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https://www.readbyqxmd.com/read/27914076/reconstructing-the-ancestral-relationships-between-bacterial-pathogen-genomes
#1
Caitlin Collins, Xavier Didelot
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#2
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913828/engineering-and-evolution-of-saccharomyces-cerevisiae-to-produce-biofuels-and-chemicals
#3
Timothy L Turner, Heejin Kim, In Iok Kong, Jing-Jing Liu, Guo-Chang Zhang, Yong-Su Jin
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology...
December 3, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27913751/new-fungal-defensin-like-peptides-provide-evidence-for-fold-change-of-proteins-in-evolution
#4
Yucheng Wu, Bin Gao, Shunyi Zhu
Defensins containing a consensus cystine framework, Cys[1]..Cys[2]X3Cys[3]..Cys[4]..Cys[5]X1Cys[6] ("X", any amino acids normally except Cys; "...", variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming a cystine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation...
December 2, 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27913727/regulated-complex-assembly-safeguards-the-fidelity-of-sleeping-beauty-transposition
#5
Yongming Wang, Diana Pryputniewicz-Dobrinska, Enikö Éva Nagy, Christopher D Kaufman, Manvendra Singh, Steve Yant, Jichang Wang, Anna Dalda, Mark A Kay, Zoltán Ivics, Zsuzsanna Izsvák
The functional relevance of the inverted repeat structure (IR/DR) in a subgroup of the Tc1/mariner superfamily of transposons has been enigmatic. In contrast to mariner transposition, where a topological filter suppresses single-ended reactions, the IR/DR orchestrates a regulatory mechanism to enforce synapsis of the transposon ends before cleavage by the transposase occurs. This ordered assembly process shepherds primary transposase binding to the inner 12DRs (where cleavage does not occur), followed by capture of the 12DR of the other transposon end...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913665/structure-and-function-of-bacterial-h-ns-protein
#6
REVIEW
David C Grainger
The histone-like nucleoid structuring (H-NS) protein is a major component of the folded chromosome in Escherichia coli and related bacteria. Functions attributed to H-NS include management of genome evolution, DNA condensation, and transcription. The wide-ranging influence of H-NS is remarkable given the simplicity of the protein, a small peptide, possessing rudimentary determinants for self-association, hetero-oligomerisation and DNA binding. In this review, I will discuss our understanding of H-NS with a focus on these structural elements...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913636/the-effect-of-temperature-on-drosophila-hybrid-fitness
#7
Charles J J Miller, Daniel R Matute
Mechanisms of reproductive isolation inhibit gene flow between species and can be broadly sorted into two categories: prezygotic and postzygotic. While comparative studies suggest that prezygotic barriers tend to evolve first, postzygotic barriers are crucial for maintaining species boundaries and impeding gene flow that might otherwise cause incipient species to merge. Most, but not all, postzygotic barriers result from genetic incompatibilities between two or more loci from different species, and occur due to divergent evolution in allopatry...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27913420/multiple-evolutionary-trajectories-have-led-to-the-emergence-of-races-in-fusarium-oxysporum-f-sp-lycopersici
#8
Biju V Chellappan, Like Fokkens, Petra M Houterman, Martijn Rep, Ben J C Cornelissen
: Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (Fol) are characterized by the presence of AVR1 in their genome. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I In Fol race 2 and race 3 isolates, AVR1 is absent and hence they are virulent on tomato cultivars carrying I In this study, we analyze an approximately 100 kb genomic fragment containing the AVR1 locus of race 1 isolate Fol004, and compare it to the sequenced genome of Fol race 2 isolate 4287 (Fol4287)...
December 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27912247/molecular-evolution-in-insect-societies-an-eco-evo-devo-synthesis
#9
Amy L Toth, Sandra M Rehan
The evolution of eusociality is a perennial issue in evolutionary biology, and genomic advances have fueled steadily growing interest in the genetic changes underlying social evolution. Along with a recent flurry of research on comparative and evolutionary genomics in different eusocial insect groups (bees, ants, wasps, and termites), several mechanistic explanations have emerged to describe the molecular evolution of eusociality from solitary behavior. These include solitary physiological ground plans, genetic toolkits of deeply conserved genes, evolutionary changes in protein-coding genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes...
November 28, 2016: Annual Review of Entomology
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#10
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
https://www.readbyqxmd.com/read/27911848/global-analysis-of-genomic-instability-caused-by-dna-replication-stress-in-saccharomyces-cerevisiae
#11
Dao-Qiong Zheng, Ke Zhang, Xue-Chang Wu, Piotr A Mieczkowski, Thomas D Petes
DNA replication stress (DRS)-induced genomic instability is an important factor driving cancer development. To understand the mechanisms of DRS-associated genomic instability, we measured the rates of genomic alterations throughout the genome in a yeast strain with lowered expression of the replicative DNA polymerase δ. By a genetic test, we showed that most recombinogenic DNA lesions were introduced during S or G2 phase, presumably as a consequence of broken replication forks. We observed a high rate of chromosome loss, likely reflecting a reduced capacity of the low-polymerase strains to repair double-stranded DNA breaks (DSBs)...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911792/transcriptomics-and-neuroanatomy-of-the-clonal-raider-ant-implicate-an-expanded-clade-of-odorant-receptors-in-chemical-communication
#12
Sean K McKenzie, Ingrid Fetter-Pruneda, Vanessa Ruta, Daniel J C Kronauer
A major aim of sociogenomic research is to uncover common principles in the molecular evolution of sociality. This endeavor has been hampered by the small number of specific genes currently known to function in social behavior. Here we provide several lines of evidence suggesting that ants have evolved a large and novel clade of odorant receptor (OR) genes to perceive hydrocarbon-based pheromones, arguably the most important signals in ant communication. This genomic expansion is also mirrored in the ant brain via a corresponding expansion of a specific cluster of glomeruli in the antennal lobe...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910910/genome-wide-characterisation-and-expression-profile-of-the-grapevine-atl-ubiquitin-ligase-family-reveal-biotic-and-abiotic-stress-responsive-and-development-related-members
#13
Pietro Ariani, Alice Regaiolo, Arianna Lovato, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Darren Wong, Simone Castellarin, Elodie Vandelle, Annalisa Polverari
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910763/il10-a-tale-of-an-evolutionarily-conserved-cytokine-across-vertebrates
#14
M Carla Piazzon, George Lutfalla, Maria Forlenza
IL10 was discovered in 1989, and since then it has been the subject of intense investigation, which has revealed its potent anti-inflammatory and regulatory activities in most immune processes during infection and disease. In 2003, the first non-mammalian IL10 sequence was identified in teleost fish, followed in 2004 by the chicken IL10 sequence. In this review, we summarize the work performed in non-mammalian vertebrates in which the IL10, IL10 receptors (IL10Rs), and their signaling components have been identified...
2016: Critical Reviews in Immunology
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#15
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27910023/array-based-comparative-genomic-hybridization-acgh
#16
Chengsheng Zhang, Eliza Cerveira, Mallory Romanovitch, Qihui Zhu
Copy number variations (CNVs) in the genomes have been suggested to play important roles in human evolution, genetic diversity, and disease susceptibility. A number of assays have been developed for the detection of CNVs, including fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (aCGH), PCR-based assays, and next-generation sequencing (NGS). In this chapter, we describe a microarray method that has been used for the detection of genome-wide CNVs, loss of heterozygosity (LOH), and uniparental disomy (UPD) associated with constitutional and neoplastic disorders...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910009/cancer-cytogenetics-an-introduction
#17
Thomas S K Wan
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908688/increased-production-of-l-serine-in-escherichia-coli-through-adaptive-laboratory-evolution
#18
Hemanshu Mundhada, Jose S Miguel, Konstantin Schneider, Anna Koza, Hanne B Christensen, Tobias Klein, Patrick V Phaneuf, Markus Herrgard, Adam M Feist, Alex T Nielsen
L-serine is a promising building block biochemical with a high theoretical production yield from glucose. Toxicity of L-serine is however prohibitive for high-titer production in E. coli. Here, E. coli lacking L-serine degradation pathways was evolved for improved tolerance by gradually increasing L-serine concentration from 3 to 100g/L using adaptive laboratory evolution (ALE). Genome sequencing of isolated clones revealed multiplication of genetic regions, as well as mutations in thrA, thereby showing a potential mechanism of serine inhibition...
November 28, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#19
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
November 28, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27906993/ancient-mitochondrial-capture-as-factor-promoting-mitonuclear-discordance-in-freshwater-fishes-a-case-study-in-the-genus-squalius-actinopterygii-cyprinidae-in-greece
#20
Silvia Perea, Jasna Vukić, Radek Šanda, Ignacio Doadrio
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data...
2016: PloS One
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