized and constructed the recombinant BmNPV that carried a single or multigene-interfering cassette...
September 18, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30203254/identification-of-the-copy-number-variant-biomarkers-for-breast-cancer-subtypes
#19
Xiaoyong Pan, XiaoHua Hu, Yu-Hang Zhang, Lei Chen, LiuCun Zhu, ShiBao Wan, Tao Huang, Yu-Dong Cai
Breast cancer is a common and threatening malignant disease with multiple biological and clinical subtypes. It can be categorized into subtypes of luminal A, luminal B, Her2 positive, and basal-like. Copy number variants (CNVs) have been reported to be a potential and even better biomarker for cancer diagnosis than mRNA biomarkers, because it is considerably more stable and robust than gene expression. Thus, it is meaningful to detect CNVs of different cancers. To identify the CNV biomarker for breast cancer subtypes, we integrated the CNV data of more than 2000 samples from two large breast cancer databases, METABRIC and The Cancer Genome Atlas (TCGA)...
September 10, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/30196354/hoxa4-regulated-mir-138-suppresses-proliferation-and-gefitinib-resistance-in-non-small-cell-lung-cancer
#20
Xiaomei Tang, Jiying Jiang, Jinbao Zhu, Nan He, Jinlong Tan
Many non-small cell lung cancer (NSCLC) patients initially benefiting from gefitinib are confronted with acquired resistance. MiR-138 was previously stated as a growth inhibitor of several cancer cell lines including NSCLC cells and its expression level was significantly lower in gefitinib-resistant cells. The role of miR-138 in NSCLC cell lines PC9 and A549 was verified using methyl thiazolyl tetrazolium (MTT) assay and colony formation assay. Quantitative real-time PCR (RT-PCR) was employed to assess the level of miR-138 in gefitinib-sensitive PC9 cells and gefitinib-resistant PC9GR cells...
September 8, 2018: Molecular Genetics and Genomics: MGG
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