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Molecular Genetics and Genomics: MGG

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https://read.qxmd.com/read/30759275/molecular-drivers-of-non-alcoholic-steatohepatitis-are-sustained-in-mild-to-late-fibrosis-progression-in-a-guinea-pig-model
#1
David Højland Ipsen, Josephine Skat-Rørdam, Maria Malvina Tsamouri, Markus Latta, Jens Lykkesfeldt, Pernille Tveden-Nyborg
Hepatic fibrosis increases mortality in humans with non-alcoholic steatohepatitis (NASH), but it remains unclear how fibrosis stage and progression affect the pathogenic mechanisms of NASH. This study investigates the transcriptional regulation and the impact of fibrosis stage, of pathways relating to hepatic lipid and cholesterol homeostasis, inflammation and fibrosis using RT-qPCR in the guinea pig NASH model. Animals were fed a chow (4% fat), a high-fat (20% fat, 0.35% cholesterol) or high-fat/high-sucrose (20% fat, 15% sucrose, 0...
February 13, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30758669/ta-gt-and-ac-are-significantly-under-represented-in-open-reading-frames-of-prokaryotic-and-eukaryotic-protein-coding-genes
#2
Yong Wang, Zhen Zeng, Tian-Lei Liu, Ling Sun, Qin Yao, Ke-Ping Chen
Genomes can be considered a combination of 16 dinucleotides. Analysing the relative abundance of different dinucleotides may reveal important features of genome evolution. In present study, we conducted extensive surveys on the relative abundances of dinucleotides in various genomic components of 28 bacterial, 20 archaean, 19 fungal, 24 plant and 29 animal species. We found that TA, GT and AC are significantly under-represented in open reading frames of all organisms and in intergenic regions and introns of most organisms...
February 13, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30739204/genome-wide-association-study-of-inflorescence-length-of-cultivated-soybean-based-on-the-high-throughout-single-nucleotide-markers
#3
Jinyang Wang, Xue Zhao, Wei Wang, Yingfan Qu, Weili Teng, Lijuan Qiu, Hongkun Zheng, Yingpeng Han, Wenbin Li
As an important and complex trait, inflorescence length (IL) of soybean [Glycine max (L.) Merr.] significantly affected seed yields. Therefore, elucidating molecular basis of inflorescence architecture, especially for IL, was important for improving soybean yield potentials. Longer IL meaned to have more pod and seed in soybean. Hence, increasing IL and improving yield are targets for soybean breeding. In this study, a association panel, comprising 283 diverse samples, was used to dissect the genetic basis of IL based on genome-wide association analysis (GWAS) and haplotype analysis...
February 9, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30739203/construction-of-genetic-linkage-map-and-genome-dissection-of-domestication-related-traits-of-moth-bean-vigna-aconitifolia-a-legume-crop-of-arid-areas
#4
Chutintorn Yundaeng, Prakit Somta, Kitiya Amkul, Alisa Kongjaimun, Akito Kaga, Norihiko Tomooka
The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F2 population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056)...
February 9, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30710177/distinct-evolutionary-origins-of-common-multi-drug-resistance-phenotypes-in-salmonella-typhimurium-dt104-a-convergent-process-for-adaptation-under-stress
#5
Le Tang, Song-Ling Zhu, Xin Fang, Yong-Guo Li, Cornelis Poppe, Randal N Johnston, Gui-Rong Liu, Shu-Lin Liu
Antimicrobial resistance makes pathogenic bacteria hard to control, but little is known about the general processes of resistance gain or loss. Here, we compared distinct S. typhimurium DT104 strains resistant to zero, two, five, or more of the tested antimicrobials. We found that common resistance phenotypes could be encoded by distinct genes, on SGI-1 or plasmid. We also demonstrated close clonality among all the tested non-resistant and differently resistant DT104 strains, demonstrating dynamic acquisition or loss (by total deletion or gradual decaying of multi-drug resistance gene clusters) of the genetic traits...
February 1, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30689096/agrobacterium-mediated-tnt1-mutagenesis-of-moss-protonemal-filaments-and-generation-of-stable-mutants-with-impaired-gametophyte
#6
Boominathan Mohanasundaram, Vyankatesh B Rajmane, Sukanya V Jogdand, Amey J Bhide, Anjan K Banerjee
The gametophyte of moss exhibits a simple body plan, yet its growth is regulated by complex developmental phenomena similar to angiosperms. Because moss can be easily maintained under laboratory conditions, amenable for gene targeting and the availability of genome sequence, P. patens has become an attractive model system for studying evolutionary traits. Until date, there has been no Agrobacterium-mediated Tnt1 mutagenesis protocol for haploid protonemal filaments of moss. Hence, we attempted to use the intact tobacco Tnt1 retrotransposon as a mutagen for P...
January 28, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30656413/a-drosophila-genetic-screen-for-suppressors-of-s6kinase-dependent-growth-identifies-the-f-box-subunit-archipelago-fbxw7
#7
Muhammad-Kashif Zahoor, Mickael Poidevin, Caroline Lecerf, Damien Garrido, Jacques Montagne
This study was designed to identify novel negative regulators of the Drosophila S6kinase (dS6K). S6K is a downstream effector of the growth-regulatory complex mTORC1 (mechanistic-Target-of-Rapamycin complex 1). Nutrients activate mTORC1, which in turn induces the phosphorylation of S6K to promote cell growth, whereas fasting represses mTORC1 activity. Here, we screened 11,000 RNA-interfering (RNAi) lines and retained those that enhanced a dS6K-dependent growth phenotype. Since RNAi induces gene knockdown, enhanced tissue growth supports the idea that the targeted gene acts as a growth suppressor...
January 17, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30635785/genome-wide-association-analysis-for-body-weight-identifies-candidate-genes-related-to-development-and-metabolism-in-rainbow-trout-oncorhynchus-mykiss
#8
Rafael Vilhena Reis Neto, Grazyella Massako Yoshida, Jean Paul Lhorente, José Manuel Yáñez
Growth is one of the most important traits from both a physiological and economic perspective in aquaculture species. Thus, identifying the genomic regions and genes underpinning genetic variation for this trait is of particular interest in several fish species, including rainbow trout. In this work, we perform a genome-wide association study (GWAS) to identify the genomic regions associated with body weight at tagging (BWT) and at 18 months (BW18M) using a dense SNP panel (57 k) and 4596 genotyped rainbow trout from 105 full-sib families belonging to a Chilean breeding population...
January 11, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30635784/genomic-copy-number-variation-of-the-chkb-gene-alters-gene-expression-and-affects-growth-traits-of-chinese-domestic-yak-bos-grunniens-breeds
#9
Habtamu Abera Goshu, Min Chu, Wu Xiaoyun, Bao Pengjia, Ding Xue Zhi, Ping Yan
Copy number variation (CNV) influences the mRNA transcription levels and phenotypic traits through gene dosage, position effects, alteration of downstream pathways, and modulation of the structure and position of chromosomes. A previous study using the read depth approach to genome resequencing analysis revealed CNVs of the choline kinase beta (CHKB) gene in the copy number variable regions (CNVRs) of yak breeds may influence muscle development and therefore the phenotypic traits of yak breeds. Further work is required to attain a more complete understanding and validate the importance of the detected CNVR of the CHKB gene found in yak breeds, because there is no association studies of the CHKB gene with yak growth traits that have been reported...
January 11, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30607602/the-mir164-dependent-regulatory-pathway-in-developing-maize-seed
#10
Lanjie Zheng, Xiangge Zhang, Haojun Zhang, Yong Gu, Xinrong Huang, Huanhuan Huang, Hanmei Liu, Junjie Zhang, Yufeng Hu, Yangping Li, Guowu Yu, Yinghong Liu, Shaneka S Lawson, Yubi Huang
MicroRNA164 (miR164) plays a key role in leaf and flower development, lateral root initiation, and stress responses. However, little is known about the regulatory roles of miR164 during seed development, particularly in maize. The aim of this study was to discover the developmental function of miR164 in maize seed. Small RNA sequencing (sRNA-seq) was performed at two key stages. The results indicated that miR164 was down-regulated during maize seed development. In addition, degradome library sequencing and transient expression assays identified the target genes for miR164...
January 3, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30604072/analysis-of-european-hazelnut-corylus-avellana-reveals-loci-for-cultivar-improvement-and-the-effects-of-domestication-and-selection-on-nut-and-kernel-traits
#11
Amy Frary, Süleyman Can Ӧztürk, Hüseyin Irfan Balık, Selda Kayalak Balık, Gökhan Kızılcı, Sami Doğanlar, Anne Frary
Turkey is a rich source of European hazelnut (Corylus avellana) germplasm with nearly 400 accessions in the national collection. This genetic material encompasses cultivars, landraces and wild genotypes which were characterized for 12 nut and 13 kernel traits over 2 years in the 1990s. Analysis of these attributes revealed both the positive and negative impacts that human selection and breeding have had on hazelnut. Thus, while selection has resulted in larger nuts and kernels, cultivars have fewer nuts per cluster and kernels with larger internal cavities...
January 3, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30604071/resolving-population-structure-and-genetic-differentiation-associated-with-rad-snp-loci-under-selection-in-tossa-jute-corchorus-olitorius-l
#12
Debabrata Sarkar, Avijit Kundu, Debajeet Das, Avrajit Chakraborty, Nur Alam Mandal, Pratik Satya, Pran Gobinda Karmakar, Chandan Sourav Kar, Jiban Mitra, Nagendra Kumar Singh
The genetic basis of selection for geographic adaptation and how it has contributed to population structure are unknown in tossa jute (Corchorus olitorius), an important bast fibre crop. We performed restriction site-associated DNA (RAD) sequencing-based (1115 RAD-SNPs) population genomic analyses to investigate genetic differentiation and population structure within a collection of 221 fibre-type lines from across nine geographic regions of the world. Indian populations, with relatively higher overall diversity, were significantly differentiated (based on FST and PCA) from the African and the other Asian populations...
January 2, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30604070/noncoding-rare-variants-of-tbx6-in-congenital-anomalies-of-the-kidney-and-urinary-tract
#13
Shuangshuang Dong, Chunyan Wang, Xueping Li, Qian Shen, Xiaoyi Fu, Mingyan Wu, Chengcheng Song, Nan Yang, Yanhua Wu, Hongyan Wang, Li Jin, Hong Xu, Feng Zhang
Congenital anomalies of the kidney and urinary tract (CAKUT) are a wide range of congenital structural renal defects. CAKUT is the leading cause of chronic renal failure and end-stage renal disease in children. Studies in humans and animal models have confirmed the large genetic contribution to CAKUT. The previous evidence suggested that human TBX6 coding mutations might cause CAKUT via gene-dosage insufficiency. However, the potential involvement of TBX6 noncoding mutations in CAKUT remains to be elucidated...
January 2, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30604069/over-expression-of-the-red-plant-gene-r1-enhances-anthocyanin-production-and-resistance-to-bollworm-and-spider-mite-in-cotton
#14
Xin Li, Xufen Ouyang, Zhengsheng Zhang, Lin He, Yi Wang, Yaohua Li, Jia Zhao, Zhong Chen, Chuannan Wang, Lingli Ding, Yan Pei, Yuehua Xiao
Anthocyanins are a class of pigments ubiquitously distributed in plants and play roles in adoption to several stresses. The red plant gene (R1) promotes light-induced anthocyanin accumulation and red/purple pigmentation in cotton. Using 11 markers developed via genome resequencing, the R1 gene was located in an interval of approximately 136 kb containing three annotated genes. Among them, a PAP1 homolog, GhPAP1D (Gohir.D07G082100) displayed differential transcript level in the red- and green-plant leaves. GhPAP1D encoded a R2R3-MYB transcription factor and its over-expression resulted in increased anthocyanin accumulation in transgenic tobaccos and cottons...
January 2, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30591960/genetic-modification-of-spikelet-arrangement-in-wheat-increases-grain-number-without-significantly-affecting-grain-weight
#15
Gizaw M Wolde, Martin Mascher, Thorsten Schnurbusch
Crop yield is determined by the acquisition and allocation of photoassimilates in sink organs. Therefore, genetic modification of sink size is essential for understanding the complex signaling network regulating sink strength and source activities. Sink size in wheat depends on the number of spikelets per spike, floret/grain number per spikelet as well as the grain weight or dry matter accumulation. Hence, increasing spikelet number and improving sink size are targets for wheat breeding. The main objective of the present work was to genetically modify the wheat spike architecture, i...
December 27, 2018: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30554378/100-years-of-phenogenetics-valentin-haecker-and-his-examination-of-the-phenotype
#16
Uwe Hoßfeld, Georgy S Levit, Elizabeth Watts
Following the 'rediscovery' of Mendel's work around 1900 the study of genetics grew rapidly and multiple new inheritance theories quickly emerged such as Hugo de Vries' "Mutation Theory" (1901) and the "Boveri-Sutton Chromosome Theory" (1902). Mendel's work also caught the attention of the German geneticist Valentin Haecker, yet he was generally dissatisfied the simplicity of Mendelian genetics as he believed that inheritance and the expression of various characteristics appeared to be much more complex than the proposed "on-off hypotheses"...
December 15, 2018: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30539301/full-length-transcriptome-and-microrna-sequencing-reveal-the-specific-gene-regulation-network-of-velvet-antler-in-sika-deer-with-extremely-different-velvet-antler-weight
#17
Pengfei Hu, Tianjiao Wang, Huamiao Liu, Jiaping Xu, Lei Wang, Pei Zhao, Xiumei Xing
Velvet antler displays the fastest and most robust tissue proliferation in the animal world, it is a model for a complete organ development/regeneration, and alternative medicine, tonic made from velvet antler, was beneficial for human. The weight of velvet antler had high biomedical and economic value, but the related regulation mechanisms controlling velvet antler weight remain unclear. In this study, extremely heavy and light velvet antler groups were selected from a sika deer population of 100 individuals with extreme velvet antler weight...
December 11, 2018: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30488322/comparative-genomics-for-non-o1-o139-vibrio-cholerae-isolates-recovered-from-the-yangtze-river-estuary-versus-v-cholerae-representative-isolates-from-serogroup-o1
#18
Li Gong, Pan Yu, Huajun Zheng, Wenyi Gu, Wei He, Yadong Tang, Yaping Wang, Yue Dong, Xu Peng, Qunxin She, Lu Xie, Lanming Chen
Vibrio cholerae, which is autochthonous to estuaries worldwide, can cause human cholera that is still pandemic in developing countries. A number of V. cholerae isolates of clinical and environmental origin worldwide have been subjected to genome sequencing to address their phylogenesis and bacterial pathogenesis, however, little genome information is available for V. cholerae isolates derived from estuaries, particularly in China. In this study, we determined the complete genome sequence of V. cholerae CHN108B (non-O1/O139 serogroup) isolated from the Yangtze River Estuary, China and performed comparative genome analysis between CHN108B and other eight representative V...
November 28, 2018: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30483896/reduced-thiamine-binding-is-a-novel-mechanism-for-tpk-deficiency-disorder
#19
Wenjie Huang, Jiao Qin, Dingdong Liu, Yan Wang, Xiaofei Shen, Na Yang, Hui Zhou, Xiao-Tang Cai, Zhi-Ling Wang, Dan Yu, Rong Luo, Qingxiang Sun, Yong-Mei Xie, Da Jia
Thiamine pyrophosphokinase (TPK) converts thiamine (vitamin B1 ) into thiamine pyrophosphate (TPP), an essential cofactor for many important enzymes. TPK1 mutations lead to a rare disorder: episodic encephalopathy type thiamine metabolism dysfunction. Yet, the molecular mechanism of the disease is not entirely clear. Here we report an individual case of episodic encephalopathy, with familial history carrying a novel homozygous TPK1 mutation (p.L28S). The L28S mutation leads to reduced enzymatic activity, both in vitro and in vivo, without impairing thiamine binding and protein stability...
November 27, 2018: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30483895/transcriptome-analysis-of-adipose-tissue-from-pigs-divergent-in-feed-efficiency-reveals-alteration-in-gene-networks-related-to-adipose-growth-lipid-metabolism-extracellular-matrix-and-immune-response
#20
Justyna Horodyska, Henry Reyer, Klaus Wimmers, Nares Trakooljul, Peadar G Lawlor, Ruth M Hamill
Adipose tissue is hypothesized to play a vital role in regulation of feed efficiency (FE; efficiency in converting energy and nutrients into tissue), of which improvement will simultaneously reduce environmental impact and feed cost per pig. The objective of the present study was to sequence the subcutaneous adipose tissue transcriptome in FE-divergent pigs (n = 16) and identify relevant biological processes underpinning observed differences in FE. We previously demonstrated that high-FE pigs were associated with lower fatness when compared to their counterparts...
November 27, 2018: Molecular Genetics and Genomics: MGG
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