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Nature Genetics

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https://www.readbyqxmd.com/read/28637337/matrix-completion-with-side-information-and-its-applications-in-predicting-the-antigenicity-of-influenza-viruses
#1
Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang
Motivation: Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition (HI) table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637269/announcing-the-genome-atlas-of-bamboo-and-rattan-gabr-project-promoting-research-in-evolution-and-in-economically-and-ecologically-beneficial-plants
#2
Hansheng Zhao, Shancen Zhao, Benhua Fei, Huan Liu, Huanming Yang, Honghai Dai, Dan Wang, Wei Jin, Feng Tang, Qiang Gao, Hang Xun, Yuwei Wang, Lianghua Qi, Xianghua Yue, Shuyan Lin, Lianfeng Gu, Lubin Li, Tiansheng Zhu, Qiang Wei, Zhen Su, Tarmeze Bin Wan Ariffin Wan, Daniel A Ofori, George Mbeva Muthike, Yigardu Mulatu Mengesha, Roberto Magno de Castro E Silva, Antonio Ludovico Beraldo, Zhimin Gao, Xin Liu, Zehui Jiang
Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of BR genetics through genome analysis...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637254/phylogeography-of-lionfishes-pterois-indicate-taxonomic-over-splitting-and-hybrid-origin-of-the-invasive-pterois-volitans
#3
Christie L Wilcox, Hiroyuki Motomura, Mizuki Matsunuma, Brian W Bowen
The lionfish is an iconic marine fish, and recently renowned for a disastrous introduction into the West Atlantic. Genetic surveys of the putative invaders (Pterois volitans and P. miles) in their natural Indo-Pacific range can illuminate both topics. Previous research indicated that P. volitans and P. miles are sister species that hybridize in the invasive range, but hybridization in the native range is unknown. Here we apply mtDNA COI and two nuclear introns (S7 RP1 and Gpd2) from 229 lionfish including the two invaders and two closely-related taxa (44 P...
June 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28637098/uncovering-the-contribution-of-epigenetics-to-plant-phenotypic-variation-in-mediterranean-ecosystems
#4
REVIEW
F Balao, O Paun, C Alonso
Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs). These ecosystems suffer recurrent stressful events (warm and dry summers with associated fire regimes) that have selected for plants with similar phenotypic complex traits, resulting in similar vegetation growth forms...
June 21, 2017: Plant Biology
https://www.readbyqxmd.com/read/28636804/new-insights-into-global-biogeography-population-structure-and-natural-selection-from-the-genome-of-the-epipelagic-copepod-oithona
#5
Mohammed-Amin Madoui, Julie Poulain, Kevin Sugier, Marc Wessner, Benjamin Noel, Leo Berline, Karine Labadie, Astrid Cornils, Leocadio Blanco-Bercial, Lars Stemmann, Jean-Louis Jamet, Patrick Wincker
In the epipelagic ocean the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about the Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation, and development, including genes coding Lin12-Notch-Repeat (LNR) domain proteins...
June 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28635289/exploring-the-drug-resistance-of-hcv-protease
#6
Garima Jindal, Dibyendu Mondal, Arieh Warshel
Hepatitis C virus (HCV) currently affects several million people across the globe. One of the major classes of drugs inhibits the NS3/4A protease of the polyprotein chain. Efficacy of these drugs is severely limited due to the high mutation rate that results in several genetically related quasispecies. The molecular mechanism of drug resistance is generally based on structural studies and binding free energies. However, prediction of new mutations requires a quantity that can define both binding free energy of the drug as well as the parameters (kcat and KM) for the natural substrate...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28635260/development-validation-and-inter-laboratory-evaluation-of-a-quantitative-multiplexing-method-to-assess-levels-of-ten-endogenous-allergens-in-soybean-seed-and-its-application-to-field-trials-spanning-three-growing-seasons
#7
Ryan Christopher Hill, Trent J Oman, Xiujuan Wang, Guomin Shan, Barry Schafer, Rod A Herman, Rowel Tobias, Jeff Shippar, Bhaskar Malayappan, Li Sheng, Austin Xu, Jason Bradshaw
As part of the regulatory approval process in Europe, comparison of endogenous soybean allergen levels between genetically engineered (GE) and non-GE plants has been requested. A quantitative multiplex analytical method using tandem mass spectrometry has been developed and validated to measure ten potential soybean allergens from soybean seed. The analytical method was implemented at six laboratories to demonstrate the robustness of the method and further applied to three soybean field studies across multiple growing seasons (including 21 non-GE soybean varieties) to assess the natural variation of allergen levels...
June 21, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28635152/a-novel-dna-structure-containing-agi-mediated-g-g-and-c-c-base-pairs
#8
Hehua Liu, Fusheng Shen, Phensinee Haruehanroengra, Qingqing Yao, Yunshan Cheng, Yiqing Chen, Chun Yang, Jing Zhang, Baixing Wu, Qiang Luo, Ruixue Cui, Jixi Li, Jinbiao Ma, Jia Sheng, Jianhua Gan
Metallo-base pairs have been extensively utilized in many research fields, including genetic code extension, novel therapeutics development, and various nanodevice designs. Compared to other cations, AgI is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-AgI-C pairs and one first time reported G-AgI-G pair in a short 8mer DNA strand. This structure not only discloses the detailed insights into these AgI-base pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by the heavy metal ions, further contributing to the structural diversity of DNA...
June 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28635123/measuring-fitness-heritability-life-history-traits-versus-morphological-traits-in-humans
#9
Alina Gavrus-Ion, Torstein Sjøvold, Miguel Hernández, Rolando González-José, María Esther Esteban Torné, Neus Martínez-Abadías, Mireia Esparza
OBJECTIVES: Traditional interpretation of Fisher's Fundamental Theorem of Natural Selection is that life history traits (LHT), which are closely related with fitness, show lower heritabilities, whereas morphological traits (MT) are less related with fitness and they are expected to show higher heritabilities. In humans, although few studies have examined the heritability of LHT and MT, none of them have analyzed the same sample for comparative purposes. Here we assessed, for the first time, the heritability, additive genetic variance (VA ), residual variance (VR ) and coefficient of genetic additive variation (CVA ) values of LHT and MT in a singular collection of identified skulls with associated demographic records from Hallstatt (Austria)...
June 21, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28634835/impact-of-mechanical-stimulation-on-the-chondrogenic-processes-in-human-bone-marrow-aspirates-modified-to-overexpress-sox9-via-raav-vectors
#10
Jagadeesh K Venkatesan, Janina Frisch, Ana Rey-Rico, Gertrud Schmitt, Henning Madry, Magali Cucchiarini
BACKGROUND: Evaluation of gene-based approaches to target human bone marrow aspirates in conditions of mechanical stimulation that aim at reproducing the natural joint environment may allow to develop improved treatments for articular cartilage injuries. In the present study, we investigated the potential of rAAV-mediated sox9 gene transfer to enhance the chondrogenic differentiation processes in human bone marrow aspirates under established hydrodynamic conditions compared with the more commonly employed static culture conditions...
December 2017: Journal of Experimental Orthopaedics
https://www.readbyqxmd.com/read/28632201/advantageous-developmental-outcomes-of-advancing-paternal-age
#11
M Janecka, F Rijsdijk, D Rai, A Modabbernia, A Reichenberg
Advanced paternal age (APA) at conception has been associated with negative outcomes in offspring, raising concerns about increasing age at fatherhood. Evidence from evolutionary and psychological research, however, suggests possible link between APA and a phenotypic advantage. We defined such advantage as educational success, which is positively associated with future socioeconomic status. We hypothesised that high IQ, strong focus on the subject of interest and little concern about 'fitting in' will be associated with such success...
June 20, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28631995/monitoring-the-effect-of-pathogenic-nematodes-on-locomotion-of-drosophila-larvae
#12
Martin Kunc, Badrul Arefin, Pavel Hyrsl, Ulrich Theopold
One of the key factors that determine the interaction between hosts and their parasites is the frequency of their interactions, which depends on the locomotory behavior of both parts. To address host behavior we used natural infections involving insect pathogenic nematodes and Drosophila melanogaster larvae as hosts. Using a modified version of a recently described method (FIMTrack) to assess several parameters in larger sets of animals, we initially detected specific differences in larval food searching when comparing Drosophila strains...
February 21, 2017: Fly
https://www.readbyqxmd.com/read/28631859/determining-the-drivers-of-population-structure-in-a-highly-urbanized-landscape-to-inform-conservation-planning
#13
Henri A Thomassen, Ryan J Harrigan, Kathleen Semple Delaney, Seth P D Riley, Laurel E K Serieys, Katherine Pease, Robert K Wayne, Thomas B Smith
Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially-explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on seven common species with diverse habitat requirements, home range sizes, and dispersal abilities...
June 20, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28631610/a-large-gene-family-in-fission-yeast-encodes-spore-killers-that-subvert-mendel-s-law
#14
Wen Hu, Zhao-Di Jiang, Fang Suo, Jin-Xin Zheng, Wan-Zhong He, Li-Lin Du
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them...
June 20, 2017: ELife
https://www.readbyqxmd.com/read/28631230/sequence-analysis-of-chromosome-1-revealed-different-selection-patterns-between-chinese-wild-mice-and-laboratory-strains
#15
Fuyi Xu, Shixian Hu, Tianzhu Chao, Maochun Wang, Kai Li, Yuxun Zhou, Hongyan Xu, Junhua Xiao
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1...
June 19, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28631029/syngas-biorefinery-and-syngas-utilization
#16
Sashini De Tissera, Michael Köpke, Sean D Simpson, Christopher Humphreys, Nigel P Minton, Peter Dürre
Autotrophic acetogenic bacteria are able to capture carbon (CO or CO2) through gas fermentation, allowing them to grow on a spectrum of waste gases from industry (e.g., steel manufacture and oil refining, coal, and natural gas) and to produce ethanol. They can also consume syn(thesis) gas (CO and H2) made from the gasification of renewable/sustainable resources, such as biomass and domestic/agricultural waste. Acetogenic gas fermentation can, therefore, produce ethanol in any geographic region without competing for food or land...
June 20, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28630911/the-genomic-mosaicism-of-hybrid-speciation
#17
Tore O Elgvin, Cassandra N Trier, Ole K Tørresen, Ingerid J Hagen, Sigbjørn Lien, Alexander J Nederbragt, Mark Ravinet, Henrik Jensen, Glenn-Peter Sætre
Hybridization is widespread in nature and, in some instances, can result in the formation of a new hybrid species. We investigate the genetic foundation of this poorly understood process through whole-genome analysis of the hybrid Italian sparrow and its progenitors. We find overall balanced yet heterogeneous levels of contribution from each parent species throughout the hybrid genome and identify areas of novel divergence in the hybrid species exhibiting signals consistent with balancing selection. High-divergence areas are disproportionately located on the Z chromosome and overrepresented in gene networks relating to key traits separating the focal species, which are likely involved in reproductive barriers and/or species-specific adaptations...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630894/next-generation-probes-particles-and-proteins-for-neural-interfacing
#18
REVIEW
Jonathan Rivnay, Huiliang Wang, Lief Fenno, Karl Deisseroth, George G Malliaras
Bidirectional interfacing with the nervous system enables neuroscience research, diagnosis, and therapy. This two-way communication allows us to monitor the state of the brain and its composite networks and cells as well as to influence them to treat disease or repair/restore sensory or motor function. To provide the most stable and effective interface, the tools of the trade must bridge the soft, ion-rich, and evolving nature of neural tissue with the largely rigid, static realm of microelectronics and medical instruments that allow for readout, analysis, and/or control...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630875/contribution-of-the-microenvironmental-niche-to-glioblastoma-heterogeneity
#19
REVIEW
Ivy A W Ho, Winston S N Shim
Glioblastoma is the most aggressive cancer of the brain. The dismal prognosis is largely attributed to the heterogeneous nature of the tumor, which in addition to intrinsic molecular and genetic changes is also influenced by the microenvironmental niche in which the glioma cells reside. The cancer stem cells (CSCs) hypothesis suggests that all cancers arise from CSCs that possess the ability to self-renew and initiate tumor formation. CSCs reside in specialized niches where interaction with the microenvironment regulates their stem cell behavior...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28630351/evolutionary-radiation-of-lanthipeptides-in-marine-cyanobacteria
#20
Andres Cubillos-Ruiz, Jessie W Berta-Thompson, Jamie W Becker, Wilfred A van der Donk, Sallie W Chisholm
Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive posttranslational modification. Prochlorosins are a group of lanthipeptides produced by certain strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus Unlike other lanthipeptide-producing bacteria, picocyanobacteria use an unprecedented mechanism of substrate promiscuity for the production of numerous and diverse lanthipeptides using a single lanthionine synthetase. Through a cross-scale analysis of prochlorosin biosynthesis genes-from genomes to oceanic populations-we show that marine picocyanobacteria have the collective capacity to encode thousands of different cyclic peptides, few of which would display similar ring topologies...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
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