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https://www.readbyqxmd.com/read/28743172/modelling-nutritional-mutualisms-challenges-and-opportunities-for-data-integration
#1
REVIEW
Teresa J Clark, Colleen A Friel, Emily Grman, Yair Shachar-Hill, Maren L Friesen
Nutritional mutualisms are ancient, widespread, and profoundly influential in biological communities and ecosystems. Although much is known about these interactions, comprehensive answers to fundamental questions, such as how resource availability and structured interactions influence mutualism persistence, are still lacking. Mathematical modelling of nutritional mutualisms has great potential to facilitate the search for comprehensive answers to these and other fundamental questions by connecting the physiological and genomic underpinnings of mutualisms with ecological and evolutionary processes...
July 25, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28743034/therapeutic-advances-in-musculoskeletal-aav-targeting-approaches
#2
REVIEW
Karen Bulaklak, Xiao Xiao
The use of recombinant adeno-associated viruses (rAAVs) is highly prevalent in musculoskeletal gene therapies due to their versatility, high transduction efficiency, natural tropism and vector genome persistence for years. As the largest organ in the body, treatment of skeletal muscle for widespread and sufficient therapeutic gene expression is highly challenging. In addition to disease-specific hurdles, vector genome loss, off-target gene transfer and immune responses to treatment can diminish the overall benefit of rAAV therapies...
July 22, 2017: Current Opinion in Pharmacology
https://www.readbyqxmd.com/read/28743024/a-method-to-evaluate-the-quality-of-clinical-gene-panel-sequencing-data-for-single-nucleotide-variant-detection
#3
Chung Lee, Joon S Bae, Gyu H Ryu, Nayoung K D Kim, Donghyun Park, Jongsuk Chung, Sungkyu Kyung, Je-Gun Joung, Hyun-Tae Shin, Seung-Ho Shin, Younglan Kim, Byung S Kim, Hojun Lee, Kyoung-Mee Kim, Jung-Sun Kim, Woong-Yang Park, Dae-Soon Son
Customized gene-panel tests, based on next-generation sequencing, have demonstrated their usefulness in a plethora of clinical settings. As with other clinical diagnostic techniques, gene-panel sequencing for clinical purposes requires precise quality control (QC) measures to ensure its reliability. Only detected variants are currently recorded in clinical reports; however, identifying whether a nondetected variant is a true or false negative is regarded essential in a clinical setting and, thus, a comprehensive QC measure is in demand...
July 22, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28743015/plant-domestication-wild-date-palms-illuminate-a%C3%A2-crop-s-sticky-origins
#4
Nathan Wales, Benjamin K Blackman
In a new study, previously unknown populations of wild date palm have been identified in remote areas of Oman. Genomic analyses indicate date palm domestication occurred in the eastern portion of the Arabian Peninsula and reveal substantial subsequent gene flow with African palm populations.
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28743002/drosophila-histone-demethylase-kdm4a-has-enzymatic-and-non-enzymatic-roles-in-controlling-heterochromatin-integrity
#5
Serafin U Colmenares, Joel M Swenson, Sasha A Langley, Cameron Kennedy, Sylvain V Costes, Gary H Karpen
Eukaryotic genomes are broadly divided between gene-rich euchromatin and the highly repetitive heterochromatin domain, which is enriched for proteins critical for genome stability and transcriptional silencing. This study shows that Drosophila KDM4A (dKDM4A), previously characterized as a euchromatic histone H3 K36 demethylase and transcriptional regulator, predominantly localizes to heterochromatin and regulates heterochromatin position-effect variegation (PEV), organization of repetitive DNAs, and DNA repair...
July 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28742982/investigation-of-orthologous-pathogen-recognition-gene-rich-regions-in-solanaceous-species
#6
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/28742980/disease-relevant-modifications-of-the-methylome-and-transcriptome-by-particulate-matter-pm2-5-from-biomass-combustion
#7
Katharina Heßelbach, Gwang-Jin Kim, Stephan Flemming, Thomas Häupl, Marc Bonin, Regina Dornhof, Stefan Günther, Irmgard Merfort, Matjaz Humar
Exposure to particulate matter (PM) is recognized as a major health hazard, but molecular responses are still insufficiently described. We analyzed the epigenetic impact of ambient PM2.5 from biomass combustion on the methylome of primary human bronchial epithelial BEAS-2B cells using the Illumina HumanMethylation450 BeadChip. The transcriptome was determined by the Affymetrix HG-U133 Plus 2.0 Array. PM2.5 induced genome wide alterations of the DNA methylation pattern, including differentially methylated CpGs in the promoter region associated with CpG islands...
July 25, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28742942/regulation-of-transposable-elements-interplay-between-te-encoded-regulatory-sequences-and-host-specific-trans-acting-factors-in-drosophila-melanogaster
#8
Ana Marija Jakšić, Robert Kofler, Christian Schlötterer
Transposable elements (TEs) are mobile genetic elements that can move around the genome and their expression is one precondition for this mobility. Because the insertion of TEs in new genomic positions is largely deleterious, the molecular mechanisms for transcriptional suppression have been extensively studied. In contrast, very little is known about their primary transcriptional regulation. Here, we characterize the expression dynamics of TE families in Drosophila melanogaster across a broad temperature range (13-29°C)...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742937/models-for-discovery-of-targeted-therapy-in-genetic-epileptic-encephalopathies
#9
REVIEW
Snezana Maljevic, Christopher A Reid, Steven Petrou
Epileptic encephalopathies are severe disorders emerging in the first days to years of life that commonly include refractory seizures, various types of movement disorders, and different levels of developmental delay. In recent years, many de novo occurring variants have been identified in individuals with these devastating disorders. To unravel disease mechanisms the functional impact of detected variants associated with epileptic encephalopathies is investigated in a range of cellular and animal models. This review addresses efforts to advance and use such models to identify specific molecular and cellular targets for the development of novel therapies...
July 25, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28742933/gene-expression-is-more-strongly-influenced-by-age-than-caste-in-the-ant-lasius-niger
#10
Eric R Lucas, Jonathan Romiguier, Laurent Keller
Phenotypic plasticity, where a single genome can give rise to different phenotypes, underlies many remarkable features of the natural world and occurs in a wide range of organisms. Understanding the transcriptional differences that underlie plastic phenotypes remains a major unsolved problem in biology. In many ants, females can develop into either queens or workers, two phenotypes with different morphology, behaviour and longevity. In comparison to workers, queens are larger, more fecund and longer-lived. Here, we study gene expression differences between queens and workers in the ant Lasius niger...
July 25, 2017: Molecular Ecology
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
#11
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/28742912/association-of-genetic-variants-related-to-serum-calcium-levels-with-coronary-artery-disease-and-myocardial-infarction
#12
Susanna C Larsson, Stephen Burgess, Karl Michaëlsson
Importance: Serum calcium has been associated with cardiovascular disease in observational studies and evidence from randomized clinical trials indicates that calcium supplementation, which raises serum calcium levels, may increase the risk of cardiovascular events, particularly myocardial infarction. Objective: To evaluate the potential causal association between genetic variants related to elevated serum calcium levels and risk of coronary artery disease (CAD) and myocardial infarction using mendelian randomization...
July 25, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28742865/a-novel-mitochondrial-genome-of-arborophila-and-new-insight-into-arborophila-evolutionary-history
#13
Chaochao Yan, Biqin Mou, Yang Meng, Feiyun Tu, Zhenxin Fan, Megan Price, Bisong Yue, Xiuyue Zhang
The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant...
2017: PloS One
https://www.readbyqxmd.com/read/28742862/plio-pleistocene-phylogeography-of-the-southeast-asian-blue-panchax-killifish-aplocheilus-panchax
#14
Samantha V Beck, Gary R Carvalho, Axel Barlow, Lukas Rüber, Heok Hui Tan, Estu Nugroho, Daisy Wowor, Siti Azizah Mohd Nor, Fabian Herder, Zainal A Muchlisin, Mark de Bruyn
The complex climatic and geological history of Southeast Asia has shaped this region's high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins...
2017: PloS One
https://www.readbyqxmd.com/read/28742856/fit-for-genomic-and-proteomic-purposes-sampling-the-fitness-of-nucleic-acid-and-protein-derivatives-from-formalin-fixed-paraffin-embedded-tissue
#15
Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules...
2017: PloS One
https://www.readbyqxmd.com/read/28742845/evaluation-of-k-ras-and-p53-expression-in-pancreatic-adenocarcinoma-using-the-cancer-genome-atlas
#16
Liming Lu, Jingchun Zeng
Genetic alterations in K-ras and p53 are thought to be critical in pancreatic cancer development and progression. However, K-ras and p53 expression in pancreatic adenocarcinoma have not been systematically examined in The Cancer Genome Atlas (TCGA) Data Portal. Information regarding K-ras and p53 alterations, mRNA expression data, and protein/protein phosphorylation abundance was retrieved from The Cancer Genome Atlas (TCGA) databases, and analyses were performed by the cBioPortal for Cancer Genomics. The mutual exclusivity analysis showed that events in K-ras and p53 were likely to co-occur in pancreatic adenocarcinoma (Log odds ratio = 1...
2017: PloS One
https://www.readbyqxmd.com/read/28742843/sequencing-of-the-complete-mitochondrial-genomes-of-eight-freshwater-snail-species-exposes-pervasive-paraphyly-within-the-viviparidae-family-caenogastropoda
#17
Ju-Guang Wang, Dong Zhang, Ivan Jakovlić, Wei-Min Wang
Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers...
2017: PloS One
https://www.readbyqxmd.com/read/28742823/genome-wide-identification-and-analysis-of-the-mads-box-gene-family-in-bread-wheat-triticum-aestivum-l
#18
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/28742818/first-identification-of-a-recombinant-form-of-hepatitis-c-virus-in-austrian-patients-by-full-genome-next-generation-sequencing
#19
Evelyn Stelzl, Bernhard Haas, Bernd Bauer, Sherry Zhang, Ellen H Fiss, Grantland Hillman, Aaron T Hamilton, Rochak Mehta, Marintha L Heil, Ed G Marins, Brigitte I Santner, Harald H Kessler
Hepatitis C virus (HCV) intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA) was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b...
2017: PloS One
https://www.readbyqxmd.com/read/28742812/broad-range-lytic-bacteriophages-that-kill-staphylococcus-aureus-local-field-strains
#20
Virginia Abatángelo, Natalia Peressutti Bacci, Carina A Boncompain, Ariel A Amadio, Soledad Carrasco, Cristian A Suárez, Héctor R Morbidoni
Staphylococcus aureus is a very successful opportunistic pathogen capable of causing a variety of diseases ranging from mild skin infections to life-threatening sepsis, meningitis and pneumonia. Its ability to display numerous virulence mechanisms matches its skill to display resistance to several antibiotics, including β-lactams, underscoring the fact that new anti-S. aureus drugs are urgently required. In this scenario, the utilization of lytic bacteriophages that kill bacteria in a genus -or even species- specific way, has become an attractive field of study...
2017: PloS One
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