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https://www.readbyqxmd.com/read/29788292/biological-processes-modulating-longevity-across-primates-a-phylogenetic-genome-phenome-analysis
#1
Gerard Muntané, Xavier Farré, Juan Antonio Rodríguez, Cinta Pegueroles, David A Hughes, João Pedro de Magalhães, Toni Gabaldón, Arcadi Navarro
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29785015/frequent-transmission-of-the-mycobacterium-tuberculosis-beijing-lineage-and-positive-selection-for-the-esxw-beijing-variant-in-vietnam
#2
Kathryn E Holt, Paul McAdam, Phan Vuong Khac Thai, Nguyen Thuy Thuong Thuong, Dang Thi Minh Ha, Nguyen Ngoc Lan, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, Hoang Thanh Hai, Vu Thi Ngoc Ha, Guy Thwaites, David J Edwards, Artika P Nath, Kym Pham, David B Ascher, Jeremy Farrar, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Maxine Caws, Sarah J Dunstan
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29782991/beneficial-and-paradoxical-roles-of-selenium-at-nutritional-levels-of-intake-in-healthspan-and-longevity
#3
REVIEW
Li Zhang, Huawei Zeng, Wen-Hsing Cheng
Accumulation of genome and macromolecule damage is a hallmark of aging, age-associated degeneration, and genome instability syndromes. Although processes of aging are irreversible, they can be modulated by genome maintenance pathways and environmental factors such as diet. Selenium (Se) confers its physiological functions mainly through selenoproteins, but Se compounds and other proteins that incorporate Se nonspecifically also impact optimal health. Bruce Ames proposed that the aging process could be mitigated by a subset of low-hierarchy selenoproteins whose levels are preferentially reduced in response to Se deficiency...
May 18, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29781921/exercise-periodization-over-the-year-improves-metabolic-syndrome-and-medication-use
#4
Felix Morales-Palomo, Miguel Ramirez-Jimenez, Juan Fernando Ortega, Ricardo Mora-Rodriguez
PURPOSE: We aimed to determine if yearly repeated exercise training reduces metabolic syndrome (MetS) and the use of medicines to control MetS components. METHODS: Fifty five MetS individuals were randomized into a TRAIN group that underwent two yearly programs of 16-week of high intensity interval training (HIIT) or a non-exercising CONT group. We measured the evolution of all five MetS components, cardiorespiratory fitness (CRF; assessed by VO2PEAK) and medicine use, at baseline (0 months), mid (12 months) and end-point (24 months)...
May 2, 2018: Medicine and Science in Sports and Exercise
https://www.readbyqxmd.com/read/29778722/phylogenomics-resolves-evolutionary-relationships-and-provides-insights-into-floral-evolution-in-the-tribe-shoreeae-dipterocarpaceae
#5
Jacqueline Heckenhauer, Rosabelle Samuel, Peter S Ashton, Kamariah Abu Salim, Ovidiu Paun
A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae...
May 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#6
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29772723/evolution-of-grain-interfaces-in-annealed-duplex-stainless-steel-after-parallel-cross-rolling-and-direct-rolling
#7
Ming Wang, Haoqing Li, Yujing Tian, Hong Guo, Xiaoying Fang, Yuebin Guo
Changes in various grain interfaces, including the grain boundary and phase boundary, are a strong indication of microstructural changes, particularly ultra-fined grains achieved by large strain deformation and subsequent annealing. After direct rolling and cross rolling with the same strain of ε = 2, the distributions of the interfaces in annealed UNS S32304 duplex stainless steel were investigated using electron backscatter diffraction (EBSD) in this study. The ferrite experienced continued recovery, and a high density of low-angle grain boundaries (LAGBs) was produced...
May 16, 2018: Materials
https://www.readbyqxmd.com/read/29769608/rapid-parallel-evolution-overcomes-global-honey-bee-parasite
#8
Melissa Oddie, Ralph Büchler, Bjørn Dahle, Marin Kovacic, Yves Le Conte, Barbara Locke, Joachim R de Miranda, Fanny Mondet, Peter Neumann
In eusocial insect colonies nestmates cooperate to combat parasites, a trait called social immunity. However, social immunity failed for Western honey bees (Apis mellifera) when the ectoparasitic mite Varroa destructor switched hosts from Eastern honey bees (Apis cerana). This mite has since become the most severe threat to A. mellifera world-wide. Despite this, some isolated A. mellifera populations are known to survive infestations by means of natural selection, largely by supressing mite reproduction, but the underlying mechanisms of this are poorly understood...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29764984/parallel-evolution-of-common-allelic-variants-confers-flowering-diversity-in-capsella-rubella
#9
Li Yang, Hui-Na Wang, Xing-Hui Hou, Yu-Pan Zou, Ting-Shen Han, Xiao-Min Niu, Jie Zhang, Zhong Zhao, Marco Todesco, Sureshkumar Balasubramanian, Ya-Long Guo
Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5' UTR region of C...
May 15, 2018: Plant Cell
https://www.readbyqxmd.com/read/29764659/mechanisms-of-aphid-adaptation-to-host-plant-resistance
#10
REVIEW
Ashley D Yates, Andy Michel
Host-plant resistant (HPR) crops can play a major role in preventing insect damage, but their durability is limited due to insect adaptation. Research in basal plant resistance provides a framework to investigate adaptation against HPR. Resistance and adaptation are predicted to follow the gene-for-gene and zigzag models of plant defense. These models also highlight the importance of insect effectors, which are small molecules that modulate host plant defense signaling. We highlight research in insect adaptation to plant resistance, and then draw parallels to virulence adaptation...
April 2018: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/29763665/selection-and-paucity-of-phylogenetic-signal-challenge-the-utility-of-alpha-tubulin-in-reconstruction-of-evolutionary-history-of-free-living-litostomateans-protista-ciliophora
#11
Ľubomír Rajter, Peter Vďačný
The class Litostomatea represents a highly diverse but monophyletic group, uniting both free-living and endosymbiotic ciliates. Ribosomal RNA genes and ITS-region sequences helped to recognize and define the main litostomatean lineages, but did not provide enough phylogenetic signal to unambiguously resolve their interrelationships. In this study, we attempted to improve the resolution among main free-living predatory lineages by adding the gene coding for alpha-tubulin. However, our phylogenetic analyses challenged the performance of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans...
May 12, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29762135/surface-morphology-of-molybdenum-silicide-films-upon-low-energy-ion-beam-sputtering
#12
Raul Gago, Miriam Jaafar, Francisco Javier Palomares Simon
The surface morphology of molybdenum silicide (Mo<sub>x</sub>Si<sub>1-x </sub>) films has been studied after low-energy Ar<sup>+</sup> ion-beam sputtering (IBS) to explore eventual pattern formation on compound targets and, simultaneously, gather information about the mechanisms behind silicide-assisted nanopatterning of silicon surfaces by IBS. For this purpose, Mo<sub>x</sub>Si<sub>1-x </sub> films with compositions below, equal and above the MoSi<sub>2</sub> stoichiometry (x = 0...
May 15, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29761150/endoscopic-retrograde-cholangiopancreatography-and-endoscopic-ultrasound-to-be-one-traveler-in-converging-roads
#13
REVIEW
Pedro Moutinho-Ribeiro, Armando Peixoto, Guilherme Macedo
Background: Endoscopic retrograde cholangiopancreatography (ERCP) and endoscopic ultrasound (EUS) were initially introduced into the world of gastroenterology as purely diagnostic procedures. With progressive evolution of intervention, both these techniques conquered fields in the treatment of many conditions that had once been exclusively surgical domains. Nowadays, more and more clinical situations have an indication to perform both EUS and ERCP, and these two techniques are frequently required at the same time for the same patient...
April 2018: GE Portuguese Journal of Gastroenterology
https://www.readbyqxmd.com/read/29760453/evolutionary-instability-of-cug-leu-in-the-genetic-code-of-budding-yeasts
#14
Tadeusz Krassowski, Aisling Y Coughlan, Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Dana A Opulente, Robert Riley, Igor V Grigoriev, Nikunj Maheshwari, Denis C Shields, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas, Kenneth H Wolfe
The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts. All three changes were reassignments of the codon CUG, which is translated as serine (in 2 yeast clades), alanine (1 clade), or the 'universal' leucine (2 clades). The newly discovered Ser2 clade is in the final stages of a genetic code transition. Most species in this clade have genes for both a novel tRNASer (CAG) and an ancestral tRNALeu (CAG) to read CUG, but only tRNASer (CAG) is used in standard growth conditions...
May 14, 2018: Nature Communications
https://www.readbyqxmd.com/read/29757159/sawtooth-structure-formation-under-nonlinear-regime-ion-bombardment
#15
Joy Clare Perkinson, Jennifer M Swenson, Alexander DeMasi, Christa Wagenbach, Karl F Ludwig, Scott A Norris, Michael J Aziz
Linear-regime Ar<sup>+</sup> bombardment of Si produces symmetrical ripple structures at ion incidence angles above 45<sup>○</sup> measured off-normal [1]. In the nonlinear regime, new behaviors emerge. In this paper, we present experimental results of ion bombardment that continues into the nonlinear regime until pattern saturation at multiple ion incidence angles, showing the evolution of their grazing incidence small-angle x-ray scattering (GISAXS) spectra as well as atomic force microscopy (AFM) topographs of the final, saturated structures...
May 14, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29755365/the-relation-between-capillary-transit-times-and-hemoglobin-saturation-heterogeneity-part-1-theoretical-models
#16
Adrien Lücker, Timothy W Secomb, Bruno Weber, Patrick Jenny
Capillary dysfunction impairs oxygen supply to parenchymal cells and often occurs in Alzheimer's disease, diabetes and aging. Disturbed capillary flow patterns have been shown to limit the efficacy of oxygen extraction and can be quantified using capillary transit time heterogeneity (CTH). However, the transit time of red blood cells (RBCs) through the microvasculature is not a direct measure of their capacity for oxygen delivery. Here we examine the relation between CTH and capillary outflow saturation heterogeneity (COSH), which is the heterogeneity of blood oxygen content at the venous end of capillaries...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29751068/multidimensional-brain-activity-dictated-by-winner-take-all-mechanisms
#17
Arturo Tozzi, James F Peters
A novel demon-based architecture is introduced to elucidate brain functions such as pattern recognition during human perception and mental interpretation of visual scenes. Starting from the topological concepts of invariance and persistence, we introduce a Selfridge pandemonium variant of brain activity that takes into account a novel feature, namely, demons that recognize short straight-line segments, curved lines and scene shapes, such as shape interior, density and texture. Low-level representations of objects can be mapped to higher-level views (our mental interpretations): a series of transformations can be gradually applied to a pattern in a visual scene, without affecting its invariant properties...
May 8, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29749630/divergent-trait-and-environment-relationships-among-parallel-radiations-in-pelargonium-geraniaceae-a-role-for-evolutionary-legacy
#18
Timothy E Moore, Carl D Schlichting, Matthew E Aiello-Lammens, Kerri Mocko, Cynthia S Jones
Functional traits in closely related lineages are expected to vary similarly along common environmental gradients as a result of shared evolutionary and biogeographic history, or legacy effects, and as a result of biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and rainfall gradients across the Greater Cape Floristic Region of South Africa...
May 11, 2018: New Phytologist
https://www.readbyqxmd.com/read/29748198/dynamic-changes-in-yeast-phosphatase-families-allow-for-specialization-in-phosphate-and-thiamine-starvation
#19
John V Nahas, Christine L Iosue, Noor F Shaik, Kathleen Selhorst, Bin Z He, Dennis D Wykoff
Convergent evolution is often due to selective pressures generating a similar phenotype. We observe relatively recent duplications in a spectrum of Saccharomycetaceae yeast species resulting in multiple phosphatases that are regulated by different nutrient conditions - thiamine and phosphate starvation. This specialization is both transcriptional and at the level of phosphatase substrate specificity. In Candida glabrata , loss of the ancestral phosphatase family was compensated by the co-option of a different histidine phosphatase family with three paralogs...
May 10, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29746459/parallel-altitudinal-clines-reveal-trends-in-adaptive-evolution-of-genome-size-in-zea-mays
#20
Paul Bilinski, Patrice S Albert, Jeremy J Berg, James A Birchler, Mark N Grote, Anne Lorant, Juvenal Quezada, Kelly Swarts, Jinliang Yang, Jeffrey Ross-Ibarra
While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance...
May 2018: PLoS Genetics
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