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landscape genetics

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https://www.readbyqxmd.com/read/28089252/practical-approaches-for-whole-genome-sequence-analysis-of-heart-and-blood-related-traits
#1
Alanna C Morrison, Zhuoyi Huang, Bing Yu, Ginger Metcalf, Xiaoming Liu, Christie Ballantyne, Josef Coresh, Fuli Yu, Donna Muzny, Elena Feofanova, Navin Rustagi, Richard Gibbs, Eric Boerwinkle
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28087782/mutation-supply-and-relative-fitness-shape-the-genotypes-of-ciprofloxacin-resistant-escherichia-coli
#2
Douglas L Huseby, Franziska Pietsch, Gerrit Brandis, Linnéa Garoff, Angelica Tegehall, Diarmaid Hughes
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087070/can-evolution-supply-what-ecology-demands
#3
REVIEW
Hanna Kokko, Anurag Chaturvedi, Daniel Croll, Martin C Fischer, Frédéric Guillaume, Sophie Karrenberg, Ben Kerr, Gregor Rolshausen, Jessica Stapley
A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate...
January 10, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28079940/reproductive-modification-in-forest-plantations-impacts-on-biodiversity-and-society
#4
REVIEW
Steven H Strauss, Kristin N Jones, Haiwei Lu, Joshua D Petit, Amy L Klocko, Matthew G Betts, Berry J Brosi, Robert J Fletcher, Mark D Needham
1000 I. 1000 II. 1001 III. 1014 IV. 1015 V. 1016 1016 References 1016 SUMMARY: Genetic engineering (GE) can be used to improve forest plantation productivity and tolerance of biotic and abiotic stresses. However, gene flow from GE forest plantations is a large source of ecological, social and legal controversy. The use of genetic technologies to mitigate or prevent gene flow has been discussed widely and should be technically feasible in a variety of plantation taxa. However, potential ecological effects of such modifications, and their social acceptability, are not well understood...
February 2017: New Phytologist
https://www.readbyqxmd.com/read/28074633/a-computational-interactome-for-prioritizing-genes-associated-with-complex-agronomic-traits-in-rice
#5
Shiwei Liu, Yihui Liu, Jiawei Zhao, Shitao Cai, Hongmei Qian, Kaijing Zuo, Lingxia Zhao, Lida Zhang
Rice is one of the most important staple foods for more than half of the world's population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet/) using machine-learning with structural relationship and functional information...
January 11, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28073919/trub1-is-the-predominant-pseudouridine-synthase-acting-on-mammalian-mrna-via-a-predictable-and-conserved-code
#6
Modi Safra, Ronit Nir, Daneyal Farouq, Schraga Schwartz
Following synthesis, RNA can be modified with over 100 chemically distinct modifications, which can potentially regulate RNA expression post-transcriptionally. Pseudouridine (Ψ) was recently established to be widespread and dynamically regulated on yeast mRNA, but less is known about Ψ presence, regulation and biogenesis in mammalian mRNA. Here, we sought to characterize the Ψ landscape on mammalian mRNA, to identify the main Ψ-synthases (PUSs) catalyzing Ψ formation, and to understand the factors governing their specificity towards selected targets...
January 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28073088/characterization-of-the-iberian-y-chromosome-haplogroup-r-df27-in-northern-spain
#7
Patricia Villaescusa, María José Illescas, Laura Valverde, Miriam Baeta, Carolina Nuñez, Begoña Martínez-Jarreta, Maria Teresa Zarrabeitia, Francesc Calafell, Marian M de Pancorbo
The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28073087/a-nearest-neighbour-approach-by-genetic-distance-to-the-assignment-of-individual-trees-to-geographic-origin
#8
Bernd Degen, Céline Blanc-Jolivet, Katrin Stierand, Elizabeth Gillet
During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin"...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28070591/-the-importance-of-conservation-of-rare-domestic-animal-breeds-using-the-example-of-arc-warder
#9
Kai Frölich, Anabell Jandowsky
The domestic animals descend from various wild ancestors. Thus, for example, of the wolf, the dog (15  000 BC), of the Bezoar goat the goat (10  000 BC), of the Asian mouflon the sheep (10  000 BC), of the wild boar the pig (8000 BC) and of the aurochs the cattle (7000 BC). Domestication has dramatically changed our culture and led to a great diversity of animal breeds. This is a unique cultural and historical treasure, which we have to preserve for future generations. The zoological park Arc Warder is Europe's largest center for rare and endangered domestic animal breeds...
January 10, 2017: Tierärztliche Praxis. Ausgabe G, Grosstiere/Nutztiere
https://www.readbyqxmd.com/read/28067020/spatial-detection-of-outlier-loci-with-moran-eigenvector-maps-mem
#10
Helene H Wagner, Mariana Chávez-Pesqueira, Brenna R Forester
The spatial signature of micro-evolutionary processes structuring genetic variation may play an important role in the detection of loci under selection. However, the spatial location of samples hasn't yet been used to quantify this. Here, we present a new two-step method of spatial outlier detection at the individual and deme levels using the power spectrum of Moran eigenvector maps (MEM). The MEM power spectrum quantifies how the variation in a variable, such as the frequency of an allele at a SNP locus, is distributed across a range of spatial scales defined by MEM spatial eigenvectors...
January 9, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28065846/the-association-of-heart-failure-related-micrornas-with-neurohormonal-signaling
#11
Yei-Tsung Chen, Juan Wang, Kai Sing Tong, Lee Lee Wong, Oi Wah Liew, Arthur Mark Richards
Heart failure (HF) is a widely prevalent syndrome imposing a significant burden of morbidity and mortality world-wide. Differential circulating microRNA profiles observed in HF cohorts suggest the diagnostic utility of microRNAs as biomarkers. Given their function in fine tuning gene expression, alternations in microRNA landscape could reflecting the underlying mechanisms of disease and present potential therapeutic targets. Using multiple computational target predicting algorithms together with the luciferase-based reporting platform, the interactions between HF-related microRNAs and the 3' untranslated regions (3'UTRs) of neurohormone associated genes were examined and compared...
January 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28063178/landscape-genetics-indicate-recently-increased-habitat-fragmentation-in-african-forest-associated-chafers
#12
Jonas Eberle, Dennis Rödder, Marc Beckett, Dirk Ahrens
Today, indigenous forests cover less than 0.6% of South Africa's land surface and are highly fragmented. Most forest relicts are very small and typically occur in fire-protected gorges along the eastern Great Escarpment. Yet, they hold a unique and valuable fauna with high endemism and ancient phylogenetic lineages, fostered by long term climatic stability and complex micro-climates. Despite numerous studies on southern African vegetation cover, the current state of knowledge about the natural extension of indigenous forests is rather fragmentary...
January 7, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28061468/the-heterogeneous-landscape-of-alk-negative-alcl
#13
Elisabetta Mereu, Elisa Pellegrino, Irene Scarfò, Giorgio Inghirami, Roberto Piva
Anaplastic Large Cell Lymphoma (ALCL) is a clinical and biological heterogeneous disease including systemic ALK positive and ALK negative entities. Whereas ALK positive ALCLs are molecularly characterized and readily diagnosed, specific immunophenotypic or genetic features to define ALK negative ALCL are missing, and their distinction from other T-cell non-Hodgkin lymphomas (T-NHLs) can be controversial. In recent years, great advances have been made in dissecting the heterogeneity of ALK negative ALCLs and in providing new diagnostic and treatment options for these patients...
January 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28059585/initiation-of-aberrant-dna-methylation-patterns-and-heterogeneity-in-precancerous-lesions-of-human-hepatocellular-cancer
#14
Ryan A Hlady, Dan Zhou, William Puszyk, Lewis R Roberts, Chen Liu, Keith D Robertson
While intratumor heterogeneity contributes to disease progression, metastasis, and resistance to chemotherapy, it also provides a route to understanding the evolution and drivers of disease. Defects in epigenetic landscapes are intimately linked to pathogenesis of a variety of human diseases, with epigenetic deregulation promoting tumorigenesis. Understanding epigenetic heterogeneity is crucial in hepatocellular carcinoma (HCC), where epigenetic alterations are frequent, early, and pathogenic events. We determined genome-wide DNA methylation and copy number variation leveraging the Infinium 450 K in a series of regenerative nodules from within single patient livers...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28057302/unraveling-the-neurobiology-of-sleep-and-sleep-disorders-using-drosophila
#15
L Chakravarti, E H Moscato, M S Kayser
Sleep disorders in humans are increasingly appreciated to be not only widespread but also detrimental to multiple facets of physical and mental health. Recent work has begun to shed light on the mechanistic basis of sleep disorders like insomnia, restless legs syndrome, narcolepsy, and a host of others, but a more detailed genetic and molecular understanding of how sleep goes awry is lacking. Over the past 15 years, studies in Drosophila have yielded new insights into basic questions regarding sleep function and regulation...
2017: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/28056824/the-emerging-landscape-of-dynamic-dna-methylation-in-early-childhood
#16
Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Ulrike Gehring, Soesma A Jankipersadsing, Pieter van der Vlies, Cleo C van Diemen, Bianca van Rijkom, Jocelyne Just, Inger Kull, Juha Kere, Josep Maria Antó, Jean Bousquet, Alexandra Zhernakova, Cisca Wijmenga, Isabella Annesi-Maesano, Jordi Sunyer, Erik Melén, Yang Li, Dirkje S Postma, Gerard H Koppelman
BACKGROUND: DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. RESULTS: By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of p < 1...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28054957/molecular-biomarkers-for-prediction-of-targeted-therapy-response-in-metastatic-breast-cancer-trick-or-treat
#17
REVIEW
Angela Toss, Marta Venturelli, Chiara Peterle, Federico Piacentini, Stefano Cascinu, Laura Cortesi
In recent years, the study of genomic alterations and protein expression involved in the pathways of breast cancer carcinogenesis has provided an increasing number of targets for drugs development in the setting of metastatic breast cancer (i.e., trastuzumab, everolimus, palbociclib, etc.) significantly improving the prognosis of this disease. These drugs target specific molecular abnormalities that confer a survival advantage to cancer cells. On these bases, emerging evidence from clinical trials provided increasing proof that the genetic landscape of any tumor may dictate its sensitivity or resistance profile to specific agents and some studies have already showed that tumors treated with therapies matched with their molecular alterations obtain higher objective response rates and longer survival...
January 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28054091/constrained-evolution-of-a-bispecific-enzyme-lessons-for-biocatalyst-design
#18
E Sugrue, C Scott, C J Jackson
One of the central goals of protein design and engineering is to be able to accurately predict the effects of a mutation on stability and activity. However, the genetic context into which mutations are introduced can lead to complex interactions between the mutation and other amino acids and unpredictable, non-additive, effects. This phenomenon is known as intramolecular epistasis and has been shown to restrict evolutionary paths through laboratory directed evolution experiments and ancestral protein reconstruction, but has rarely been studied at a quantitative level in naturally evolving enzymes...
January 5, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28052389/infectious-hematopoietic-necrosis-virus-virological-and-genetic-surveillance-2000-2012
#19
Rachel Breyta, Ilana Brito, Gael Kurath, Shannon LaDeau
Surveillance records of the acute RNA pathogen of Pacific salmonid fish infectious hematopoietic necrosis virus are combined for the first time to enable landscape-level ecological analyses and modeling. The study area is the freshwater ecosystems of the large Columbia River watershed in the U.S. states of Washington, Oregon, and Idaho, as well as coastal rivers in Washington and Oregon. The study period is 2000-2012, and records were contributed by all five resource management agencies that operate conservation hatcheries in the study area...
January 2017: Ecology
https://www.readbyqxmd.com/read/28051182/nesting-of-colon-and-ovarian-cancer-cells-in-the-endothelial-niche-is-associated-with-alterations-in-glycan-and-lipid-metabolism
#20
Anna Halama, Bella S Guerrouahen, Jennifer Pasquier, Noothan J Satheesh, Karsten Suhre, Arash Rafii
The metabolic phenotype of a cancer cell is determined by its genetic makeup and microenvironment, which dynamically modulates the tumor landscape. The endothelial cells provide both a promoting and protective microenvironment - a niche for cancer cells. Although metabolic alterations associated with cancer and its progression have been fairly defined, there is a significant gap in our understanding of cancer metabolism in context of its microenvironment. We deployed an in vitro co-culture system based on direct contact of cancer cells with endothelial cells (E4(+)EC), mimicking the tumor microenvironment...
January 4, 2017: Scientific Reports
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