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https://www.readbyqxmd.com/read/29773666/ancient-genomes-document-multiple-waves-of-migration-in-southeast-asian-prehistory
#1
Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, Michael Pietrusewsky, Thomas Oliver Pryce, Anna Willis, Hirofumi Matsumura, Hallie Buckley, Kate Domett, Nguyen Giang Hai, Trinh Hoang Hiep, Aung Aung Kyaw, Tin Tin Win, Baptiste Pradier, Nasreen Broomandkhoshbacht, Francesca Candilio, Piya Changmai, Daniel Fernandes, Matthew Ferry, Beatriz Gamarra, Eadaoin Harney, Jatupol Kampuansai, Wibhu Kutanan, Megan Michel, Mario Novak, Jonas Oppenheimer, Kendra Sirak, Kristin Stewardson, Zhao Zhang, Pavel Flegontov, Ron Pinhasi, David Reich
Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from eighteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages...
May 17, 2018: Science
https://www.readbyqxmd.com/read/29773654/genetic-code-expansion-and-live-cell-imaging-reveal-that-thr308-phosphorylation-is-irreplaceable-and-sufficient-for-akt1-activity
#2
Nileeka Balasuriya, Maya T Kunkel, Xuguang Liu, Kyle K Biggar, Shawn S-C Li, Alexandra C Newton, Patrick O'Donoghue
The proto-oncogene Akt/protein kinase B (PKB) is a pivotal signal transducer for growth and survival. Growth factor stimulation leads to Akt phosphorylation at two regulatory sites (Thr308, Ser473), acutely activating Akt signaling. Delineating the exact role of each regulatory site is, however, technically challenging and has remained elusive. Here, we used genetic code expansion to produce site-specifically phosphorylated Akt1 in order to dissect the contribution of each regulatory site to Akt1 activity. We achieved recombinant production of full length Akt1 containing site-specific pThr and pSer residues for the first time...
May 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29773336/seasonal-dynamics-geographical-range-size-hosts-genetic-diversity-and-phylogeography-of-amblyomma-sculptum-in-argentina
#3
Evelina L Tarragona, Patrick S Sebastian, María N Saracho Bottero, Emilia I Martinez, Valeria N Debárbora, Atilio J Mangold, Alberto A Guglielmone, Santiago Nava
The aim of this work was to generate knowledge on ecological aspects of Amblyomma sculptum in Argentina, such as seasonal dynamics, geographical range size, hosts, genetic diversity and phylogeography. Adult and immature A. sculptum ticks were collected in different localities of Argentina to know the geographical range size and hosts. The genetic diversity of this tick was studied through analyses of 16S rDNA sequences. To describe the seasonal dynamics, free-living ticks were monthly collected from October 2013 to October 2015...
April 27, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29772713/genetic-optimization-algorithm-for-metabolic-engineering-revisited
#4
Tobias B Alter, Lars M Blank, Birgitta E Ebert
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research...
May 16, 2018: Metabolites
https://www.readbyqxmd.com/read/29770273/westwards-and-northwards-dispersal-of-triosteum-himalayanum-caprifoliaceae-from-the-hengduan-mountains-region-based-on-chloroplast-dna-phylogeography
#5
Hai-Rui Liu, Qing-Bo Gao, Fa-Qi Zhang, Gulzar Khan, Shi-Long Chen
The varying topography and environment that resulted from paleoorogeny and climate fluctuations of the Himalaya-Hengduan Mountains (HHM) areas had a considerable impact on the evolution of biota during the Quaternary. To understand the phylogeographic pattern and historical dynamics of Triosteum himalayanum (Caprifoliaceae), we sequenced three chloroplast DNA fragments ( rbcL-accD , rps15-ycf1 , and trnH-psbA ) from 238 individuals representing 20 populations. Nineteen haplotypes (H1-H19) were identified based on 23 single-site mutations and eight indels...
2018: PeerJ
https://www.readbyqxmd.com/read/29769162/increased-pregnancy-losses-following-serial-somatic-cell-nuclear-transfer-in-goats
#6
Min Yang, Iuri Perisse, Zhiqiang Fan, Misha Regouski, Mirella Meyer-Ficca, Irina A Polejaeva
Serial cloning by somatic cell nuclear transfer (SCNT) is a critical tool for the expansion of precious transgenic lines or resetting the lifespan of primary transgenic cells for multiple genetic modifications. We successfully produced second-generation cloned goats using donor neonatal fibroblasts from first-generation clones. However, our attempts to produce any third-generation clones failed. SCNT efficiency decreased progressively with the clonal generations. The rate of pregnancy loss was significantly greater in recloning groups (P<0...
May 17, 2018: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/29768530/ns1-codon-usage-adaptation-to-humans-in-pandemic-zika-virus
#7
Caio César de Melo Freire, Giuseppe Palmisano, Carla T Braconi, Fernanda R Cugola, Fabiele B Russo, Patricia Cb Beltrão-Braga, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Livia Rosa-Fernandes, Martin R Larsen, Paolo Marinho de Andrade Zanotto
BACKGROUND: Zika virus (ZIKV) was recognised as a zoonotic pathogen in Africa and southeastern Asia. Human infections were infrequently reported until 2007, when the first known epidemic occurred in Micronesia. After 2013, the Asian lineage of ZIKV spread along the Pacific Islands and Americas, causing severe outbreaks with millions of human infections. The recent human infections of ZIKV were also associated with severe complications, such as an increase in cases of Guillain-Barre syndrome and the emergence of congenital Zika syndrome...
May 10, 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29768404/tissue-specific-activities-of-the-fat1-cadherin-cooperate-to-control-neuromuscular-morphogenesis
#8
Françoise Helmbacher
Muscle morphogenesis is tightly coupled with that of motor neurons (MNs). Both MNs and muscle progenitors simultaneously explore the surrounding tissues while exchanging reciprocal signals to tune their behaviors. We previously identified the Fat1 cadherin as a regulator of muscle morphogenesis and showed that it is required in the myogenic lineage to control the polarity of progenitor migration. To expand our knowledge on how Fat1 exerts its tissue-morphogenesis regulator activity, we dissected its functions by tissue-specific genetic ablation...
May 16, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29768211/long-term-persistence-of-exhausted-cd8-t-cells-in-chronic-infection-is-regulated-by-microrna-155
#9
Erietta Stelekati, Zeyu Chen, Sasikanth Manne, Makoto Kurachi, Mohammed-Alkhatim Ali, Keith Lewy, Zhangying Cai, Kito Nzingha, Laura M McLane, Jennifer L Hope, Adam J Fike, Peter D Katsikis, E John Wherry
Persistent viral infections and tumors drive development of exhausted T (TEX ) cells. In these settings, TEX cells establish an important host-pathogen or host-tumor stalemate. However, TEX cells erode over time, leading to loss of pathogen or cancer containment. We identified microRNA (miR)-155 as a key regulator of sustained TEX cell responses during chronic lymphocytic choriomeningitis virus (LCMV) infection. Genetic deficiency of miR-155 ablated CD8 T cell responses during chronic infection. Conversely, enhanced miR-155 expression promoted expansion and long-term persistence of TEX cells...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29765696/behavioural-divergence-during-biological-invasions-a-study-of-cane-toads-rhinella-marina-from-contrasting-environments-in-hawai-i
#10
Jodie Gruber, Gregory Brown, Martin J Whiting, Richard Shine
Invasive species must deal with novel challenges, both from the alien environment and from pressures arising from range expansion per se (e.g. spatial sorting). Those conditions can create geographical variation in behaviour across the invaded range, as has been documented across regions of Australia invaded by cane toads; range-edge toads are more exploratory and willing to take risks than are conspecifics from the range-core. That behavioural divergence might be a response to range expansion and invasion per se , or to the different environments encountered...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765016/b-cell-activation-and-plasma-cell-differentiation-are-inhibited-by-de-novo-dna-methylation
#11
Benjamin G Barwick, Christopher D Scharer, Ryan J Martinez, Madeline J Price, Alexander N Wein, Robert R Haines, Alexander P R Bally, Jacob E Kohlmeier, Jeremy M Boss
B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29764451/phenotypic-and-genotypic-characterization-of-thai-isolates-of-plasmodium-falciparum-after-an-artemisinin-resistance-containment-project
#12
Thunyapit Thita, Pimrat Jadsri, Jarupatr Thamkhantho, Toon Ruang-Areerate, Nantana Suwandittakul, Naruemon Sitthichot, Kittiya Mahotorn, Peerapan Tan-Ariya, Mathirut Mungthin
BACKGROUND: In Thailand, artemisinin-based combination therapy (ACT) has been used to treat uncomplicated falciparum malaria since 1995. Unfortunately, artemisinin resistance has been reported from Thailand and other Southeast Asian countries since 2003. Malarone® , a combination of atovaquone-proguanil (ATQ-PG), has been used to cease artemisinin pressure in some areas along Thai-Cambodia border, as part of an artemisinin resistance containment project since 2009. This study aimed to determine genotypes and phenotypes of Plasmodium falciparum isolates collected from the Thai-Cambodia border after the artemisinin resistance containment project compared with those collected before...
May 15, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29763307/genetic-code-expansion-in-rhodobacter-sphaeroides-to-incorporate-non-canonical-amino-acids-into-photosynthetic-reaction-centers
#13
Jared Weaver, Steven G Boxer
Photosynthetic reaction centers (RCs) are the membrane proteins responsible for the initial charge separation steps central to photosynthesis. As a complex and spectroscopically complicated membrane protein, the RC (and other associated photosynthetic proteins) would benefit greatly from the insight offered by site-specifically encoded non-canonical amino acids in the form of probes and an increased chemical range in key amino acid analogues. Towards that goal, we developed a method to transfer amber codon suppression machinery developed for E...
May 15, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29760713/human-leukocyte-antigen-class-i-alleles-and-the-autoreactive-t-cell-response-in-psoriasis-pathogenesis
#14
REVIEW
Jörg Christoph Prinz
Psoriasis is a complex immune-mediated inflammatory skin disease characterized by T-cell-driven epidermal hyperplasia. It occurs on a strong genetic predisposition. The human leukocyte antigen (HLA)-class I allele HLA-C*06:02 on psoriasis susceptibility locus 1 (PSORS1 on 6p21.3) is the main psoriasis risk gene. Other HLA-class I alleles encoding HLA molecules presenting overlapping peptide repertoires show associations with psoriasis as well. Outside the major histocompatibility complex region, genome-wide association studies identified more than 60 psoriasis-associated common gene variants exerting only modest individual effects...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29758422/clonal-expansion-of-environmentally-adapted-escherichia-coli-contributes-to-propagation-of-antibiotic-resistance-genes-in-beef-cattle-feedlots
#15
Lisa Tymensen, Rahat Zaheer, Shaun R Cook, Kingsley K Amoako, Noriko Goji, Ron Read, Calvin W Booker, Sherry J Hannon, Norman Neumann, Tim A McAllister
Livestock wastewater lagoons represent important environmental reservoirs of antibiotic resistance genes (ARGs), although factors contributing to their proliferation within these reservoirs remain poorly understood. Here, we characterized Escherichia coli from feedlot cattle feces and associated wastewater lagoons using CRISPR1 subtyping, and demonstrated that while generic E. coli were genetically diverse, populations were dominated by several 'feedlot-adapted' CRISPR types (CTs) that were widely distributed throughout the feedlot...
May 11, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29758334/genetic-inactivation-of-nrf2-prevents-clonal-expansion-of-initiated-cells-in-a-nutritional-model-of-rat-hepatocarcinogenesis
#16
Claudia Orrù, Marta Szydlowska, Keiko Taguchi, Patrizia Zavattari, Andrea Perra, Masayuki Yamamoto, Amedeo Columbano
BACKGROUND & AIMS: Dysregulation of the Keap1-Nrf2 pathway has been observed in experimental and human tumors, suggesting possible roles of the pathway in cancer development. Here we examined whether Nrf2 activation occurs at early steps of rat hepatocarcinogenesis, to assess critical contributions of Nrf2 to the onset of hepatocellular carcinoma (HCC). METHODS: We used wild type (WT) and Nrf2 knockout (Nrf2KO) rats treated with a single injection of diethylnitrosamine (DENA) followed by choline-devoid methionine-deficient (CMD) diet...
May 11, 2018: Journal of Hepatology
https://www.readbyqxmd.com/read/29758256/reduction-of-protein-kinase-a-mediated-phosphorylation-of-atxn1-s776-in-purkinje-cells-delays-onset-of-ataxia-in-a-sca1-mouse-model
#17
Judit M Pérez Ortiz, Nissa Mollema, Nicholas Toker, Carolyn J Adamski, Brennon O'Callaghan, Lisa Duvick, Jillian Friedrich, Michael A Walters, Jessica Strasser, Jon E Hawkinson, Huda Y Zoghbi, Christine Henzler, Harry T Orr, Sarita Lagalwar
Spinocerebellar ataxia type 1 (SCA1) is a polyglutamine (polyQ) repeat neurodegenerative disease in which a primary site of pathogenesis are cerebellar Purkinje cells. In addition to polyQ expansion of ataxin-1 protein (ATXN1), phosphorylation of ATXN1 at the serine 776 residue (ATXN1-pS776) plays a significant role in protein toxicity. Utilizing a biochemical approach, pharmacological agents and cell-based assays, including SCA1 patient iPSC-derived neurons, we examine the role of Protein Kinase A (PKA) as an effector of ATXN1-S776 phosphorylation...
May 11, 2018: Neurobiology of Disease
https://www.readbyqxmd.com/read/29757513/genetic-characters-of-the-globally-spread-tiger-mosquito-aedes-albopictus-diptera-culicidae-implications-from-mitochondrial-gene-coi
#18
Zhang Ruiling, Liu Tongkai, Ma Dezhen, Zhang Zhong
There has been a rapid global expansion of Aedes albopictus, with varying biological characters and vector competence according to geographic and evolutionary origins of the invading populations. Based on mitochondrial gene cytochrome c oxidase I (COI) sequences from both native and invasive regions, genetic characters of Ae. albopictus were examined. Phylogenetic analyses indicate lineage differentiation in the original areas, and only one of the lineages was involved in the worldwide expansion. Multiple invasions were detected in populations in Africa and the Americas, whereas no obvious genetic structure was found in European populations...
June 2018: Journal of Vector Ecology: Journal of the Society for Vector Ecology
https://www.readbyqxmd.com/read/29757393/snpnexus-assessing-the-functional-relevance-of-genetic-variation-to-facilitate-the-promise-of-precision-medicine
#19
Abu Z Dayem Ullah, Jorge Oscanoa, Jun Wang, Ai Nagano, Nicholas R Lemoine, Claude Chelala
Broader functional annotation of genetic variation is a valuable means for prioritising phenotypically-important variants in further disease studies and large-scale genotyping projects. We developed SNPnexus to meet this need by assessing the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models. Since its previous release in 2012, we have made significant improvements to the annotation categories and updated the query and data viewing systems...
May 11, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29757291/virus-delivery-of-crispr-guides-to-the-murine-prostate-for-gene-alteration
#20
Maria Riedel, Martin F Berthelsen, Latifa Bakiri, Erwin F Wagner, Martin K Thomsen
With an increasing incidence of prostate cancer, identification of new tumor drivers or modulators is crucial. Genetically engineered mouse models (GEMM) for prostate cancer are hampered by tumor heterogeneity and its complex microevolution dynamics. Traditional prostate cancer mouse models include, amongst others, germline and conditional knockouts, transgenic expression of oncogenes, and xenograft models. Generation of de novo mutations in these models is complex, time-consuming, and costly. In addition, most of traditional models target the majority of the prostate epithelium, whereas human prostate cancer is well known to evolve as an isolated event in only a small subset of cells...
April 27, 2018: Journal of Visualized Experiments: JoVE
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