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Genome evolution

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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/28641092/nuclear-mechanotransduction-sensing-the-force-from-within
#2
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/28640911/evolution-of-microrna-in-primates
#3
Jennifer C McCreight, Sean E Schneider, Damien B Wilburn, Willie J Swanson
MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely uncharacterized. A particular miRNA can have one to thousands of messenger RNA targets, establishing the potential for a small change in sequence or overall miRNA structure to have profound phenotypic effects. However, the majority of non-human primate miRNA is predicted solely by homology to the human genome and lacks experimental validation. In the present study, we sequenced thirteen species representing a wide range of the primate phylogeny...
2017: PloS One
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/28640696/insights-from-molecular-profiling-of-adult-glioma
#5
Phedias Diamandis, Kenneth D Aldape
The comprehensive molecular profiling of cancer has resulted in new insights into the biology and classification of numerous tumor types. In the case of primary brain tumors that commonly affect adults, an emerging set of disease-defining biomarker sets is reshaping existing diagnostic entities that had previously been defined on the basis of their microscopic appearance. Substantial progress has been made in this regard for common primary brain tumors in adults, especially diffuse gliomas, where large-scale profiling efforts have led to the incorporation of highly prevalent molecular alterations that promote a biologically based classification as an adjunct to the traditional histopathologic approach...
June 22, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28637269/announcing-the-genome-atlas-of-bamboo-and-rattan-gabr-project-promoting-research-in-evolution-and-in-economically-and-ecologically-beneficial-plants
#6
Hansheng Zhao, Shancen Zhao, Benhua Fei, Huan Liu, Huanming Yang, Honghai Dai, Dan Wang, Wei Jin, Feng Tang, Qiang Gao, Hang Xun, Yuwei Wang, Lianghua Qi, Xianghua Yue, Shuyan Lin, Lianfeng Gu, Lubin Li, Tiansheng Zhu, Qiang Wei, Zhen Su, Tarmeze Bin Wan Ariffin Wan, Daniel A Ofori, George Mbeva Muthike, Yigardu Mulatu Mengesha, Roberto Magno de Castro E Silva, Antonio Ludovico Beraldo, Zhimin Gao, Xin Liu, Zehui Jiang
Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of BR genetics through genome analysis...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637261/further-simulations-and-analyses-demonstrate-open-problems-of-phylostratigraphy
#7
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
#8
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
#9
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
#10
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/28636447/emerging-viral-infections-in-pakistan-issues-concerns-and-future-prospects
#11
Ali Talha Khalil, Muhammad Ali, Faouzia Tanveer, Muhammad Ovais, Muhammad Idrees, Zabta Khan Shinwari, James E Hollenbeck
Emerging infectious diseases pose a serious threat to public health security; this is especially true in the underdeveloped world because of limited resources to combat them. These emerging pathogens are characterized by a novel mode of pathogenesis and, in some cases, a broad host range. Over the past few decades, Pakistan has suffered a great deal from infectious diseases such as dengue, Crimean-Congo fever, hepatitis, measles, and polio. Changing climate conditions, environmental degradation, global warming, loss of biodiversity, and other ecological determinants have a direct effect on these diseases and result in the emergence and reemergence of infectious entities...
May 2017: Health Security
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#12
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28635103/uncovering-the-dispersion-history-adaptive-evolution-and-selection-of-wheat-in-china
#13
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/28634423/tumor-ras-gene-expression-levels-are-influenced-by-the-mutational-status-of-ras-genes-and-both-upstream-and-downstream-ras-pathway-genes
#14
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/28634337/evolutionary-and-network-analysis-of-virus-sequences-from-infants-infected-with-an-australian-recombinant-strain-of-human-parechovirus-type-3
#15
Soren Alexandersen, Tiffanie M Nelson, Jason Hodge, Julian Druce
We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012-2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634269/human-development-heredity-and-evolution
#16
REVIEW
Ryuichi Nishinakamura, Minoru Takasato
From March 27-29 2017, the RIKEN Center for Developmental Biology held a symposium entitled 'Towards Understanding Human Development, Heredity, and Evolution' in Kobe, Japan. Recent advances in technologies including stem cell culture, live imaging, single-cell approaches, next-generation sequencing and genome editing have led to an expansion in our knowledge of human development. Organized by Yoshiya Kawaguchi, Mitinori Saitou, Mototsugu Eiraku, Tomoya Kitajima, Fumio Matsuzaki, Takashi Tsuji and Edith Heard, the symposium covered a broad range of topics including human germline development, epigenetics, organogenesis and evolution...
June 15, 2017: Development
https://www.readbyqxmd.com/read/28634106/biology-evolution-and-medical-importance-of-polyomaviruses-an-update
#17
REVIEW
Ugo Moens, Andi Krumbholz, Bernhard Ehlers, Roland Zell, Reimar Johne, Sébastien Calvignac-Spencer, Chris Lauber
The family Polyomaviridae encompasses non-enveloped viruses with a circular dsDNA genome that is typically approximately 5000bp in length. Originally isolated from mammals, polyomavirus sequences have now been detected in invertebrates, fish, amphibians, reptiles and birds, although it remains to be determined whether all these animals are genuine hosts. The genomes of all polyomaviruses encode at least two regulatory proteins (large and small tumour antigen) and two structural proteins (capsid proteins VP1 and VP2) whose functions have been defined...
June 17, 2017: Infection, Genetics and Evolution
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/28633473/experimental-evolution-and-the-adjustment-of-metabolic-strategies-in-lactic-acid-bacteria
#20
Herwig Bachmann, Douwe Molenaar, Filipe Branco Dos Santos, Bas Teusink
Experimental evolution of microbes has gained lots of interest in recent years, mainly due to the ease of strain characterisation through next-generation sequencing. While evolutionary and systems biologists use experimental evolution to address fundamental questions in their respective fields, studies with lactic acid bacteria are often more directed by applied questions. Insight into population and genome dynamics are valuable for experimental design and data interpretation, and it is becoming increasingly apparent how different constraints limit and govern the outcome of microbial adaptation to a selective environment...
June 19, 2017: FEMS Microbiology Reviews
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