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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28331962/sex-combs-reduced-scr-regulatory-region-of-drosophila-revisited
#1
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
The Hox gene Sex combs reduced (Scr) is responsible for the differentiation of the labial and prothoracic segments in Drosophila. Scr is expressed in several specific tissues throughout embryonic development, following a complex path that must be coordinated by an equally complex regulatory region. Although some cis-regulatory modules (CRMs) have been identified in the Scr regulatory region (~75 kb), there has been no detailed and systematic study of the distinct regulatory elements present within this region...
March 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28321510/dna-methylation-patterns-of-behavior-related-gene-promoter-regions-dissect-the-gray-wolf-from-domestic-dog-breeds
#2
Zsofia Banlaki, Giulia Cimarelli, Zsofia Viranyi, Eniko Kubinyi, Maria Sasvari-Szekely, Zsolt Ronai
A growing body of evidence highlights the relationship between epigenetics, especially DNA methylation, and population divergence as well as speciation. However, little is known about how general the phenomenon of epigenetics-wise separation of different populations is, or whether population assignment is, possible based on solely epigenetic marks. In the present study, we compared DNA methylation profiles between four different canine populations: three domestic dog breeds and their ancestor the gray wolf...
March 21, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28315961/qtl-mapping-with-different-genetic-systems-for-nine-non-essential-amino-acids-of-cottonseeds
#3
Haiying Liu, Alfred Quampah, Jinhong Chen, Jinrong Li, Zhuangrong Huang, Qiuling He, Chunhai Shi, Shuijin Zhu
Amino acid is an important nutrient resource for both human and animals. Using a set of 188 RILs population derived from an elite hybrid cross of upland cotton cultivars 'HS46' × 'MARCABUCAG8US-1-88' and their immortal F2 (IF2) with reciprocal backcrosses BC1F1 and BC2F1 (BC) populations in two environments, the QTLs located on the embryo genome and maternal plant genome for nine amino acids of cottonseed were studied across environments. The QTL Network-CL-2.0-seed software was used to analyze the QTLs and their genetic effects for nine amino acids...
March 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28314937/phylogenetic-analysis-of-idd-gene-family-and-characterization-of-its-expression-in-response-to-flower-induction-in-malus
#4
Sheng Fan, Dong Zhang, Libo Xing, Siyan Qi, Lisha Du, Haiqin Wu, Hongxia Shao, Youmei Li, Juanjuan Ma, Mingyu Han
Although INDETERMINATE DOMAIN (IDD) genes encoding specific plant transcription factors have important roles in plant growth and development, little is known about apple IDD (MdIDD) genes and their potential functions in the flower induction. In this study, we identified 20 putative IDD genes in apple and named them according to their chromosomal locations. All identified MdIDD genes shared a conserved IDD domain. A phylogenetic analysis separated MdIDDs and other plant IDD genes into four groups. Bioinformatic analysis of chemical characteristics, gene structure, and prediction of protein-protein interactions demonstrated the functional and structural diversity of MdIDD genes...
March 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28314936/distribution-of-divo-in-coffea-genomes-a-poorly-described-family-of-angiosperm-ltr-retrotransposons
#5
Mathilde Dupeyron, Rogerio Fernandes de Souza, Perla Hamon, Alexandre de Kochko, Dominique Crouzillat, Emmanuel Couturon, Douglas Silva Domingues, Romain Guyot
Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains...
March 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28289846/a-deletion-in-the-hermansky-pudlak-syndrome-4-hps4-gene-appears-to-be-responsible-for-albinism-in-channel-catfish
#6
Yueru Li, Xin Geng, Lisui Bao, Ahmed Elaswad, Kevin W Huggins, Rex Dunham, Zhanjiang Liu
Albinism is caused by a series of genetic abnormalities leading to reduction of melanin production. Albinism is quite frequent in catfish, but the causative gene and the molecular basis were unknown. In this study, we conducted a genome-wide association study (GWAS) using the 250 K SNP array. The GWAS analysis allowed mapping of the albino phenotype in the Hermansky-Pudlak syndrome 4 (Hps4) gene, which is known to be involved in melanosome biosynthesis. Sequencing analysis revealed that a 99-bp deletion was present in all analyzed albino catfish at the intron 2 and exon 3 junction...
March 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28271161/dna-methylation-profiling-reveals-the-presence-of-population-specific-signatures-correlating-with-phenotypic-characteristics
#7
Anil K Giri, Soham Bharadwaj, Priyanka Banerjee, Shraddha Chakraborty, Vaisak Parekatt, Donaka Rajashekar, Abhishek Tomar, Aarthi Ravindran, Analabha Basu, Nikhil Tandon, Dwaipayan Bharadwaj
Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups...
March 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28255762/semax-an-analog-of-acth-4-7-regulates-expression-of-immune-response-genes-during-ischemic-brain-injury-in-rats
#8
Ekaterina V Medvedeva, Veronika G Dmitrieva, Svetlana A Limborska, Nikolay F Myasoedov, Lyudmila V Dergunova
Brain stroke continues to claim the lives of million people every year. To build the effective strategies for stroke treatment it is necessary to understand the neuroprotective mechanisms that are able to prevent the ischemic injury. Consisting of the ACTH(4-7) fragment and the tripeptide Pro-Gly-Pro (PGP), the synthetic peptide Semax effectively protects brain against ischemic stroke. However, the molecular mechanisms underlying its neuroprotection and participation of PGP in them are still needed to be clarified...
March 2, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28251317/crispr-cas9-mediated-gene-editing-in-human-zygotes-using-cas9-protein
#9
Lichun Tang, Yanting Zeng, Hongzi Du, Mengmeng Gong, Jin Peng, Buxi Zhang, Ming Lei, Fang Zhao, Weihua Wang, Xiaowei Li, Jianqiao Liu
Previous works using human tripronuclear zygotes suggested that the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system could be a tool in correcting disease-causing mutations. However, whether this system was applicable in normal human (dual pronuclear, 2PN) zygotes was unclear. Here we demonstrate that CRISPR/Cas9 is also effective as a gene-editing tool in human 2PN zygotes. By injection of Cas9 protein complexed with the appropriate sgRNAs and homology donors into one-cell human embryos, we demonstrated efficient homologous recombination-mediated correction of point mutations in HBB and G6PD...
March 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28251316/editor-s-comment-on-crispr-cas9-mediated-gene-editing-in-human-zygotes-using-cas9-protein
#10
EDITORIAL
Stefan Hohmann
No abstract text is available yet for this article.
March 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28251315/genome-wide-analysis-of-the-hd-zip-iv-transcription-factor-family-in-gossypium-arboreum-and-gahdg11-involved-in-osmotic-tolerance-in-transgenic-arabidopsis
#11
Eryong Chen, Xueyan Zhang, Zhaoen Yang, Xiaoqian Wang, Zuoren Yang, Chaojun Zhang, Zhixia Wu, Depei Kong, Zhao Liu, Ge Zhao, Hamama Islam Butt, Xianlong Zhang, Fuguang Li
HD-ZIP IV proteins belong to the homeodomain-leucine zipper (HD-ZIP) transcription factor family and are involved in trichome development and drought stress in plants. Although some functions of the HD-ZIP IV group are well understood in Arabidopsis, little is known about their function in cotton. In this study, HD-ZIP genes were identified from three Gossypium species (G. arboreum, G. raimondii and G. hirsutum) and clustered into four families (HD-ZIP I, II, III and IV) to separate HD-ZIP IV from the other three families...
March 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28247040/transcriptome-wide-identification-phylogenetic-analysis-and-expression-profiling-of-zinc-finger-transcription-factors-from-crocus-sativus-l
#12
Aubid Hussain Malik, Nasheeman Ashraf
Crocus sativus belongs to Iridaceae family and is the only plant species which produces apocarotenoids like crocin, picrocrocin, and safranal in significant quantities. Besides their organoleptic properties, Crocus apocarotenoids have been found to possess remarkable pharmacological potential. Although apocarotenoid biosynthetic pathway has been worked out to a great degree, but the mechanism that regulates the tissue and developmental stage-specific production of Crocus apocarotenoids is not known. To identify the genes regulating apocarotenoid biosynthesis in Crocus, transcriptome wide identification of zinc-finger transcription factors was undertaken...
February 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28243735/new-insights-into-vitamin-d-anticancer-properties-focus-on-mirna-modulation
#13
REVIEW
Katarina Zeljic, Gordana Supic, Zvonko Magic
Vitamin D anticancer properties are well known and have been demonstrated in many in vitro and in vivo studies. Mechanistic insights have given an explanation on how vitamin D exerts antineoplastic functions, which are mainly conducted via the canonical vitamin D receptor (VDR)-vitamin D response elements (VDRE) pathway. Numerous findings indicate that dietary components, including vitamin D, could exert chemopreventive effects through alterations of microRNA (miRNA) expression. As miRNAs have important roles in regulating diverse and vital cellular processes, it has been speculated that vitamin D's non-classical effects, including anticancer effects, could be mediated through alterations of miRNA expression level...
February 27, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28229227/population-structure-and-infectious-disease-risk-in-southern-africa
#14
REVIEW
Caitlin Uren, Marlo Möller, Paul D van Helden, Brenna M Henn, Eileen G Hoal
The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles...
February 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28214997/the-human-rit2-core-promoter-short-tandem-repeat-predominant-allele-is-species-specific-in-length-a-selective-advantage-for-human-evolution
#15
Babak Emamalizadeh, Abofazl Movafagh, Hossein Darvish, Somayeh Kazeminasab, Monavvar Andarva, Pegah Namdar-Aligoodarzi, Mina Ohadi
Evolutionary analyses of the critical core promoter interval support a selective advantage for expanding the length of certain short tandem repeats (STRs) in humans. We recently reported genome-wide data on human core promoter STRs that are "exceptionally long" (≥6-repeats). Near the top of the list, the neuron-specific gene, RIT2, contains one of the longest GA-STRs at 11-repeats. In the present study, we analyzed the evolutionary implications of this STR across species. We also studied this STR in a sample of 2,143 Iranian human subjects that encompassed a number of neuropsychiatric disorders and controls...
February 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28204924/genome-wide-analysis-of-transposable-elements-in-the-coffee-berry-borer-hypothenemus-hampei-coleoptera-curculionidae-description-of-novel-families
#16
Eric M Hernandez-Hernandez, Rita Daniela Fernández-Medina, Lucio Navarro-Escalante, Jonathan Nuñez, Pablo Benavides-Machado, Claudia M A Carareto
The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron)...
February 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28190082/association-of-recently-identified-type-2-diabetes-gene-variants-with-gestational-diabetes-in-asian-indian-population
#17
Sekar Kanthimathi, Manickam Chidambaram, Dhanasekaran Bodhini, Samuel Liju, Aruyerchelvan Bhavatharini, Ram Uma, Ranjit Mohan Anjana, Viswanathan Mohan, Venkatesan Radha
Earlier studies have provided evidence that the gestational diabetes mellitus (GDM) and Type 2 diabetes mellitus (T2DM) share common genetic background. A recent genome wide association study (GWAS) showed a strong association of six novel gene variants with T2DM among south Asians but not with Europeans. The aim of this study was to investigate whether these variants that confer susceptibility to T2DM in Asian Indian population also correlate with GDM in Asian Indian population. In addition to these novel variants, three T2DM associated SNPs that were previously identified by GWAS in Caucasian populations, which also showed association with T2DM in south Indian population in our previous study were also evaluated for their susceptibility to GDM in our population...
February 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28160081/ecl1-is-a-zinc-binding-protein-involved-in-the-zinc-limitation-dependent-extension-of-chronological-life-span-in-fission-yeast
#18
Takafumi Shimasaki, Hokuto Ohtsuka, Chikako Naito, Kenko Azuma, Takeshi Tenno, Hidekazu Hiroaki, Hiroshi Murakami, Hirofumi Aiba
Overexpression of Ecl1-family genes (ecl1 (+), ecl2 (+), and ecl3 (+)) results in the extension of the chronological life span in Schizosaccharomyces pombe. However, the mechanism for this extension has not been defined clearly. Ecl1-family proteins consist of approximately 80 amino acids, and four cysteine residues are conserved in their N-terminal domains. This study focused on the Ecl1 protein, mutating its cysteine residues sequentially to confirm their importance. As a result, all mutated Ecl1 proteins nearly lost the function to extend the chronological life span, suggesting that these four cysteine residues are essential for the Ecl1 protein...
February 3, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28160080/genome-wide-mining-and-comparative-analysis-of-microsatellites-in-three-macaque-species
#19
Sanxu Liu, Wei Hou, Tianlin Sun, Yongtao Xu, Peng Li, Bisong Yue, Zhenxin Fan, Jing Li
Microsatellites are found in taxonomically different organisms, and such repeats are related with genomic structure, function and certain diseases. To characterize microsatellites for macaques, we searched and compared SSRs with 1-6 bp nucleotide motifs in rhesus, cynomolgus and pigtailed macaque. A total of 1395671, 1284929 and 1266348 perfect SSRs were mined, respectively. The most frequent perfect SSRs were mononucleotide SSRs. The most GC-content was in dinucleotide SSRs and the least was in the mononucleotide SSRs...
February 3, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28160079/development-and-dissection-of-diagnostic-snp-markers-for-the-downy-mildew-resistance-genes-pl-arg-and-pl-8-and-maker-assisted-gene-pyramiding-in-sunflower-helianthus-annuus-l
#20
L L Qi, Z I Talukder, B S Hulke, M E Foley
Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers...
February 3, 2017: Molecular Genetics and Genomics: MGG
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