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https://www.readbyqxmd.com/read/29055226/generation-of-an-induced-pluripotent-stem-cell-line-ibms-ipsc-014-05-from-a-female-autosomal-dominant-polycystic-kidney-disease-patient-carrying-a-common-mutation-of-r803x-in-pkd2
#1
Ming-Ching Ho, Ching-Ying Huang, Jia-Jung Lee, Shih-Han Hsu, Yu-Che Cheng, Yu-Hung Hsu, Daw-Yang Hwang, Huai-En Lu, Hung-Chun Chen, Patrick C H Hsieh
Autosomal dominant polycystic kidney disease (ADPKD) is one of the most commonly inherited forms of polycystic kidney disease, and is characterized by the growth of numerous cysts in both kidneys. Here we generated an induced pluripotent stem cell (iPSC) line from the peripheral blood mononuclear cells (PBMCs) of a 63-year-old female ADPKD patient carrying an R803X mutation in the PKD2 gene using the Sendai-virus delivery system. Downstream characterization of these iPSCs showed that they possessed normal karyotyping, were free of genomic integration, retained the disease-causing PKD2 mutation, expressed pluripotency markers and could differentiate into three germ layers...
October 10, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29055225/generation-and-characterization-of-a-human-ipsc-line-sani005-a-containing-the-gray-platelet-associated-heterozygous-mutation-p-q287-in-gfi1b
#2
Marten Hansen, Eszter Varga, Tatjana Wüst, Clemens Mellink, Anne-Marie van der Kevie-Kersemaekers, Anne E Marneth, Marieke von Lindern, Bert van der Reijden, Emile van den Akker
Peripheral blood mononuclear cells were isolated from an individual harboring a heterozygous c.859C→T p.Q287* mutation in GFI1B, causing an autosomal dominant bleeding disorder, platelet type, 17 (BDPLT17). PBMCs were differentiated to erythroblasts and reprogrammed by lentiviral delivery of a self-silencing hOKSM polycistronic vector. Pluripotency of iPSC line was confirmed by expression of associated markers and by in vitro spontaneous differentiation towards the 3 germ layers. Normal karyotype confirmed the genomic integrity of iPSCs and the presence of disease causing mutation was shown by Sanger sequencing...
October 12, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29055182/computational-drug-repositioning-for-rare-diseases-in-the-era-of-precision-medicine
#3
REVIEW
Brian Delavan, Ruth Roberts, Ruili Huang, Wenjun Bao, Weida Tong, Zhichao Liu
There are tremendous unmet needs in drug development for rare diseases. Computational drug repositioning is a promising approach and has been successfully applied to the development of treatments for diseases. However, how to utilize this knowledge and effectively conduct and implement computational drug repositioning approaches for rare disease therapies is still an open issue. Here, we focus on the means of utilizing accumulated genomic data for accelerating and facilitating drug repositioning for rare diseases...
October 18, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/29055167/genomic-differentiation-and-patterns-of-gene-flow-between-two-long-tailed-tit-species-aegithalos
#4
Dezhi Zhang, Gang Song, Bin Gao, Yalin Cheng, Yanhua Qu, Shaoyuan Wu, Shimiao Shao, Yongjie Wu, Per Alström, Fumin Lei
Patterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions ("genomic differentiation islands") spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29055159/genomics-of-natural-populations-evolutionary-forces-that-establish-and-maintain-gene-arrangements-in-drosophila-pseudoobscura
#5
Zachary L Fuller, Gwilym D Haynes, Stephen Richards, Stephen W Schaeffer
The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29055150/distinct-sources-of-gene-flow-produce-contrasting-population-genetic-dynamics-at-different-range-boundaries-of-a-choristoneura-budworm
#6
Gwylim S Blackburn, Bryan M T Brunet, Kevin Muirhead, Michel Cusson, Catherine Béliveau, Roger C Levesque, Lisa M Lumley, Felix A H Sperling
Populations are often exposed to multiple sources of gene flow, but accounts are lacking of the population genetic dynamics that result from these interactions or their effects on local evolution. Using a genomic clines framework applied to 1195 SNPs, we documented genome-wide, locus-specific patterns of introgression between Choristoneura occidentalis biennis spruce budworms and two ecologically divergent relatives, C. o. occidentalis and C. fumiferana, that it interacts with at alternate boundaries of its range...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29055111/genetic-based-dissection-of-arsenic-accumulation-in-maize-using-a-genome-wide-association-analysis-method
#7
Zhan Zhao, Huaisheng Zhang, Zhongjun Fu, Hao Chen, Yanan Lin, Pengshuai Yan, Weihua Li, Huiling Xie, Zhanyong Guo, Xuehai Zhang, Jihua Tang
Understanding the mechanism of arsenic (As) accumulation in plants is important in reducing As's toxicity to plants and its potential risks to human health. Here, we performed a genome-wide association study to dissect the genetic basis of the As contents of different maize tissues in Xixian, which was irrigated with As-rich surface water, and Changge using an association population consisting of 230 representative inbred maize lines. Phenotypic data revealed a wide normal distribution and high repeatability for the As contents in maize tissues...
October 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29055020/subtype-specific-cancer-associated-fibroblasts-contribute-to-the-pathogenesis-of-uterine-leiomyoma
#8
Xin Wu, Vanida Ann Serna, Justin Thomas, Wenan Qiang, Michael L Blumenfeld, Takeshi Kurita
Recent genomic studies have identified subtypes of uterine leiomyoma (LM) with distinctive genetic alterations. Here we report the elucidation of the biological characteristics of the two most prevalent LM subtypes, MED12 mutant (MED12-LM) and HMGA2-overexpressing (HMGA2-LM) LM. Since each tumor carries only one genetic alteration, both subtypes are considered to be monoclonal. Approximately 90% of cells in HMGA2-LM were smooth muscle cells (SMC) with HMGA2 overexpression. In contrast, MED12-LM consisted of similar numbers of SMC and non-SMC, which were mostly tumor-associated fibroblasts (TAF)...
October 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/29055006/posttranscriptional-regulation-of-hla-a-protein-expression-by-alternative-polyadenylation-signals-involving-the-rna-binding-protein-syncrip
#9
Smita Kulkarni, Veron Ramsuran, Marijana Rucevic, Sukhvinder Singh, Alexandra Lied, Viraj Kulkarni, Colm O'hUigin, Sylvie Le Gall, Mary Carrington
Genomic variation in the untranslated region (UTR) has been shown to influence HLA class I expression level and associate with disease outcomes. Sequencing of the 3'UTR of common HLA-A alleles indicated the presence of two polyadenylation signals (PAS). The proximal PAS is conserved, whereas the distal PAS is disrupted within certain alleles by sequence variants. Using 3'RACE, we confirmed expression of two distinct forms of the HLA-A 3'UTR based on use of either the proximal or the distal PAS, which differ in length by 100 bp...
October 20, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29054994/study-identifies-subtypes-of-pediatric-high-grade-gliomas
#10
(no author information available yet)
A molecular analysis that included genome sequencing, methylation profiling, and copy-number analysis divides pediatric glioma into 10 different categories. Tumors in each category carry distinct mutations, grow in different parts of the brain, and have varying impact on survival. The findings could lead to more effective treatments.
October 20, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/29054977/synthesis-and-degradation-of-camp-in-giardia-lamblia-possible-role-and-characterization-of-a-nucleotidyl-cyclase-with-a-single-cyclase-homology-domain
#11
Vanina Saraullo, Nicolas Di Siervi, Belen Jerez, Carlos Davio, Adolfo Zurita
Despite its importance in the regulation of growth and differentiation processes of a variety of organisms, the mechanism of synthesis and degradation of cAMP has not yet been described in Giardia lamblia In this work, we measured significant quantities of cAMP in trophozoites of G. lamblia incubated in vitro and later detected how it increases during the first hours of encystation, and how it then returns to basal levels at 24 h. Through an analysis of the genome of G. lamblia , we found sequences of three putative enzymes -one phosphodiesterase (gPDE) and two nucleotydyl cyclases (gNC1 and gNC2)- that should be responsible for the regulation of cAMP in G...
October 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29054926/biomolecular-coevolution-and-its-applications-going-from-structure-prediction-toward-signaling-epistasis-and-function
#12
REVIEW
Mehari B Zerihun, Alexander Schug
Evolution leads to considerable changes in the sequence of biomolecules, while their overall structure and function remain quite conserved. The wealth of genomic sequences, the 'Biological Big Data', modern sequencing techniques provide allows us to investigate biomolecular evolution with unprecedented detail. Sophisticated statistical models can infer residue pair mutations resulting from spatial proximity. The introduction of predicted spatial adjacencies as constraints in biomolecular structure prediction workflows has transformed the field of protein and RNA structure prediction toward accuracies approaching the experimental resolution limit...
October 20, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29054875/a-novel-steroid-coenzyme-a-ligase-from-novosphingobium-sp-strain-chol11-is-essential-for-an-alternative-degradation-pathway-for-bile-salts
#13
Onur Yücel, Johannes Holert, Kevin Christopher Ludwig, Sven Thierbach, Bodo Philipp
Bile salts such as cholate are steroid compounds with a C5 carboxylic side chain and occur ubiquitously in vertebrates. Upon their excretion into soils and waters bile salts can serve as growth substrates for diverse bacteria. Novosphingobium sp. strain Chol11 degrades 7-hydroxy bile salts via 3-keto-7-deoxy-Δ(4,6) metabolites by dehydration of the 7-hydroxyl group catalyzed by the 7α-hydroxysteroid dehydratase Hsh2. This reaction has not been observed in the well-studied 9-10-seco degradation pathway used by other steroid-degrading bacteria indicating that strain Chol11 uses an alternative pathway...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054873/the-enigmatic-genome-of-an-obligate-ancient-spiroplasma-symbiont-in-a-hadal-holothurian
#14
Li-Sheng He, Pei-Wei Zhang, Jiao-Mei Huang, Fang-Chao Zhu, Antoine Danchin, Yong Wang
Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their host are unclear. Here, we sequenced the 424-Kbp genome of "Candidatus Spiroplasma holothuricola" that dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana trench (6140m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of Spiroplasma sp. In this organism, the genes responsible for biosynthesis of amino acids, glycolysis and sugar transporters were lost, strongly suggesting endosymbiosis...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054864/heterogeneous-patterns-of-genetic-diversity-and-differentiation-in-european-and-siberian-chiffchaff-phylloscopus-collybita-abietinus-p-tristis
#15
Venkat Talla, Faheema Kalsoom, Daria Shipilina, Irina Marova, Niclas Backström
Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps towards understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations since they allow for studying how genomes evolve as species exchange genetic material and for associating particular genetic regions with phenotypic traits of interest. Here we use whole-genome resequencing of both allopatric and hybridising populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P...
October 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29054852/selective-base-excision-repair-of-dna-damage-by-the-non-base-flipping-dna-glycosylase-alkc
#16
Rongxin Shi, Elwood A Mullins, Xing-Xing Shen, Kori T Lay, Philip K Yuen, Sheila S David, Antonis Rokas, Brandt F Eichman
DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA)...
October 20, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29054826/viral-infections-in-common-carp-lead-to-a-disturbance-of-mucin-expression-in-mucosal-tissues
#17
Mikolaj Adamek, Dennis Hazerli, Marek Matras, Felix Teitge, Michal Reichert, Dieter Steinhagen
In response to the constant challenge by potential pathogens, external surfaces of fish, their skin, gills and intestinal tract, are coated with mucus, a gel like substance which largely prevents the entry of pathogens. This mucus gel consists mainly of water and mucins, large O-glycosylated proteins, which are responsible for forming a gel like mixture. A modulation of the mRNA expression of mucins, was described in viral diseases in mammals however there is a knowledge gap about the regulation of mucins during viral infection in fish...
October 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29054765/characterization-of-germline-mutations-in-familial-lung-cancer-from-the-chinese-population
#18
Madiha Kanwal, Xiao-Jie Ding, Zhans-Han Ma, Lian-Wei Li, Ping Wang, Ying Chen, Yun-Chao Huang, Yi Cao
Compared with numerous studies of somatic mutations using sporadic lung cancer, the research into germline mutations using familial lung cancer (FLC) is limited. In the present study, we used FLC samples obtained from the Chinese population in highly air-polluted regions to screen for novel germline mutations in lung cancer. Through a whole genome sequencing (WGS) analysis of the nine subjects (four lung cancer patients and five normal family members of FLC), we obtained a whole genome dataset of DNA alterations in FLC samples...
October 17, 2017: Gene
https://www.readbyqxmd.com/read/29054677/expression-of-the-ppm1f-gene-is-regulated-by-stress-and-associated-with-anxiety-and-depression
#19
Aliza P Wingo, Eric R Velasco, Antonio Florido, Adriana Lori, Dennis C Choi, Tanja Jovanovic, Kerry J Ressler, Raül Andero
BACKGROUND: Molecular mechanisms underlying psychological sequelae of exposure to stressful experiences, such as posttraumatic stress disorder (PTSD) and depression, are not well understood. METHODS: Using convergent evidence from animal and human transcriptomic and genomic studies, we aimed to identify genetic mechanisms underlying depression and anxiety after traumatic experiences. RESULTS: From a transcriptome-wide analysis in mice, we found the Ppm1f gene to be differentially expressed in the amygdala and medial prefrontal cortex (mPFC) a week after immobilization stress...
August 30, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29054638/the-persistent-organochlorine-pesticide-endosulfan-modulates-multiple-epigenetic-regulators-with-oncogenic-potential-in-mcf-7-cells
#20
Krishna Ghosh, Biji Chatterjee, Aparna Geetha Jayaprasad, Santosh R Kanade
Environmental cues and chemicals can potentially modulate the phenotypic expression of genome through alterations in the epigenetic mechanisms. Endosulfan is one of the extensively used organochlorine pesticides around the world which is known for its endocrine, neuro- and reproductive toxicity. This study was aimed to investigate the potential of α-endosulfan in modulation of multiple epigenetic enzymes in MCF-7 cells. The cells were treated with DMSO (control) or α-endosulfan (1 and 10μM) and the expression of various epigenetic enzymes was assayed by real-time PCR and immunoblotting, in addition to their activity assays...
October 17, 2017: Science of the Total Environment
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