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Evolution analysis

Michael R Gillings, Ian T Paulsen, Sasha G Tetu
Antibiotic resistance arises as a consequence of complex interactions among genes, mobile elements, and their bacterial hosts, coupled with the intense selection pressures imposed by humans in an attempt to control bacterial growth. Understanding the evolution of resistance requires an understanding of interacting cellular and genetic components. Here, we review how DNA analysis has helped reconstruct the origins of the mosaic, multiresistant mobile elements that have spread through pathogens in the last 60 years...
October 21, 2016: Annals of the New York Academy of Sciences
Akira Shiraishi, Jun Murata, Erika Matsumoto, Shin Matsubara, Eiichiro Ono, Honoo Satake
Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform...
2016: PloS One
Elena Sugrue, Paul D Carr, Colin Scott, Colin J Jackson
The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little is known regarding how enzymes can naturally evolve active sites with highly reactive and desolvated charges. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214, Tyr215), whereas TrzN from Nocardioides sp...
October 21, 2016: Biochemistry
Dongliang Chao, Pei Liang, Zhen Chen, Linyi Bai, He Shen, Xiaoxu Liu, Xinhui Xia, Yanli Zhao, Serguei V Savilov, Jianyi Lin, Ze Xiang Shen
The abundant reservation and low cost of sodium have provoked tremendous evolution of Na-ion batteries (SIBs) in the past few years, but their performances were still limited either by the specific capacity or rate capability. Attempts to pursuit high-rate ability with maintained high-capacity in a single electrode remains even more challenging. Here, an elaborate self-branched 2D SnS2 (B-SnS2) nanoarrays electrode is designed by a facile hot bath method for Na storage. This interesting electrode exhibits areal reversible capacity of ca...
October 21, 2016: ACS Nano
Vi Khanh Truong, Miljan Stefanovic, Shane Maclaughlin, Mark Tobin, Jitraporn Vongsvivut, Mohammad Al Kobaisi, Russell J Crawford, Elena P Ivanova
Corrosion of metallic surfaces is prevalent in the environment and is of great concern in many areas, including the military, transport, aviation, building and food industries, amongst others. Polyester and coatings containing both polyester and silica nanoparticles (SiO2NPs) have been widely used to protect steel substrata from corrosion. In this study, we utilized X-ray photoelectron spectroscopy, attenuated total reflection infrared micro-spectroscopy, water contact angle measurements, optical profiling and atomic force microscopy to provide an insight into how exposure to sunlight can cause changes in the micro- and nanoscale integrity of the coatings...
October 11, 2016: Journal of Visualized Experiments: JoVE
Qingwang Lian, Gang Zhou, Xiaohui Zeng, Chen Wu, Yuehua Wei, Chao Cui, Weifeng Wei, Libao Chen, Cheng-Chao Li
Carbon coated SnS/SnO2 heterostructures wrapping on the carbon nanofibers (C@SnS/SnO2@CNFs) was demonstrated to have excellent performance as an anode material for Li-ion batteries. C@SnS/SnO2@CNFs electrode deliver high reversible capacity of 826.8 mAh g(-1) (500(th) cycle) at the current density of 1.0 A g(-1). However, an interesting phenomenon of increasing capacity on cycling can be observed. According to the analysis of the evolution of structure and electrochemical property, C@SnS/SnO2@CNFs is demonstrated to experience the progress of conversion from nanowalls containing polycrystals into amorphous nanosheets with high porosity and larger surface upon cycling...
October 21, 2016: ACS Applied Materials & Interfaces
Qiu-Ning Liu, Zhao-Zhe Xin, Dan-Dan Bian, Xin-Yue Chai, Chun-Lin Zhou, Bo-Ping Tang
The mitochondrial genome (mitogenome) provides important information for understanding molecular evolution and phylogeny. To determine the systematic status of the family Limacodidae within Lepidoptera, we infer a phylogenetic hypothesis based on the complete mitogenome of Monema flavescens (Lepidoptera: Limacodidae). The mitogenome of M. flavescens is 15,396 base pairs (bp), and includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR)...
October 21, 2016: Scientific Reports
Pierre E Affaticati, Shao-Bo Dai, Panwajee Payongsri, Helen C Hailes, Kai Tittmann, Paul A Dalby
The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation...
October 21, 2016: Scientific Reports
Yanling Zhang, Aizhi Liu, Changyin Sun
For large quantities of spatial models, the multi-strategy selection under weak selection is the sum of two competition terms: the pairwise competition and the competition of multiple strategies with equal frequency. Two parameters σ1 and σ2 quantify the dependence of the multi-strategy selection on these two terms, respectively. Unlike previous studies, we here do not require large populations for calculating σ1 and σ2, and perform the first quantitative analysis of the effect of migration on them in group-structured populations of any finite sizes...
October 21, 2016: Scientific Reports
Sonia Duarte de Azevedo Bittencourt, Rosa Maria Soares Madeira Domingues, Lenice Gnocchi da Costa Reis, Márcia Melo Ramos, Maria do Carmo Leal
BACKGROUND: In Brazil, hospital childbirth care is available to all, but differences in access and quality of care result in inequalities of maternal health. The objective of this study is to assess the infrastructure and staffing of publicly financed labor and birth care in Brazil and its adequacy according to clinical and obstetric conditions potentially associated with obstetric emergencies. METHODS: Nationwide cross-sectional hospital-based study "Birth in Brazil: national survey into labor and birth" conducted in 2011-2012...
October 17, 2016: Reproductive Health
Xavier Flecher, Benjamin Appy, Sébastien Parratte, Matthieu Ollivier, Jean-Noel Argenson
INTRODUCTION: Recent studies have reported short-term favourable results of tantalum-made components in acetabular revisions with bone loss. However, there is a lack of information regarding the mid to long-term results of such components. OBJECTIVES: The objective of this study was to analyse the outcome and survivorship of acetabular revision hip arthroplasty using tantalum components for loosening associated with bone loss at a minimum of five-year follow-up...
October 21, 2016: International Orthopaedics
Lêniféré Chantal Soro, Sylvie Munier, Yves Pelissier, Lidwine Grosmaire, Rickey Yada, David Kitts, Anin Louise Ocho-Anin Atchibri, Caroline Guzman, Frédéric Boudard, Chantal Menut, Jean Charles Robinson, Patrick Poucheret
ETHNOPHARMACOLOGICAL RELEVANCE: Lippia multiflora is a plant with nutritional and pharmaco-therapeutic properties that is native to central and occidental Africa. The potential effects of plants on health are associated with their chemical composition. Therefore, the present study aimed to identify chemical variations in essential oils of Lippia multiflora as a function of geographic origin and time of annual harvest to determine optimal chemical profiles for ethno-pharmacotherapeutic applications...
October 17, 2016: Journal of Ethnopharmacology
Jingzhong Xie, Naxin Huo, Shenghui Zhou, Yi Wang, Guanghao Guo, Karin R Deal, Shuhong Ouyang, Yong Liang, Zhenzhong Wang, Lichan Xiao, Tingting Zhu, Tiezhu Hu, Vijay Tiwari, Jianwei Zhang, Hongxia Li, Zhongfu Ni, Yingyin Yao, Huiru Peng, Shengli Zhang, Olin D Anderson, Patrick E McGuire, Jan Dvorak, Ming-Cheng Luo, Zhiyong Liu, Yong Q Gu, Qixin Sun
Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4...
October 5, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
Sandra A Heldstab, Carel P van Schaik, Karin Isler
Humans stand out among non-aquatic mammals by having both an extremely large brain and a relatively large amount of body fat. To understand the evolution of this human peculiarity we report a phylogenetic comparative study of 120 mammalian species, including 30 primates, using seasonal variation in adult body mass as a proxy of the tendency to store fat. Species that rely on storing fat to survive lean periods are expected to be less active because of higher costs of locomotion and have increased predation risk due to reduced agility...
November 2016: Journal of Human Evolution
Saura R Silva, Yani C A Diaz, Helen Alves Penha, Daniel G Pinheiro, Camila C Fernandes, Vitor F O Miranda, Todd P Michael, Alessandro M Varani
Lentibulariaceae is the richest family of carnivorous plants spanning three genera including Pinguicula, Genlisea, and Utricularia. Utricularia is globally distributed, and, unlike Pinguicula and Genlisea, has both aquatic and terrestrial forms. In this study we present the analysis of the chloroplast (cp) genome of the terrestrial Utricularia reniformis. U. reniformis has a standard cp genome of 139,725bp, encoding a gene repertoire similar to essentially all photosynthetic organisms. However, an exclusive combination of losses and pseudogenization of the plastid NAD(P)H-dehydrogenase (ndh) gene complex were observed...
2016: PloS One
Lucas C Wheeler, Micah T Donor, James S Prell, Michael J Harms
The S100 proteins are a large family of signaling proteins that play critical roles in biology and disease. Many S100 proteins bind Zn2+, Cu2+, and/or Mn2+ as part of their biological functions; however, the evolutionary origins of binding remain obscure. One key question is whether divalent transition metal binding is ancestral, or instead arose independently on multiple lineages. To tackle this question, we combined phylogenetics with biophysical characterization of modern S100 proteins. We demonstrate an earlier origin for established S100 subfamilies than previously believed, and reveal that transition metal binding is widely distributed across the tree...
2016: PloS One
Noor-Ul-Huda Ghori, Atif Shafique, Muhammad Qasim Hayat, Sadia Anjum
Hepatitis C Virus (HCV) is the most prevalent human pathogen in Pakistan and is the major cause of liver cirrhosis and hepatocellular carcinoma in infected patients. It has shifted from being hypo-endemic to being hyper-endemic. There was no information about the origin and evolution of the local variants. Here we use newly developed phyloinformatic methods of sequence analysis to conduct the first comprehensive investigation of the evolutionary and biogeographic history in unprecedented detail and breadth...
2016: PloS One
Oscar Claveria, Alessio Poluzzi
The first decade of the present century has been characterized by several economic shocks such as the 2008 financial crisis. In this data article we present the annual percentage growth rates of the main tourism indicators in the world׳s top tourist destinations: the United States, China, France, Spain, Italy, United Kingdom, Germany, Turkey, Mexico and Austria. We use data from the Compendium of Tourism Statistics provided by the World Tourism Organization ( It has been demonstrated that the dynamics of growth in the tourism industry pose different challenges to each destination in the previous study "Positioning and clustering of the world׳s top tourist destinations by means of dimensionality reduction techniques for categorical data" (Claveria and Poluzzi, 2016, [1])...
June 2016: Data in Brief
Nashmiah Aid Alrashedy, Jeanmaire Molina
Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful...
2016: PeerJ
Kate Stringaris, David Marin, A John Barrett, Robert Hills, Catherine Sobieski, Kai Cao, Jerome G Saltarrelli, May Daher, Hila Shaim, Nathaniel Smith, David Linch, Rosemary Gale, Christopher Allen, Takuya Sekine, Rohtesh Mehta, Richard Champlin, Elizabeth J Shpall, Hagop Kantarjian, Guillermo Garcia-Manero, Katayoun Rezvani
Myelodysplastic syndromes (MDS) are a group of hematopoietic disorders affecting the myeloid lineage, characterized by cytopenias and clonal evolution to acute myeloid leukemia (AML). We hypothesized that natural killer (NK) cells and their activating killer immunoglobulin-like receptors (aKIRs) influence the immune surveillance and clinical outcome of patients with MDS. Here, we first examined the distribution of aKIR genes and haplotype in two independent cohorts of MDS and AML patients. The median number of aKIR genes was lower in MDS patients than healthy controls (2 vs...
October 19, 2016: Blood
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