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https://www.readbyqxmd.com/read/28641396/geneticization-in-mim-omim%C3%A2-exploring-historic-and-epistemic-drivers-of-contemporary-understandings-of-genetic-disease
#1
Rachel A Ankeny
Prior to the genomic sequencing era, the bible for those working in clinical genetics was McKusick's Mendelian Inheritance in Man (MIM), which appeared in multiple editions between the 1960s and the late 1990s. This catalogue was organized according to general patterns of inheritance and focused on phenotypes. Beginning in the mid-1980s, it was replaced by Online Mendelian Inheritance in Man (OMIM®), a continuously updated catalogue documenting molecular relationships between genetic variation and phenotypic expression...
June 21, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28641277/association-of-the-cfh-y402h-polymorphism-with-the-1-year-response-of-exudative-amd-to-intravitreal-anti-vegf-treatment-in-the-brazilian-population
#2
Flavio Mac Cord Medina, Augusto Alves Lopes da Motta, Walter Yukihiko Takahashi, Pedro Carlos Carricondo, Mario Martins Dos Santos Motta, Monica B Melo, Jose Paulo C Vasconcellos
AIM: Evidence of the relationship between the polymorphism of the complement factor H (CFH) gene at position 402 (Y402H) and the response to the treatment of wet AMD is controversial. The aim of this study was to compare the functional and morphological 1-year evolution of patients with exudative AMD treated with antivascular endothelial growth factor (VEGF) drugs with the CFH Y402H polymorphism in the Brazilian population. METHODS: Forty-six patients treated for wet AMD with bevacizumab or ranibizumab in a pro re nata regimen were included...
June 23, 2017: Ophthalmic Research
https://www.readbyqxmd.com/read/28641092/nuclear-mechanotransduction-sensing-the-force-from-within
#3
REVIEW
Avathamsa Athirasala, Nivi Hirsch, Amnon Buxboim
The cell nucleus is a hallmark of eukaryotic evolution, where gene expression is regulated and the genome is replicated and repaired. Yet, in addition to complex molecular processes, the nucleus has also evolved to serve physical tasks that utilize its optical and mechanical properties. Nuclear mechanotransduction of externally applied forces and extracellular stiffness is facilitated by the physical connectivity of the extracellular environment, the cytoskeleton and the nucleoskeletal matrix of lamins and chromatin...
June 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28640886/epigenomic-diversification-within-the-genus-lupinus
#4
Karolina Susek, Agnieszka Braszewska-Zalewska, Adam J Bewick, Robert Hasterok, Robert J Schmitz, Barbara Naganowska
Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organisation of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment...
2017: PloS One
https://www.readbyqxmd.com/read/28640838/next-generation-sequencing-of-the-clonal-igh-rearrangement-detects-ongoing-mutations-and-interfollicular-trafficking-in-in-situ-follicular-neoplasia
#5
Perikles Kosmidis, Irina Bonzheim, Claudia Dufke, Sema Colak, Thomas Hentrich, Christopher Schroeder, Peter Bauer, Patrick Adam, Falko Fend
Follicular lymphoma (FL) is characterized genetically by a significant intraclonal diversity of rearranged immunoglobulin heavy chain (IGH) genes and a substantial cell migration activity (follicular trafficking). Recently, in situ follicular neoplasia (ISFN), characterized by accumulations of immunohistochemically strongly BCL2-positive, t(14;18)+ clonal B cells confined to germinal centers in reactive lymph nodes, has been identified as a precursor lesion of FL with low risk of progression to manifest FL...
2017: PloS One
https://www.readbyqxmd.com/read/28637323/evolution-of-transcription-activator-like-effectors-in-xanthomonas-oryzae
#6
Annett Erkes, Maik Reschke, Jens Boch, Jan Grau
Transcription activator-like effectors (TALEs) are secreted by plant-pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid tandem repeats, where amino acid 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28637270/in-planta-recapitulation-of-isoprene-synthases-evolution-from-ocimene-synthases
#7
Mingai Li, Jia Xu, Alberto Algarra Alarcon, Silvia Carlin, Enrico Barbaro, Luca Cappellin, Violeta Velikova, Urska Vrhovsek, Francesco Loreto, Claudio Varotto
Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated.We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases...
June 16, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28637261/further-simulations-and-analyses-demonstrate-open-problems-of-phylostratigraphy
#8
Bryan A Moyers, Jianzhi Zhang
Phylostratigraphy, originally designed for gene age estimation by BLAST-based protein homology searches of sequenced genomes, has been widely used for studying patterns and inferring mechanisms of gene origination and evolution. We previously showed by computer simulation that phylostratigraphy underestimates gene age for a non-negligible fraction of genes and that the underestimation is severer for genes with certain properties such as fast evolution and short protein sequences. Consequently, many previously reported age distributions of gene properties may have been methodological artifacts rather than biological realities...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28637205/evolution-and-comparative-genomics-of-paqu-like-conjugative-plasmids-in-vibrio-species
#9
Ruichao Li, Lianwei Ye, Marcus Ho Yin Wong, Zhiwei Zheng, Edward Wai Chi Chan, Sheng Chen
Objectives: To investigate a set of MDR conjugative plasmids found in Vibrio species and characterize the underlying evolution process. Methods: pAQU-type plasmids from Vibrio species were sequenced using both Illumina and PacBio platforms. Bioinformatics tools were utilized to analyse the typical MDR regions and core genes in the plasmids. Results: The nine pAQU-type plasmids ranged from ∼160 to 206 kb in size and were found to harbour as many as 111 core genes encoding conjugative, replication and maintenance functions...
June 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28637190/evolution-of-the-sperm-methylome-of-primates-is-associated-with-retrotransposon-insertions-and-genome-instability
#10
Kei Fukuda, Yukihiro Inoguchi, Kenji Ichiyanagi, Tomoko Ichiyanagi, Yasuhiro Go, Masashi Nagano, Yojiro Yanagawa, Noboru Takaesu, Yasuyuki Ohkawa, Hiroo Imai, Hiroyuki Sasaki
Changes in gene expression resulting from epigenetic and/or genetic changes play an important role in the evolutionary divergence of phenotypes. To explore how epigenetic and genetic changes are linked during primate evolution, we have compared the genome-wide DNA methylation profiles (methylomes) of humans and chimpanzees, which have a 1.2% DNA sequence divergence, of sperm, the frontal cortices, B cells, and neutrophils. We revealed that species-specific differentially methylated regions (S-DMRs), ranging from several hundred bp to several kb, were frequently associated with sequence changes in transcription factor binding sites and insertions of Alu and SVA retrotransposons...
June 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28636881/mitochondrial-genome-of-helice-tientsinensis-brachyura-grapsoidea-varunidae-gene-rearrangements-and-higher-level-phylogeny-of-the-brachyura
#11
Zhao-Zhe Xin, Yu-Liu, Dai-Zhen Zhang, Zheng-Fei Wang, Hua-Bin Zhang, Bo-Ping Tang, Chun-Lin Zhou, Xin-Yue Chai, Qiu-Ning Liu
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogeny. The further understand the molecular evolution and phylogeny of Helice tientsinensis, the complete mt genome was determined. It is 16,212bp long and includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a control region. The genome composition of H. tientsinensis was highly A+T biased 69.0% and showed negative AT skew (-0.017) and GC skew (-0.289). One PCG, all rRNAs and 12 of the tRNAs appeared to be rearranged with respect to the pancrustacean ground pattern gene order...
June 18, 2017: Gene
https://www.readbyqxmd.com/read/28636368/probing-the-mechanism-of-lal-32-a-gold-nanoparticle-based-antibiotic-discovered-through-small-molecule-variable-ligand-display
#12
Rose Byrne-Nash, Danielle Lucero, Niki Osbaugh, Roberta J Melander, Christian Melander, Daniel L Feldheim
The unrelenting rise of antimicrobial resistant bacteria has necessitated the search for novel antibiotic solutions. Herein we describe further mechanistic studies on a 2.0 nm diameter gold nanoparticle-based antibiotic (designated LAL-32). This antibiotic exhibits bactericidal activity against the Gram-negative bacterium Escherichia coli at 1.0 μΜ, a concentration significantly lower than several clinically available antibiotics (such as ampicillin and gentamicin), and acute treatment with LAL-32 does not give rise to spontaneous resistant mutants...
June 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28635965/identification-genealogical-structure-and-population-genetics-of-s-alleles-in-malus-sieversii-the-wild-ancestor-of-domesticated-apple
#13
X Ma, Z Cai, W Liu, S Ge, L Tang
The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris...
June 21, 2017: Heredity
https://www.readbyqxmd.com/read/28635103/uncovering-the-dispersion-history-adaptive-evolution-and-selection-of-wheat-in-china
#14
Yong Zhou, Zhongxu Chen, Mengping Cheng, Jian Chen, Tingting Zhu, Rui Wang, Yaxi Liu, Pengfei Qi, Guoyue Chen, Qiantao Jiang, Yuming Wei, Ming-Cheng Luo, Eviatar Nevo, Robin G Allaby, Dengcai Liu, Jirui Wang, Jan Dvorák, Youliang Zheng
Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27,933 DArTseq (for 717 landraces) and 312,831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces...
June 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28634583/circular-rnas-biogenesis-function-and-role-in-human-diseases
#15
REVIEW
John Greene, Anne-Marie Baird, Lauren Brady, Marvin Lim, Steven G Gray, Raymond McDermott, Stephen P Finn
Circular RNAs (circRNAs) are currently classed as non-coding RNA (ncRNA) that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28634423/tumor-ras-gene-expression-levels-are-influenced-by-the-mutational-status-of-ras-genes-and-both-upstream-and-downstream-ras-pathway-genes
#16
Robert M Stephens, Ming Yi, Bailey Kessing, Dwight V Nissley, Frank McCormick
The 3 human RAS genes play pivotal roles regulating proliferation, differentiation, and survival in normal cells and become mutated in 15% to 20% of all human tumors and amplified in many others. In this report, we examined data from The Cancer Genome Atlas to investigate the relationship between RAS gene mutational status and messenger RNA expression. We show that all 3 RAS genes exhibit increased expression when they are mutated in a context-dependent manner. In the case of KRAS, this increase is manifested by a larger proportional increase in KRAS4A than KRAS4B, although both increase significantly...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28634236/alternative-evolutionary-pathways-for-drug-resistant-small-colony-variant-mutants-in-staphylococcus-aureus
#17
Sha Cao, Douglas L Huseby, Gerrit Brandis, Diarmaid Hughes
Staphylococcus aureus is known to generate small colony variants (SCVs) that are resistant to aminoglycoside antibiotics and can cause persistent and recurrent infections. The SCV phenotype is unstable, and compensatory mutations lead to restored growth, usually with loss of resistance. However, the evolution of improved growth, by mechanisms that avoid loss of antibiotic resistance, is very poorly understood. By selection with serial passaging, we isolated and characterized different classes of extragenic suppressor mutations that compensate for the slow growth of small colony variants...
June 20, 2017: MBio
https://www.readbyqxmd.com/read/28634029/discovery-of-scors-anciently-derived-highly-conserved-gene-associated-repeats-in-stony-corals
#18
Huan Qiu, Ehud Zelzion, Hollie M Putnam, Ruth D Gates, Nicole E Wagner, Diane K Adams, Debashish Bhattacharya
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA...
June 17, 2017: Genomics
https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-non-coding-sequences-on-embryonic-brain-development
#19
Morteza Mahmoudi Saber, Naruya Saitou
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633361/evolution-of-mirna-tailing-by-3-terminal-uridylyl-transferases-in-metazoa
#20
Vengamanaidu Modepalli, Yehu Moran
In bilaterian animals the 3' ends of microRNAs (miRNAs) are frequently modified by tailing and trimming. These modifications affect miRNA-mediated gene regulation by modulating miRNA stability. Here we analyzed data from three non-bilaterian animals: two cnidarians (Nematostella vectensis and Hydra magnipapillata) and one poriferan (Amphimedon queenslandica). Our analysis revealed that non-bilaterian miRNAs frequently undergo modifications like the bilaterian counterparts: the majority are expressed as different length isoforms and frequent modifications of the 3' end by mono U or mono A tailing are observed...
June 14, 2017: Genome Biology and Evolution
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