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https://www.readbyqxmd.com/read/29935353/a-new-method-to-cluster-genomes-based-on-cumulative-fourier-power-spectrum
#1
Rui Dong, Ziyue Zhu, Changchuan Yin, Rong L He, Stephen S-T Yau
Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences...
June 20, 2018: Gene
https://www.readbyqxmd.com/read/29935338/pathogenicity-population-genetics-and-dissemination-of-bacillus-anthracis
#2
REVIEW
Paola Pilo, Joachim Frey
Bacillus anthracis, the etiological agent of anthrax, procures its particular virulence by a capsule and two AB type toxins: the lethal factor LF and the edema factor EF. These toxins primarily disable immune cells. Both toxins are translocated to the host cell by the adhesin-internalin subunit called protective antigen PA. PA enables LF to reach intra-luminal vesicles, where it remains active for long periods. Subsequently, LF translocates to non-infected cells, leading to inefficient late therapy of anthrax...
June 20, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29931325/early-arrival-and-climatically-linked-geographic-expansion-of-new-world-monkeys-from-tiny-african-ancestors
#3
Daniele Silvestro, Marcelo F Tejedor, Martha L Serrano-Serrano, Oriane Loiseau, Victor Rossier, Jonathan Rolland, Alexander Zizka, Sebastian Höhna, Alexandre Antonelli, Nicolas Salamin
New World monkeys (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Here we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines...
June 20, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29929489/quantitative-evolutionary-proteomics-of-seminal-fluid-from-primates-with-different-mating-systems
#4
Katrina G Claw, Renee D George, Michael J MacCoss, Willie J Swanson
BACKGROUND: Genomic data from various organisms have been used to study how sexual selection has shaped genetic diversity in reproductive proteins, and in particular, to elucidate how mating systems may have influenced evolution at the molecular and phenotypic levels. However, large-scale proteomic data including protein identifications and abundances are only now entering the field of evolutionary and comparative genomics. Variation in both protein sequence and expression level may play important roles in the evolution of sexual traits and behaviors...
June 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29925657/recurrent-loss-of-apobec3h-activity-during-primate-evolution
#5
Erin I Garcia, Michael Emerman
Genes in the APOBEC3 family encode cytidine deaminases that provide a barrier against viral infection and retrotransposition. Of all APOBEC3 genes in humans, APOBEC3H ( A3H ) is the most polymorphic: some haplotypes encode stable and active A3H proteins, while others are unstable and poorly antiviral. Such variation in human A3H affects interactions with the lentiviral antagonist Vif, which counteracts A3H via proteasomal degradation. In order to broaden our understanding of A3H-Vif interactions, as well as its evolution in Old World monkeys, we characterized A3H variation within four African green monkey (AGM) subspecies...
June 20, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29925616/adaptive-developmental-plasticity-in-rhesus-macaques-the-serotonin-transporter-gene-interacts-with-maternal-care-to-affect-juvenile-social-behaviour
#6
Jesus E Madrid, Tara M Mandalaywala, Sean P Coyne, Jamie Ahloy-Dallaire, Joseph P Garner, Christina S Barr, Dario Maestripieri, Karen J Parker
Research has increasingly highlighted the role that developmental plasticity-the ability of a particular genotype to produce variable phenotypes in response to different early environments-plays as an adaptive mechanism. One of the most widely studied genetic contributors to developmental plasticity in humans and rhesus macaques is a serotonin transporter gene-linked polymorphic region (5-HTTLPR), which determines transcriptional efficiency of the serotonin transporter gene in vitro and modifies the availability of synaptic serotonin in these species...
June 27, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29913352/recent-insights-into-the-evolution-of-quantitative-traits-in-non-human-primates
#7
REVIEW
Leslea J Hlusko
The past few years of genetic research on primate quantitative trait variation have been notable in the diversity of phenotypes explored, ranging from classic skeletal measurements to behavior, through to levels of gene expression, and with observations from both captive and wild populations. These studies demonstrate the importance of captive pedigreed breeding colonies, populations that can be matched to their wild counterparts to enable comparison of genetic architectures. Non-human primate genotype:phenotype maps are essential for placing human variation within an evolutionary framework as well as for gaining insight to human biology...
June 15, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29905829/two-hormones-for-one-receptor-evolution-biochemistry-actions-and-pathophysiology-of-lh-and-hcg
#8
Livio Casarini, Daniele Santi, Giulia Brigante, Manuela Simoni
Luteinizing hormone (LH) and chorionic gonadotropin (CG) are glycoproteins fundamental for sexual development and reproduction. Since they act on the same receptor (LHCGR), there is a general consensus that LH and hCG are equivalent. However, separate evolution of LHβ and hCGβ subunits occurred in primates, resulting in two molecules sharing ∼85% identity and regulating different physiological events. Pituitary, pulsatile LH production results in a ∼90 min half-life molecule targeting the gonads, to regulate gametogenesis and androgen synthesis...
June 13, 2018: Endocrine Reviews
https://www.readbyqxmd.com/read/29905781/association-between-genomic-instability-and-evolutionary-chromosomal-rearrangements-in-neotropical-primates
#9
Fiona Puntieri, Nancy B Andrioli, Mariela Nieves
During the last decades the mammalian genome has been proposed to have regions prone to breakage and reorganization concentrated in certain chromosomal bands that seem to correspond to evolutionary breakpoints. These bands are likely to be involved in chromosome fragility or instability. In Primates, some biomarkers of genetic damage may be associated with various degrees of genomic instability. Here, we investigated the usefulness of Sister Chromatid Exchange (SCE) as a biomarker of potential sites of frequent chromosome breakage and rearrangement in Alouatta caraya, Ateles chamek, Ateles paniscus and Cebus cay...
June 14, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29898898/human-specific-features-of-special-gene-expression-and-regulation-in-eight-brain-regions
#10
Chuan Xu, Qian Li, Olga Efimova, Liu He, Shoji Tatsumoto, Vita Stepanova, Takao Oishi, Toshifumi Udono, Katsushi Yamaguchi, Shuji Shigenobu, Akiyoshi Kakita, Hiroyuki Nawa, Philipp Khaitovich, Yasuhiro Go
Molecular maps of the human brain alone do not inform us of the features unique to humans. Yet, the identification of these features is important for understanding both the evolution and nature of human cognition. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, a gibbon and macaques. An analysis of spatial transcriptome trajectories across eight brain regions in four primate species revealed 1,851 genes showing human-specific transcriptome differences in one or multiple brain regions, in contrast to 240 chimpanzee-specific ones...
June 13, 2018: Genome Research
https://www.readbyqxmd.com/read/29894995/primate-brain-anatomy-new-volumetric-mri-measurements-for-neuroanatomical-studies
#11
Ana F Navarrete, Erwin L A Blezer, Murillo Pagnotta, Elizabeth S M de Viet, Orlin S Todorov, Patrik Lindenfors, Kevin N Laland, Simon M Reader
Since the publication of the primate brain volumetric dataset of Stephan and colleagues in the early 1980s, no major new comparative datasets covering multiple brain regions and a large number of primate species have become available. However, technological and other advances in the last two decades, particularly magnetic resonance imaging (MRI) and the creation of institutions devoted to the collection and preservation of rare brain specimens, provide opportunities to rectify this situation. Here, we present a new dataset including brain region volumetric measurements of 39 species, including 20 species not previously available in the literature, with measurements of 16 brain areas...
June 12, 2018: Brain, Behavior and Evolution
https://www.readbyqxmd.com/read/29888138/adaptive-genetic-variation-at-three-loci-in-south-african-vervet-monkeys-chlorocebus-pygerythrus-and-the-role-of-selection-within-primates
#12
Willem G Coetzer, Trudy R Turner, Christopher A Schmitt, J Paul Grobler
Vervet monkeys ( Chlorocebus pygerythrus ) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor ( TLR ) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research...
2018: PeerJ
https://www.readbyqxmd.com/read/29876698/the-function-of-primate-multimodal-communication
#13
REVIEW
Marlen Fröhlich, Carel P van Schaik
Language is commonly narrowed down to speech, but human face-to-face communication is in fact an intrinsically multimodal phenomenon. Despite growing evidence that the communication of non-human primates, our main model for the evolution of language, is also inherently multimodal, most studies on primate communication have focused on either gestures or vocalizations in isolation. Accordingly, the biological function of multimodal signalling remains poorly understood. In this paper, we aim to merge the perspectives of comparative psychology and behavioural ecology on multimodal communication, and review existing studies in great apes for evidence of multimodal signal function based on content-based, efficacy-based and inter-signal interaction hypotheses...
June 6, 2018: Animal Cognition
https://www.readbyqxmd.com/read/29873392/facial-expressions-and-pair-bonds-in-hylobatids
#14
Brittany Florkiewicz, Gabriella Skollar, Ulrich H Reichard
OBJECTIVES: Facial expressions are an important component of primate communication that functions to transmit social information and modulate intentions and motivations. Chimpanzees and macaques, for example, produce a variety of facial expressions when communicating with conspecifics. Hylobatids also produce various facial expressions; however, the origin and function of these facial expressions are still largely unclear. It has been suggested that larger facial expression repertoires may have evolved in the context of social complexity, but this link has yet to be tested at a broader empirical basis...
June 6, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29873035/the-influence-of-a-demographic-change-on-social-relationships-among-male-golden-snub-nosed-monkeys-rhinopithecus-roxellana
#15
Pengzhen Huang, Endi Zhang, Min Chen
It has been suggested that social relationships are more likely to be prone to variation in the dispersing sex than the philopatric sex. However, we know less about the dynamics of all-male groups in male-dispersing species than we do about other types of primate groups. We studied male sociality in a captive group of golden snub-nosed monkeys (Rhinopithecus roxellana), which was composed of a one-male unit (OMU, N = 7) and an all-male unit (AMU, N = 7 or 8), in Shanghai Wild Animal Park, China. Using data collected for 6 months, during which there was a demographic change in the AMU and the alpha male was replaced by a newcomer, we found that a dramatic change in social ranks occurred accompanied by elevated aggression following this social upheaval...
June 5, 2018: Primates; Journal of Primatology
https://www.readbyqxmd.com/read/29872426/comprehensive-antiretroviral-restriction-factor-profiling-reveals-the-evolutionary-imprint-of-the-ex-vivo-and-in-vivo-ifn-%C3%AE-response-in-htlv-1-associated-neuroinflammation
#16
Fabio E Leal, Soraya Maria Menezes, Emanuela A S Costa, Phillip M Brailey, Lucio Gama, Aluisio C Segurado, Esper G Kallas, Douglas F Nixon, Tim Dierckx, Ricardo Khouri, Jurgen Vercauteren, Bernardo Galvão-Castro, Rui Andre Saraiva Raposo, Johan Van Weyenbergh
HTLV-1-Associated Myelopathy (HAM/TSP) is a progressive neuroinflammatory disorder for which no disease-modifying treatment exists. Modest clinical benefit from type I interferons (IFN-α/β) in HAM/TSP contrasts with its recently identified IFN-inducible gene signature. In addition, IFN-α treatment in vivo decreases proviral load and immune activation in HAM/TSP, whereas IFN-β therapy decreases tax mRNA and lymphoproliferation. We hypothesize this "IFN paradox" in HAM/TSP might be explained by both cell type- and gene-specific effects of type I IFN in HTLV-1-associated pathogenesis...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29870801/construction-expression-and-characterization-of-ag1-1-843-and-ag1-1-1581
#17
Yan Xie, Yan-Tao Yang, Wei Shi, Xia Ai, Xu-Guang Xi
AG1, a member of the DUF1220 protein family, exhibits the most extreme human lineage-specific copy number expansion of any protein-coding sequence in the genome. These variations in copy number have been linked to both brain evolution among primates and brain size in humans. Unfortunately, our current understanding of the structure and function of these proteins is limited because current cloning and expression techniques fail to consistently produce recombinant protein for in vitro studies. The present work describes a method for amino acid and DNA sequence optimization and synthesis, recombinant protein expression and analysis of two AG1 fragments, AG11-843 and AG11-1581 ...
June 2, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29866924/feeding-decisions-under-contamination-risk-in-bonobos
#18
Cecile Sarabian, Raphael Belais, Andrew J J MacIntosh
Threats from parasites and pathogens are ubiquitous, and many use pathways that exploit host trophic interactions for their transmission. As such, host organisms have evolved a behavioural immune system to facilitate contamination-risk assessment and avoidance of potential contaminants in various contexts, including feeding. Detecting pathogen threats can rely on different sensory modalities allowing animals to screen for a wide array of contaminants. Here, we present a series of experiments in which bonobos showed clear avoidance of contaminated food items, and were sensitive to risk along a contamination probability gradient...
July 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29862519/the-gut-microbiome-of-nonhuman-primates-lessons-in-ecology-and-evolution
#19
REVIEW
Jonathan B Clayton, Andres Gomez, Katherine Amato, Dan Knights, Dominic A Travis, Ran Blekhman, Rob Knight, Steven Leigh, Rebecca Stumpf, Tiffany Wolf, Kenneth E Glander, Francis Cabana, Timothy J Johnson
The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa...
June 4, 2018: American Journal of Primatology
https://www.readbyqxmd.com/read/29850465/evolution-of-substrate-specificity-in-the-nucleobase-ascorbate-transporter-nat-protein-family
#20
Anezia Kourkoulou, Alexandros A Pittis, George Diallinas
L-ascorbic acid (vitamin C) is an essential metabolite in animals and plants due to its role as an enzyme co-factor and antioxidant activity. In most eukaryotic organisms, L-ascorbate is biosynthesized enzymatically, but in several major groups, including the primate suborder Haplorhini, this ability is lost due to gene truncations in the gene coding for L-gulonolactone oxidase. Specific ascorbate transporters (SVCTs) have been characterized only in mammals and shown to be essential for life. These belong to an extensively studied transporter family, called Nucleobase-Ascorbate Transporters (NAT)...
March 22, 2018: Microbial Cell
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