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Human evolutionary genetics

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https://www.readbyqxmd.com/read/29341142/evolutionary-and-genetic-features-of-drug-targets
#1
REVIEW
Yuan Quan, Zhong-Yi Wang, Xin-Yi Chu, Hong-Yu Zhang
In the modern drug discovery pipeline, identification of novel drug targets is a critical step. Despite rapid progress in developing biomedical techniques, it is still a great challenge to find promising new targets from the ample space of human genes. This fact is partially responsible for the situation of "more investments, fewer drugs" in the pharmaceutical industry. A series of recent researches revealed that successfully targeted genes share some common evolutionary and genetic features, which means that the knowledge accumulated in modern evolutionary biology and genetics is very helpful to identify potential drug targets and to find new drugs as well...
January 17, 2018: Medicinal Research Reviews
https://www.readbyqxmd.com/read/29335803/contribution-of-transposable-elements-and-distal-enhancers-to-evolution-of-human-specific-features-of-interphase-chromatin-architecture-in-embryonic-stem-cells
#2
Gennadi V Glinsky
Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs...
January 15, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29334950/will-human-influences-on-evolutionary-dynamics-in-the-wild-pervade-the-anthropocene
#3
REVIEW
Fanie Pelletier, David W Coltman
The five most pervasive anthropogenic threats to biodiversity are over-exploitation, habitat changes, climate change, invasive species, and pollution. Since all of these threats can affect intraspecific biodiversity-including genetic variation within populations-humans have the potential to induce contemporary microevolution in wild populations. We highlight recent empirical studies that have explored the effects of these anthropogenic threats to intraspecific biodiversity in the wild. We conclude that it is critical that we move towards a predictive framework that integrates a better understanding of contemporary microevolution to multiple threats to forecast the fate of natural populations in a changing world...
January 15, 2018: BMC Biology
https://www.readbyqxmd.com/read/29332164/skewing-of-the-genetic-architecture-at-the-zmym3-human-specific-5-utr-short-tandem-repeat-in-schizophrenia
#4
F Alizadeh, A Bozorgmehr, J Tavakkoly-Bazzaz, M Ohadi
Differential expansion of a number of human short tandem repeats (STRs) at the critical core promoter and 5' untranslated region (UTR) support the hypothesis that at least some of these STRs may provide a selective advantage in human evolution. Following a genome-wide screen of all human protein-coding gene 5' UTRs based on the Ensembl database ( http://www.ensembl.org ), we previously reported that the longest STR in this interval is a (GA)32, which belongs to the X-linked zinc finger MYM-type containing 3 (ZMYM3) gene...
January 13, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29316927/global-sequence-diversity-of-the-lactate-dehydrogenase-gene-in-plasmodium-falciparum
#5
Phumin Simpalipan, Sittiporn Pattaradilokrat, Pongchai Harnyuttanakorn
BACKGROUND: Antigen-detecting rapid diagnostic tests (RDTs) have been recommended by the World Health Organization for use in remote areas to improve malaria case management. Lactate dehydrogenase (LDH) of Plasmodium falciparum is one of the main parasite antigens employed by various commercial RDTs. It has been hypothesized that the poor detection of LDH-based RDTs is attributed in part to the sequence diversity of the gene. To test this, the present study aimed to investigate the genetic diversity of the P...
January 9, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29315643/characterization-of-unusual-ds-1-like-g3p-8-rotavirus-strains-in-children-with-diarrhea-in-japan
#6
Satoshi Komoto, Tomihiko Ide, Manami Negoro, Takaaki Tanaka, Kazutoyo Asada, Masakazu Umemoto, Haruo Kuroki, Hiroaki Ito, Shigeki Tanaka, Mitsue Ito, Saori Fukuda, Shigeru Suga, Hajime Kamiya, Takashi Nakano, Koki Taniguchi
The emergence and rapid spread of novel DS-1-like intergenogroup reassortant rotaviruses having the equine-like G3 genotype (DS-1-like G3P[8] strains) have been recently reported from several countries. During rotavirus surveillance in Japan in 2015-2016, three DS-1-like G3P[8] strains were identified from children with severe diarrhea. In the present study, we sequenced and characterized the full genomes of these three strains. On full-genomic analysis, all three strains showed a unique genotype constellation including both genogroup 1 and 2 genes: G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2...
January 9, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29311597/putative-functional-genes-in-idiopathic-dilated-cardiomyopathy
#7
Nishanth Ulhas Nair, Avinash Das, Uri Amit, Welles Robinson, Seung Gu Park, Mahashweta Basu, Alex Lugo, Jonathan Leor, Eytan Ruppin, Sridhar Hannenhalli
Idiopathic dilated cardiomyopathy (DCM) is a complex disorder with a genetic and an environmental component involving multiple genes, many of which are yet to be discovered. We integrate genetic, epigenetic, transcriptomic, phenotypic, and evolutionary features into a method - Hridaya, to infer putative functional genes underlying DCM in a genome-wide fashion, using 213 human heart genomes and transcriptomes. Many genes identified by Hridaya are experimentally shown to cause cardiac complications. We validate the top predicted genes, via five different genome-wide analyses: First, the predicted genes are associated with cardiovascular functions...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29306351/dissection-of-ancestral-genetic-contributions-to-creole-goat-populations
#8
N Sevane, O Cortés, L T Gama, A Martínez, P Zaragoza, M Amills, D O Bedotti, C Bruno de Sousa, J Cañon, S Dunner, C Ginja, M R Lanari, V Landi, P Sponenberg, J V Delgado
Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus' arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds...
January 8, 2018: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29305858/identification-of-a-candidate-enhancer-for-dmrt3-involved-in-spastic-cerebral-palsy-pathogenesis
#9
Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama
Cerebral palsy (CP) is a major neuronal disease and the most common movement disorder in children. Although environmental factors leading to CP have been greatly investigated, the genetic mechanism underlying CP is not well understood. Here we focused on two clinical reports that characterized a deletion involving the KANK1 gene locus in the 9p24.3 region. One report shows spastic CP and the other shows no spastic CP phenotype. Based on the epigenetic status and evolutionary conservation, we first found a functional genomic element at the noncoding region that was deleted only in patients with spastic CP...
January 3, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29302275/rapid-evolution-leads-to-differential-population-dynamics-and-top-down-control-in-resurrected-daphnia-populations
#10
Eyerusalem Goitom, Laurens J Kilsdonk, Kristien Brans, Mieke Jansen, Pieter Lemmens, Luc De Meester
There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco-evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow-up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top-down control of phytoplankton...
January 2018: Evolutionary Applications
https://www.readbyqxmd.com/read/29299963/extending-genome-wide-association-study-results-to-test-classic-anthropological-hypotheses-human-third-molar-agenesis-and-the-probable-mutation-effect
#11
Adrijana Vukelic, Jacob A Cohen, Alexis P Sullivan, George H Perry
A genome-wide association study (GWAS) identifies regions of the genome that likely affect the variable state of a phenotype of interest. These regions can then be studied with population genetic methods to make inferences about the evolutionary history of the trait. There are increasing opportunities to use GWAS results-even from clinically motivated studies-for tests of classic anthropological hypotheses. One such example, presented here as a case study for this approach, involves tooth development variation related to dental crowding...
April 2017: Human Biology
https://www.readbyqxmd.com/read/29285971/leveraging-multiple-populations-across-time-helps-define-accurate-models-of-human-evolution-a-reanalysis-of-the-lactase-persistence-adaptation
#12
Chenling Xu Antelope, Davide Marnetto, Fergal Casey, Emilia Huerta-Sanchez
Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continue to improve and enable tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred and to revise previous conjectures...
January 2017: Human Biology
https://www.readbyqxmd.com/read/29277877/comparative-genomics-in-drosophila
#13
Martin Oti, Attilio Pane, Michael Sammeth
Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying animal genetics, development, behavior, evolution, and human disease. Recent advances in DNA sequencing technologies launched Drosophila into the post-genomic era and paved the way for unprecedented comparative genomics investigations. The complete sequencing and systematic comparison of the genomes from 12 Drosophila species represents a milestone achievement in modern biology, which allowed a plethora of different studies ranging from the annotation of known and novel genomic features to the evolution of chromosomes and, ultimately, of entire genomes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29277311/targeting-gut-microbiome-a-novel-and-potential-therapy-for-autism
#14
REVIEW
Yongshou Yang, Jinhu Tian, Bo Yang
Autism spectrum disorder (ASD) is a severely neurodevelopmental disorder that impairs a child's ability to communicate and interact with others. Children with neurodevelopmental disorder, including ASD, are regularly affected by gastrointestinal problems and dysbiosis of gut microbiota. On the other hand, humans live in a co-evolutionary association with plenty of microorganisms that resident on the exposed and internal surfaces of our bodies. The microbiome, refers to the collection of microbes and their genetic material, confers a variety of physiologic benefits to the host in many key aspects of life as well as being responsible for some diseases...
December 22, 2017: Life Sciences
https://www.readbyqxmd.com/read/29273026/genetic-diversity-and-structure-related-to-expansion-history-and-habitat-isolation-stone-marten-populating-rural-urban-habitats
#15
Anna Wereszczuk, Raphaël Leblois, Andrzej Zalewski
BACKGROUND: Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species' ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions...
December 22, 2017: BMC Ecology
https://www.readbyqxmd.com/read/29259610/domesticated-genetically-engineered-and-wild-plant-relatives-exhibit-unintended-phenotypic-differences-a-comparative-meta-analysis-profiling-rice-canola-maize-sunflower-and-pumpkin
#16
Alejandra Hernández-Terán, Ana Wegier, Mariana Benítez, Rafael Lira, Ana E Escalante
Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE). Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29259589/complete-genome-sequencing-of-mycobacterium-bovis-sp38-and-comparative-genomics-of-mycobacterium-bovis-and-m-tuberculosis-strains
#17
Cristina Kraemer Zimpel, Paulo E Brandão, Antônio F de Souza Filho, Robson F de Souza, Cássia Y Ikuta, José Soares Ferreira Neto, Naila C Soler Camargo, Marcos Bryan Heinemann, Ana M S Guimarães
Mycobacterium bovis causes bovine tuberculosis and is the main organism responsible for zoonotic tuberculosis in humans. We performed the sequencing, assembly and annotation of a Brazilian strain of M. bovis named SP38, and performed comparative genomics of M. bovis genomes deposited in GenBank. M. bovis SP38 has a traditional tuberculous mycobacterium genome of 4,347,648 bp, with 65.5% GC, and 4,216 genes. The majority of CDSs (2,805, 69.3%) have predictive function, while 1,206 (30.07%) are hypothetical. For comparative analysis, 31 M...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29258326/origin-and-spread-of-hiv-1-subtype-b-among-heterosexual-individuals-in-bulgaria
#18
Ivailo Alexiev, Alessandra Lo Presti, Reneta Dimitrova, Brian Thomas Foley, Anna Gancheva, Asya Kostadinova, Lora Nikolova, Silvia Angeletti, Eleonora Cella, Ivaylo Elenkov, Mariana Stoycheva, Daniela Nikolova, Tsetsa Doychinova, Liliya Pekova, Massimo Ciccozzi
Human Immunodeficiency Virus (HIV) was originally introduced in Bulgaria through heterosexual transmission (HET) and later transferred to other vulnerable groups along with numerous more recent introductions from outside Bulgaria. To define the diversity, origins and dynamics of the HIV-1 subtypes prevalent in HET population in Bulgaria we applied phylogenetic and phylodynamic analyses using polymerase (pol) sequences from HET individuals to infer the spatiotemporal evolutionary history of the HIV-1 epidemic in this population in Bulgaria...
December 19, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29246100/investigating-population-continuity-with-ancient-dna-under-a-spatially-explicit-simulation-framework
#19
Nuno Miguel Silva, Jeremy Rio, Mathias Currat
BACKGROUND: Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times...
December 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29244562/learning-to-cooperate-the-evolution-of-social-rewards-in-repeated-interactions
#20
Slimane Dridi, Erol Akçay
Understanding the behavioral and psychological mechanisms underlying social behaviors is one of the major goals of social evolutionary theory. In particular, a persistent question about animal cooperation is to what extent it is supported by other-regarding preferences-the motivation to increase the welfare of others. In many situations, animals adjust their behaviors through learning by responding to the rewards they experience as a consequence of their actions. Therefore, we may ask whether learning in social situations can be driven by evolved other-regarding rewards...
January 2018: American Naturalist
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