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https://www.readbyqxmd.com/read/28749478/molecular-autopsy-in-maternal-fetal-medicine
#1
Hanan E Shamseldin, Wesam Kurdi, Fatima Almusafri, Maha Alnemer, Alya Alkaff, Zeneb Babay, Amal Alhashem, Maha Tulbah, Nada Alsahan, Rubina Khan, Bahauddin Sallout, Elham Al Mardawi, Mohamed Zain Seidahmed, Niema Meriki, Yasser Alsaber, Alya Qari, Ola Khalifa, Wafaa Eyaid, Zuhair Rahbeeni, Ahmed Kurdi, Mais Hashem, Tarfa Alshidi, Eman Al-Obeid, Firdous Abdulwahab, Niema Ibrahim, Nour Ewida, Karen El-Akouri, Mariam Al Mulla, Tawfeg Ben-Omran, Matthias Pergande, Sebahattin Cirak, Saeed Al Tala, Ranad Shaheen, Eissa Faqeih, Fowzan S Alkuraya
PurposeThe application of genomic sequencing to investigate unexplained death during early human development, a form of lethality likely enriched for severe Mendelian disorders, has been limited.MethodsIn this study, we employed exome sequencing as a molecular autopsy tool in a cohort of 44 families with at least one death or lethal fetal malformation at any stage of in utero development. Where no DNA was available from the fetus, we performed molecular autopsy by proxy, i.e., through parental testing.ResultsPathogenic or likely pathogenic variants were identified in 22 families (50%), and variants of unknown significance were identified in further 15 families (34%)...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28748223/phenoplasm-a-database-of-disruption-phenotypes-for-malaria-parasite-genes
#2
Theo Sanderson, Julian C Rayner
Two decades after the first Plasmodium transfection, attempts have been made to disrupt more than 3,151 genes in malaria parasites, across five Plasmodium species. While results from rodent malaria transfections have been curated and systematised, empowering large-scale analysis, phenotypic data from human malaria parasite transfections currently exists as individual reports scattered across a the literature. To facilitate systematic analysis of published experimental genetic data across Plasmodium species, we have built PhenoPlasm ( http://www...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28748083/lactadherin-orthologs-inhibit-migration-of-human-porcine-and-murine-intestinal-epithelial-cells
#3
Steffen Nyegaard, Trine Andreasen, Jan Trige Rasmussen
Lactadherin was originally described due to its appearance in milk, but is abundantly expressed especially by professional and nonprofessional phagocytes. The proteins has been shown to have a multitude of bioactive effects, including inhibition of inflammatory phospholipases, induction of effero- and phagocytosis, prevent rotavirus induced gastroenteritis, and modulate intestinal homeostasis by regulating epithelial cell migration. The level of expression seems to be important in a row of serious pathologies linked to the intestinal epithelial barrier function, vascular- and autoimmune disease...
July 2017: Food Science & Nutrition
https://www.readbyqxmd.com/read/28747726/association-of-micrornas-with-argonaute-proteins-in-the-malaria-mosquito-anopheles-gambiae-after-blood-ingestion
#4
Xiaonan Fu, George Dimopoulos, Jinsong Zhu
Drastic changes in gene expression occur after adult female mosquitoes take a blood meal and use the nutrients for egg maturation. A growing body of evidence indicates that microRNAs (miRNAs) contribute to this tightly controlled tissue- and stage-specific gene expression. To investigate the role of miRNAs, we monitored miRNA expression in the mosquito Anopheles gambiae during the 72-h period immediately after blood feeding. We also measured the association of miRNAs with Argonaute 1 (Ago1) and Argonaute 2 (Ago2) to assess the functional status of individual miRNA species...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747659/porcine-familial-adenomatous-polyposis-model-enables-systematic-analysis-of-early-events-in-adenoma-progression
#5
Tatiana Flisikowska, Monika Stachowiak, Hongen Xu, Alexandra Wagner, Alejandra Hernandez-Caceres, Christine Wurmser, Carolin Perleberg, Hubert Pausch, Anna Perkowska, Konrad Fischer, Dmitrij Frishman, Ruedi Fries, Marek Switonski, Alexander Kind, Dieter Saur, Angelika Schnieke, Krzysztof Flisikowski
We compared gene expression in low and high-grade intraepithelial dysplastic polyps from pigs carrying an APC (1311) truncating mutation orthologous to human APC (1309) , analysing whole samples and microdissected dysplastic epithelium. Gene set enrichment analysis revealed differential expression of gene sets similar to human normal mucosa versus T1 stage polyps. Transcriptome analysis of whole samples revealed many differentially-expressed genes reflecting immune infiltration. Analysis of microdissected dysplastic epithelium was markedly different and showed increased expression in high-grade intraepithelial neoplasia of several genes known to be involved in human CRC; and revealed possible new roles for GBP6 and PLXND1...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747644/active-nuclear-transcriptome-analysis-reveals-inflammasome-dependent-mechanism-for-early-neutrophil-response-to-mycobacterium-marinum
#6
Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka-Spengler
The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747502/permissivity-of-dpp4-orthologs-to-mers-coronavirus-is-governed-by-glycosylation-and-other-complex-determinants
#7
Kayla M Peck, Trevor Scobey, Jesica Swanstrom, Kara L Jensen, Christina L Burch, Ralph S Baric, Mark T Heise
Middle East respiratory syndrome coronavirus (MERS-CoV) utilizes dipeptidyl peptidase 4 (DPP4) as an entry receptor. While bat, camel, and human DPP4 support MERS-CoV infection, several DPP4 orthologs, including mouse, ferret, hamster, and guinea pig, do not. Previous work revealed that glycosylation of mouse DPP4 plays a role in blocking MERS-CoV infection. Here, we test whether glycosylation also acts as a determinant of permissivity for ferret, hamster, and guinea pig DPP4. We find that while glycosylation plays an important role in these orthologs, additional sequence and structural determinants impact their ability to act as functional receptors for MERS-CoV...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28746874/glycolytic-enzymes-coalesce-in-g-bodies-under-hypoxic-stress
#8
Meiyan Jin, Gregory G Fuller, Ting Han, Yao Yao, Amelia F Alessi, Mallory A Freeberg, Nathan P Roach, James J Moresco, Alla Karnovsky, Misuzu Baba, John R Yates, Aaron D Gitler, Ken Inoki, Daniel J Klionsky, John K Kim
Glycolysis is upregulated under conditions such as hypoxia and high energy demand to promote cell proliferation, although the mechanism remains poorly understood. We find that hypoxia in Saccharomyces cerevisiae induces concentration of glycolytic enzymes, including the Pfk2p subunit of the rate-limiting phosphofructokinase, into a single, non-membrane-bound granule termed the "glycolytic body" or "G body." A yeast kinome screen identifies the yeast ortholog of AMP-activated protein kinase, Snf1p, as necessary for G-body formation...
July 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28745839/transcription-factor-agseb1-affects-development-osmotic-stress-response-and-secondary-metabolism-in-marine-derived-aspergillus-glaucus
#9
Yuan Wu, Yanna Ren, Xiangshan Zhou, Menghao Cai, Yuanxing Zhang
Fungi possess sophisticated regulatory systems to respond to a vast array of environmental signals. Among these responsive networks, some genes play critical roles in the regulation of various cellular processes. Here, we identified a putative transcriptional factor Agseb1 in Aspergillus glaucus, a marine-derived filamentous fungus. Agseb1 encodes a protein with two C2 H2 zinc fingers at the C-terminus, similar to the placement of these motifs in msn2/4 of Saccharomyces cerevisia, where they are positioned to allow binding to the CCCCT-box of stress-specific genes...
July 26, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28745435/mapk-15-is-a-ciliary-protein-required-for-pkd-2-localization-and-male-mating-behavior-in-caenorhabditis-elegans
#10
Brian P Piasecki, Thomas A Sasani, Alexander T Lessenger, Nicholas Huth, Shane Farrell
Cilia are conserved cellular structures that facilitate sensory-based processes, including those required for neuronal and kidney functions. Here, we show that the human mitogen activated kinase-15 (MAPK-15) ortholog in Caenorhabditis elegans encodes a ciliary protein. A strain harboring a mutation in the catalytic site of the kinase domain results in ciliary-specific defects in tail neurons of both hermaphrodite and male worms, manifesting in dye uptake, dendrite extension, and male mating behavior defects...
July 26, 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28744961/the-lexa-transcription-factor-regulates-fatty-acid-biosynthetic-genes-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#11
Ayumi Kizawa, Akihito Kawahara, Kosuke Takashima, Yasushi Takimura, Yoshitaka Nishiyama, Yukako Hihara
In various heterotrophic bacterial species, specific transcription factors have been identified that regulate the sets of genes required for fatty acid metabolism. Here, we report that expression of the fab genes, encoding fatty acid biosynthetic enzymes, is regulated by the global regulator LexA in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803. Sll1626, an ortholog of the well-known LexA repressor involved in the SOS response in heterotrophic bacteria, was isolated from crude extracts of Synechocystis by DNA affinity chromatography, reflecting its binding to the upstream region of the acpP-fabF and fabI genes...
July 26, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28743883/metabolic-pathway-and-cell-adaptation-mechanisms-revealed-through-genomic-proteomic-and-transcription-analysis-of-a-sphingomonas-haloaromaticamans-strain-degrading-ortho-phenylphenol
#12
Perruchon Chiara, Vasileiadis Sotirios, Rousidou Constantina, Papadopoulou S Evangelia, Tanou Georgia, Samiotaki Martina, Garagounis Constantinos, Molassiotis Athanassios, Papadopoulou K Kalliope, Karpouzas G Dimitrios
Ortho-phenylphenol (OPP) is a fungicide contained in agro-industrial effluents produced by fruit-packaging plants. Within the frame of developing bio-strategies to detoxify these effluents, an OPP-degrading Sphingomonas haloaromaticamans strain was isolated. Proteins/genes with a putative catabolic role and bacterium adaptation mechanisms during OPP degradation were identified via genomic and proteomic analysis. Transcription analysis of all putative catabolic genes established their role in the metabolism of OPP...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743801/foxq2-has-a-key-role-in-anterior-head-and-central-brain-patterning-in-insects
#13
Peter Kitzmann, Matthias Weißkopf, Magdalena Ines Schacht, Gregor Bucher
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the foxQ2 ortholog of the red flour beetle Tribolium castaneum as novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression...
July 25, 2017: Development
https://www.readbyqxmd.com/read/28743231/genome-wide-comparative-analysis-of-putative-pth11-related-g-protein-coupled-receptors-in-fungi-belonging-to-pezizomycotina
#14
Xihui Xu, Guopeng Li, Lu Li, Zhenzhu Su, Chen Chen
BACKGROUND: G-protein coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi, where they play important roles in signal transduction. Among them, the Pth11-related GPCRs form a large and divergent protein family, and are only found in fungi in Pezizomycotina. However, the evolutionary process and potential functions of Pth11-related GPCRs remain largely unknown. RESULTS: Twenty genomes of fungi in Pezizomycotina covering different nutritional strategies were mined for putative Pth11-related GPCRs...
July 25, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28742982/investigation-of-orthologous-pathogen-recognition-gene-rich-regions-in-solanaceous-species
#15
A Di Donato, Giuseppe Andolfo, A Ferrarini, M Delledonne, M R Ercolano
The genome architecture of pathogen receptor genes (PRGs) was extensively investigated in several plant species. However, we still know little about their elaborate reorganization arose during the plant speciation process. Using recently released pepper and eggplant genome sequences we were able to identify 1097 pathogen recognition genes in pepper Zunla-1 and 775 in eggplant Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping...
July 25, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28742928/shotgun-mitogenomics-across-body-size-classes-in-a-local-assemblage-of-tropical-diptera-phylogeny-species-diversity-and-mitochondrial-abundance-spectrum
#16
Le Qin Choo, Alex Crampton-Platt, Alfried P Vogler
Mitochondrial genomes can be assembled readily from shotgun sequenced DNA mixtures of mass-trapped arthropods ('mitochondrial metagenomics'), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy-fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body-size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742823/genome-wide-identification-and-analysis-of-the-mads-box-gene-family-in-bread-wheat-triticum-aestivum-l
#17
Jian Ma, Yujie Yang, Wei Luo, Congcong Yang, Puyang Ding, Yaxi Liu, Linyi Qiao, Zhijian Chang, Hongwei Geng, Penghao Wang, Qiantao Jiang, Jirui Wang, Guoyue Chen, Yuming Wei, Youliang Zheng, Xiujin Lan
The MADS-box genes encode transcription factors with key roles in plant growth and development. A comprehensive analysis of the MADS-box gene family in bread wheat (Triticum aestivum) has not yet been conducted, and our understanding of their roles in stress is rather limited. Here, we report the identification and characterization of the MADS-box gene family in wheat. A total of 180 MADS-box genes classified as 32 Mα, 5 Mγ, 5 Mδ, and 138 MIKC types were identified. Evolutionary analysis of the orthologs among T...
2017: PloS One
https://www.readbyqxmd.com/read/28740502/the-amp-activated-protein-kinase-kin10-is-involved-in-the-regulation-of-autophagy-in-arabidopsis
#18
Liang Chen, Ze-Zhuo Su, Li Huang, Fan-Nv Xia, Hua Qi, Li-Juan Xie, Shi Xiao, Qin-Fang Chen
Autophagy is a highly conserved system in eukaryotes for the bulk degradation and recycling of intracellular components. Autophagy is involved in many physiological processes including development, senescence, and responses to abiotic and biotic stress. The adenosine 5'-monophosphate (AMP)-activated protein kinase AMPK positively regulates autophagy in mammals; however, the potential function of AMPK in plant autophagy remains largely unknown. Here, we identified KIN10, a plant ortholog of the mammalian AMPK, as a positive regulator of plant autophagy and showed that it acts by affecting the phosphorylation of ATG1 (AUTOPHAGY-RELATED GENE 1) proteins in Arabidopsis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28739599/evolutionary-dynamics-of-male-reproductive-genes-in-the-drosophila-virilis-subgroup
#19
Yasir H Ahmed-Braimah, Robert L Unckless, Andrew G Clark
Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739598/sequence-based-mapping-and-genome-editing-reveal-mutations-in-stickleback-hps5-cause-oculocutaneous-albinism-and-the-casper-phenotype
#20
Craig T Miller, James C Hart
Here we present and characterize the spontaneous X-linked recessive mutation casper, which causes oculocutaneous albinism in threespine sticklebacks (Gasterosteus aculeatus). In humans, Hermansky-Pudlak syndrome results in pigmentation defects due to disrupted formation of the melanin-containing lysosomal-related organelle (LRO), the melanosome. casper mutants display not only reduced pigmentation of melanosomes in melanophores, but also reductions in the iridescent silver color from iridophores, while the yellow pigmentation from xanthophores appears unaffected...
July 24, 2017: G3: Genes—Genomes—Genetics
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