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https://www.readbyqxmd.com/read/27923069/characterization-in-helicobacter-pylori-of-a-nickel-transporter-essential-for-colonization-that-was-acquired-during-evolution-by-gastric-helicobacter-species
#1
Frédéric Fischer, Marie Robbe-Saule, Evelyne Turlin, Francesco Mancuso, Valérie Michel, Pierre Richaud, Frédéric J Veyrier, Hilde De Reuse, Daniel Vinella
Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27920204/studies-on-the-detection-expression-glycosylation-dimerization-and-ligand-binding-properties-of-mouse-siglec-e
#2
Shoib Siddiqui, Flavio Schwarz, Stevan Springer, Zahra Khedri, Hai Yu, Lingquan Deng, Andrea Verhagen, Yuko Naito-Matsui, Weiping Jiang, Daniel Kim, Jie Zhou, Beibei Ding, Xi Chen, Nissi Varki, Ajit Varki
CD33-related Siglecs are a family of proteins widely expressed on innate immune cells. Binding of sialylated glycans or other ligands triggers signals that inhibit or activate inflammation. Immunomodulation by Siglecs has been extensively studied, but relationships between structure and functions are poorly explored. Here we present new data relating the structure and function of Siglec-E, the major CD33-related Siglec expressed on mouse neutrophils, monocytes, macrophages, and dendritic cells. We generated nine new rat monoclonal antibodies specific to mouse Siglec-E, with no cross-reactivity to Siglec-F...
December 5, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27918435/piecemeal-buildup-of-the-genetic-code-ribosomes-and-genomes-from-primordial-trna-building-blocks
#3
Derek Caetano-Anollés, Gustavo Caetano-Anollés
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains...
December 2, 2016: Life
https://www.readbyqxmd.com/read/27917941/comparative-phylogenomic-analysis-provides-insights-into-tcp-gene-functions-in-sorghum
#4
Aleena Francis, Namrata Dhaka, Mohit Bakshi, Ki-Hong Jung, Manoj K Sharma, Rita Sharma
Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917320/the-complete-chloroplast-genome-sequence-of-helwingia-himalaica-helwingiaceae-aquifoliales-and-a-chloroplast-phylogenomic-analysis-of-the-campanulidae
#5
Xin Yao, Ying-Ying Liu, Yun-Hong Tan, Yu Song, Richard T Corlett
Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels...
2016: PeerJ
https://www.readbyqxmd.com/read/27917315/the-first-complete-plastid-genomes-of-melastomataceae-are-highly-structurally-conserved
#6
Marcelo Reginato, Kurt M Neubig, Lucas C Majure, Fabian A Michelangeli
BACKGROUND: In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. METHODS: Genome skimming was performed for 16 species spread across the Melastomataceae...
2016: PeerJ
https://www.readbyqxmd.com/read/27917155/aerobic-lineage-of-the-oxidative-stress-response-protein-rubrerythrin-emerged-in-an-ancient-microaerobic-hyper-thermophilic-environment
#7
Juan P Cardenas, Raquel Quatrini, David S Holmes
Rubrerythrins (RBRs) are non-heme di-iron proteins belonging to the ferritin-like superfamily. They are involved in oxidative stress defense as peroxide scavengers in a wide range of organisms. The vast majority of RBRs, including classical forms of this protein, contain a C-terminal rubredoxin-like domain involved in electron transport that is used during catalysis in anaerobic conditions. Rubredoxin is an ancient and large protein family of short length (<100 residues) that contains a Fe-S center involved in electron transfer...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27911898/bilaterian-giant-ankyrins-have-a-common-evolutionary-origin-and-play-a-conserved-role-in-patterning-the-axon-initial-segment
#8
Timothy Jegla, Michelle M Nguyen, Chengye Feng, Daniel J Goetschius, Esteban Luna, Damian B van Rossum, Bishoy Kamel, Aditya Pisupati, Elliott S Milner, Melissa M Rolls
In vertebrate neurons, the axon initial segment (AIS) is specialized for action potential initiation. It is organized by a giant 480 Kd variant of ankyrin G (AnkG) that serves as an anchor for ion channels and is required for a plasma membrane diffusion barrier that excludes somatodendritic proteins from the axon. An unusually long exon required to encode this 480Kd variant is thought to have been inserted only recently during vertebrate evolution, so the giant ankyrin-based AIS scaffold has been viewed as a vertebrate adaptation for fast, precise signaling...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27908741/resolving-interspecific-relationships-within-evolutionarily-young-lineages-using-rna-seq-data-an-example-from-pedicularis-section-cyathophora-orobanchaceae
#9
Hong-Juan Wang, Wei-Tao Li, Ya-Nan Liu, Fu-Sheng Yang, Xiao-Quan Wang
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species...
November 28, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#10
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903602/whole-genome-sequencing-of-mycobacterium-tuberculosis-provides-insight-into-the-evolution-and-genetic-composition-of-drug-resistant-tuberculosis-in-belarus
#11
Kurt R Wollenberg, Christopher A Desjardins, Aksana Zalutskaya, Vervara Slodovnikova, Andrew J Oler, Mariam Quiñones, Thomas Abeel, Sinead B Chapman, Michael Tartakovsky, Andrei Gabrielian, Sven Hoffner, Aliaksandr Skrahin, Bruce W Birren, Alexander Rosenthal, Alena Skrahina, Ashlee M Earl
The emergence and spread of drug resistant Mycobacterium tuberculosis (DR-TB) is a critical global health issue. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB...
November 30, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27902180/phylogenomic-analysis-of-the-family-peptostreptococcaceae-clostridium-cluster-xi-and-proposal-for-reclassification-of-clostridium-litorale-fendrich-et-al-1991-and-eubacterium-acidaminophilum-zindel-et-al-1989-as-peptoclostridium-litorale-gen-nov-comb-nov-and
#12
Michael Y Galperin, Vyacheslav Brover, Igor Tolstoy, Natalya Yutin
In 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18 species to Clostridium cluster XI, separating them from Clostridium sensu stricto (Clostridium cluster I). Subsequently, most cluster XI species have been assigned to the family Peptostreptococcaceae; some of them have been reassigned to new genera. However, several Clostridium species were left with their old names, creating a taxonomic conundrum and confusion regarding their status. Here, we have re-examined the phylogeny of cluster XI species by comparing the 16S rRNA gene-based trees with protein- and genome-based trees, where available...
October 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27898825/complete-chloroplast-genome-sequence-of-corroborates-structural-heterogeneity-of-inverted-repeats-in-wild-progenitors-of-cultivated-bananas-and-plantains
#13
Santoshkumar M Shetty, Maria Ulfa Md Shah, Kavyashree Makale, Yusmin Mohd-Yusuf, Norzulaani Khalid, Rofina Yasmin Othman
Complete genome sequencing of cytoplasmically inherited chloroplast DNA provides novel insights into the origins of clonally propagated crops such as banana and plantain ( spp.). This study describes the structural organization of the chloroplast genome of Colla and its phylogenetic relationship with other wild progenitors of the domesticated banana cultivars. The chloroplast genome was sequenced using Illumina HiSeq 2000 platform, followed by a combination of de novo short-read assembly and reference-guided mapping of contigs to generate complete plastome sequence...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27886369/genomic-data-reveals-potential-for-hybridization-introgression-and-incomplete-lineage-sorting-to-confound-phylogenetic-relationships-in-an-adaptive-radiation-of-narrow-mouth-frogs
#14
A M Alexander, Y-C Su, C H Oliveros, K V Olson, S L Travers, R M Brown
The microhylid frog genus Kaloula is an adaptive radiation spanning the edge of the Asian mainland and multiple adjacent island archipelagos, with much of the clade's diversity associated with an endemic Philippine radiation. Relationships among clades from the Philippines, however, remain unresolved. With ultraconserved element (UCE) and mitogenomic data, we identified highly-supported differences in topology and areas of poor resolution, for each marker set. Using the UCE data, we then identified possible instances of contemporary hybridization, past introgression and incomplete lineage sorting (ILS) within the Philippine Kaloula...
November 25, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27876901/nematodes-ultrastructure-complex-systems-and-processes
#15
REVIEW
Maha M A Basyoni, Enas M A Rizk
Nematode worms are among the most ubiquitous organisms on earth. They include free-living forms as well as parasites of plants, insects, humans and other animals. Recently, there has been an explosion of interest in nematode biology, including the area of nematode ultrastructure. Nematodes are round with a body cavity. They have one way guts with a mouth at one end and an anus at the other. They have a pseudocoelom that is lined on one side with mesoderm and on the other side with endoderm. It appears that the cuticle is a very complex and evolutionarily plastic feature with important functions involving protection, body movement and maintaining shape...
December 2016: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
https://www.readbyqxmd.com/read/27872617/bacterial-genomics-reveal-the-complex-epidemiology-of-an-emerging-pathogen-in-arctic-and-boreal-ungulates
#16
Taya L Forde, Karin Orsel, Ruth N Zadoks, Roman Biek, Layne G Adams, Sylvia L Checkley, Tracy Davison, Jeroen De Buck, Mathieu Dumond, Brett T Elkin, Laura Finnegan, Bryan J Macbeth, Cait Nelson, Amanda Niptanatiak, Shane Sather, Helen M Schwantje, Frank van der Meer, Susan J Kutz
Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27871225/genomic-epidemiology-of-lineage-4-mycobacterium-tuberculosis-subpopulations-in-new-york-city-and-new-jersey-1999-2009
#17
Tyler S Brown, Apurva Narechania, John R Walker, Paul J Planet, Pablo J Bifani, Sergios-Orestis Kolokotronis, Barry N Kreiswirth, Barun Mathema
BACKGROUND: Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27864136/the-underlying-mechanisms-of-genetic-innovation-and-speciation-in-the-family-corynebacteriaceae-a-phylogenomics-approach
#18
Xiao-Yang Zhi, Zhao Jiang, Ling-Ling Yang, Ying Huang
The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach...
November 15, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27863094/resources-for-phylogenomic-analyses-of-australian-terrestrial-vertebrates
#19
Jason G Bragg, Sally Potter, Ke Bi, Renee Catullo, Stephen C Donnellan, Mark D B Eldridge, Leo Joseph, J Scott Keogh, Paul Oliver, Kevin C Rowe, Craig Moritz
High throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci and we now know that many lineages also exhibit substantial cryptic diversity. Here, we present a set of phylogenetically diverse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for 4 species of birds, 4 frogs, 7 lizards and 7 mammals...
November 8, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27862822/type%C3%A2-iii-polyketide-synthases-functional-classification-and-phylogenomics
#20
REVIEW
Yugo Shimizu, Hiroyuki Ogata, Susumu Goto
Polyketide synthases (PKSs) catalyze the sequential condensation of simple acetate units to produce a large class of natural products, including pharmacologically valuable compounds. PKSs are classified into three types on the basis of their domain structures; type III PKSs have the simplest domain structure, although their products have various structures and functions. The sequence-function relationship is fundamental for predicting enzyme functions, but it has not been well investigated in type III PKSs to date...
November 14, 2016: Chembiochem: a European Journal of Chemical Biology
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