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Neutral evolution

Alexander C Cameron, Jeffry J Anderson, Robert B Page
The red-backed salamander (Plethodon cinereus) has long-served as a model system in ecology, evolution, and behavior, and studies surveying molecular variation in this species have become increasingly common over the past decade. However, difficulties are commonly encountered when extending microsatellite markers to populations that are unstudied from a genetic perspective due to high levels of genetic differentiation across this species' range. To ameliorate this issue, we used 454 pyrosequencing to identify hundreds of microsatellite loci...
2017: PloS One
Steven D Aird, Jigyasa Arora, Agneesh Barua, Lijun Qiu, Kouki Terada, Alexander S Mikheyev
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested...
October 1, 2017: Genome Biology and Evolution
Ahmed Sayadi, Elina Immonen, Christian Tellgren-Roth, Göran Arnqvist
Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution...
October 1, 2017: Genome Biology and Evolution
Chenguang Shen, Junyu Chen, Rui Li, Mengya Zhang, Guosong Wang, Svetlana Stegalkina, Limin Zhang, Jing Chen, Jianli Cao, Xingjian Bi, Stephen F Anderson, Timothy Alefantis, Minwei Zhang, Xiaoyang Cai, Kunyu Yang, Qingbing Zheng, Mujing Fang, Hai Yu, Wenxin Luo, Zizheng Zheng, Quan Yuan, Jun Zhang, James Wai-Kuo Shih, Harry Kleanthous, Honglin Chen, Yixin Chen, Ningshao Xia
Influenza B virus causes considerable disease burden worldwide annually, highlighting the limitations of current influenza vaccines and antiviral drugs. In recent years, broadly neutralizing antibodies (bnAbs) against hemagglutinin (HA) have emerged as a new approach for combating influenza. We describe the generation and characterization of a chimeric monoclonal antibody, C12G6, that cross-neutralizes representative viruses spanning the 76 years of influenza B antigenic evolution since 1940, including viruses belonging to the Yamagata, Victoria, and earlier lineages...
October 18, 2017: Science Translational Medicine
Kristin M Lee, Graham Coop
Geographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene ow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes...
October 18, 2017: Genetics
Matthias Hoetzinger, Martin W Hahn
BACKGROUND: In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P...
October 16, 2017: BMC Genomics
Yan Fan, Chenglin Zhang, Wendan Wu, Wei He, Li Zhang, Xiao Ma
Indigofera pseudotinctoria Mats is an agronomically and economically important perennial legume shrub with a high forage yield, protein content and strong adaptability, which is subject to natural habitat fragmentation and serious human disturbance. Until now, our knowledge of the genetic relationships and intraspecific genetic diversity for its wild collections is still poor, especially at small spatial scales. Here amplified fragment length polymorphism (AFLP) technology was employed for analysis of genetic diversity, differentiation, and structure of 364 genotypes of I...
October 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Chao Xie, Yanyong Wang, Dafeng Yan, Li Tao, Shuangyin Wang
Development of efficient non-noble metal electrocatalysts for oxygen evolution reaction (OER) is still a crucial issue for renewable energy technologies. Herein, we report a core-shell-like catalyst of amorphous cobalt borate nanosheets grown on metallic cobalt deposited on Ti-mesh (Co@Co-Bi/Ti) by an in situ conversion strategy. Benefiting from the high activity, large surface area of Co-Bi nanosheets, outstanding electronic conductivity of metallic Co and the 3D structure inherited from Ti-mesh substrate, Co@Co-Bi/Ti shows high OER activity with a relatively small overpotential of 329 mV to obtain a current density of 10 mA cm(-2), a low Tafel slope of 46 mV dec(-1) and an accessible large current density of 500 mA cm(-2) in alkaline solution...
October 16, 2017: Nanoscale
Frederic Bertels, Alex Marzel, Gabriel Leventhal, Venelin Mitov, Jacques Fellay, Huldrych F Günthard, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Manuel Battegay, Andri Rauch, Matthias Cavassini, Alexandra Calmy, Enos Bernasconi, Patrick Schmid, Alexandra U Scherrer, Viktor Müller, Sebastian Bonhoeffer, Roger Kouyos, Roland R Regoes
Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as" per-parasite pathogenicity". Using viral load and CD4+ T cell measures from 2014 HIV-1 subtype B infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence - measured as the rate of decline of CD4+ T cells - and per-parasite pathogenicity are heritable from donor to recipient...
October 3, 2017: Molecular Biology and Evolution
S Drouet, J Creus, V Collière, C Amiens, J García-Antón, X Sala, K Philippot
A porous Ru nanomaterial exhibits high electrocatalytic performance and excellent durability for the hydrogen evolution reaction (HER) under both acidic and neutral conditions. It displays a low overpotential of 83 mV at a current density of 10 mA cm(-2) and an excellent durability up to 12 h in 0.5 M H2SO4.
October 12, 2017: Chemical Communications: Chem Comm
Ben J Mans, Jonathan Featherston, Minique H de Castro, Ronel Pienaar
Ticks modulate their hosts' defense responses by secreting a biopharmacopiea of hundreds to thousands of proteins and bioactive chemicals into the feeding site (tick-host interface). These molecules and their functions evolved over millions of years as ticks adapted to blood-feeding, tick lineages diverged, and host-shifts occurred. The evolution of new proteins with new functions is mainly dependent on gene duplication events. Central questions around this are the rates of gene duplication, when they occurred and how new functions evolve after gene duplication...
2017: Frontiers in Cellular and Infection Microbiology
David S Ojala, Sabrina Sun, Jorge L Santiago-Ortiz, Mikhail G Shapiro, Philip A Romero, David V Schaffer
Directed evolution continues to expand the capabilities of complex biomolecules for a range of applications, such as adeno-associated virus vectors for gene therapy; however, advances in library design and selection strategies are key to develop variants that overcome barriers to clinical translation. To address this need, we applied structure-guided SCHEMA recombination of the multimeric adeno-associated virus (AAV) capsid to generate a highly diversified chimeric library with minimal structural disruption...
September 8, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
Georgy A Semenov, Elizabeth S C Scordato, David R Khaydarov, Chris C R Smith, Nolan C Kane, Rebecca J Safran
Phenotypic differentiation plays an important role in the formation and maintenance of reproductive barriers. In some cases, variation in a few key aspects of phenotype can promote and maintain divergence; hence the identification of these traits and their associations with patterns of genomic divergence are crucial for understanding the patterns and processes of population differentiation. We studied hybridization between the alba and personata subspecies of the white wagtail (Motacilla alba), and quantified divergence and introgression of multiple morphological traits and 19,437 SNP loci on a 3000 km transect...
October 7, 2017: Molecular Ecology
Zhonghui Chen, Song Li, Yong Qiu, Zezhang Zhu, Xi Chen, Liang Xu, Xu Sun
OBJECTIVE Although the vertical expandable prosthetic titanium rib (VEPTR) and growing rod instrumentation (GRI) encourage spinal growth via regular lengthening, they can create different results because of their different fixation patterns and mechanisms in correcting scoliosis. Previous studies have focused comparisons on coronal plane deformity with minimal attention to the sagittal profile. In this retrospective study, the authors aimed to compare the evolution of the sagittal spinal profile in early-onset scoliosis (EOS) treated with VEPTR versus GRI...
October 6, 2017: Journal of Neurosurgery. Pediatrics
Hua Cui, Chunlian Wang, Tengfei Qin, Feifei Xu, Yongchao Tang, Ying Gao, Kaijun Zhao
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region...
2017: PloS One
Krastan B Blagoev, Julia Wilkerson, Mauricio Burotto, Chul Kim, Edward Espinal-Domínguez, Pilar García-Alfonso, Meghna Alimchandani, Markku Miettinen, Montserrat Blanco-Codesido, Tito Fojo
Emergence of tumor resistance to an anti-cancer therapy directed against a putative target raises several questions including: (1) do mutations in the target/pathway confer resistance? (2) Are these mutations pre-existing? (3) What is the relative fitness of cells with/without the mutation? We addressed these questions in patients with metastatic colorectal cancer (mCRC). We conducted an exhaustive review of published data to establish a median doubling time for CRCs and stained a cohort of CRCs to document mitotic indices...
2017: PloS One
Lisa C Lindesmith, Jacob F Kocher, Eric F Donaldson, Kari Debbink, Michael L Mallory, Excel W Swann, Paul D Brewer-Jenson, Ralph S Baric
Background: Human norovirus is a significant public health burden with >30 genotypes causing endemic levels of disease and strains from the GII.4 genotype causing serial pandemics as the virus evolves new ligand binding and antigenicity features. During 2014-2015, genotype GII.17 cluster IIIb strains emerged as the leading cause of norovirus infection in select global locations. Comparison of capsid sequences indicate that GII.17 is evolving at previously defined GII.4 antibody epitopes...
August 3, 2017: Journal of Infectious Diseases
Amanda J Craig, Johann von Felden, Augusto Villanueva
Liver cancer has the highest increase in incidence and mortality of all cancers in the United States in recent decades. A major effort has been taken over the last 10 years to understand molecular heterogeneity between tumors of different patients through the development of mutation signatures and molecular classifications. More recently, attention has shifted to understanding intra-tumor heterogeneity (ITH). Several possibilities exist as to the underlying mechanisms that drive ITH in liver cancer, including cancer stem cells (CSCs) and neutral and clonal evolution...
September 2017: Discovery Medicine
Yongming Liu, Jia Li, Gui Wei, Yonghao Sun, Yanli Lu, Hai Lan, Chuan Li, Suzhi Zhang, Moju Cao
The transcription factor ZmbHLH16, the maize ortholog of OsTIP2 (OsbHLH142), was isolated in the present experiment. Tissue expression analysis showed that ZmbHLH16 is preferentially expressed in male reproductive organs. Subcellular location analysis of ZmbHLH16 via rice protoplast indicated it is located in the nucleus. Through nucleotide variation analysis, 36 polymorphic sites in ZmbHLH16, including 23 SNPs and 13 InDels, were detected among 78 maize inbred lines. Neutrality tests and linkage disequilibrium analysis showed that ZmbHLH16 experienced no significant evolutionary pressure...
October 2, 2017: Biology Open
Masashi Tsuge, Chih-Yu Tseng, Yuan-Pern Lee
para-Hydrogen (p-H2) serves as a new host in matrix-isolation experiments for an investigation of species of astrochemical interest. Protonated and mono-hydrogenated species are produced upon electron bombardment during deposition of p-H2 containing a precursor in a small proportion. The applications of this novel technique to generate protonated polycyclic aromatic hydrocarbons (H(+)PAH), protonated polycyclic nitrogen heterocycles (H(+)PANH), and their neutral counterparts, which are important in the identification of interstellar unidentified infrared emission bands, demonstrate its superiority over other methods...
October 2, 2017: Physical Chemistry Chemical Physics: PCCP
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