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https://www.readbyqxmd.com/read/28645195/mutational-biases-influence-parallel-adaptation
#1
Arlin Stoltzfus, David M McCandlish
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be over-represented among documented adaptive substitutions. To test this hypothesis, we assembled 2 sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645188/temporal-variation-of-the-microbiome-is-dependent-on-body-region-in-a-wild-mammal-tamiasciurus-hudsonicus
#2
Colleen B Bobbie, Nadia C S Mykytczuk, Albrecht I Schulte-Hostedde
Microbial communities are increasingly being recognized as important to host health in wild mammals, but how these communities are characterized can have important consequences on the results of these studies. Previous research has explored temporal variation in microbial communities in humans and lab mammals, but few have investigated how microbiomes fluctuate in wild populations and none have examined the temporal dynamics of these fluctuations in different body regions on a wild mammal. Using Illumina MiSeq sequencing of the V3-V4 16S rRNA gene regions, we characterized the buccal and gut microbiomes of wild North American red squirrels, Tamiasciurus hudsonicus, to measure changes in these two microbiomes over short (< 2 weeks), medium (2-4 weeks) and long (> 1 month) term sampling periods...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28645169/heterodimerization-of-arabidopsis-calcium-proton-exchangers-contributes-to-regulation-of-guard-cell-dynamics-and-plant-defense-responses
#3
Bradleigh Hocking, Simon J Conn, Murli Manohar, Bo Xu, Asmini Athman, Matthew A Stancombe, Alex R Webb, Kendal D Hirschi, Matthew Gilliham
Arabidopsis thaliana cation exchangers (CAX1 and CAX3) are closely related tonoplast-localized calcium/proton (Ca2+/H+) antiporters that contribute to cellular Ca2+ homeostasis. CAX1 and CAX3 were previously shown to interact in yeast; however, the function of this complex in plants has remained elusive. Here, we demonstrate that expression of CAX1 and CAX3 occurs in guard cells. Additionally, CAX1 and CAX3 are co-expressed in mesophyll tissue in response to wounding or flg22 treatment, due to the induction of CAX3 expression...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28645155/features-of-genomic-organization-in-a-nucleotide-resolution-molecular-model-of-the-escherichia-coli-chromosome
#4
William C Hacker, Shuxiang Li, Adrian H Elcock
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases...
June 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645146/analysis-of-in-vitro-evolution-reveals-the-underlying-distribution-of-catalytic-activity-among-random-sequences
#5
Abe Pressman, Janina E Moretti, Gregory W Campbell, Ulrich F Müller, Irene A Chen
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645089/drug-resistance-mechanism-of-l10f-l10f-n88s-and-l90m-mutations-in-crf01_ae-hiv-1-protease-molecular-dynamics-simulations-and-binding-free-energy-calculations
#6
C S Vasavi, Ramasamy Tamizhselvi, Punnagai Munusami
HIV-1 protease plays a crucial role in viral replication and maturation, which makes it one of the most attractive targets for anti-retroviral therapy. The majority of HIV infections in developing countries are due to non-B subtype. Subtype AE is spreading rapidly and infecting huge population worldwide. The mutations in the active site of subtype AE directly impair the interactions with the inhibitor. The non-active site mutations influence the binding of the inhibitor indirectly and their resistance mechanism is not well understood...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28645069/controlled-single-bubble-cavitation-collapse-results-in-jet-induced-injury-in-brain-tissue
#7
Saranya Canchi, Karen Kelly, Yu Hong, Michael A King, Ghatu Subhash, Malisa Sarntinoranont
Multiscale damage due to cavitation is considered as a potential mechanism of traumatic brain injury (TBI) associated with explosion. In this study, we employed a TBI relevant hippocampal ex vivo slice model to induce bubble cavitation. Placement of single reproducible seed bubbles allowed control of size, number, and tissue location to visualize and measure deformation parameters. Maximum strain value was measured at 45 µs after bubble collapse, presented with a distinct contour and coincided temporally and spatially with the liquid jet...
June 15, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28645050/land-use-affects-total-dissolved-nitrogen-and-nitrate-concentrations-in-tropical-montane-streams-in-kenya
#8
Suzanne R Jacobs, Lutz Breuer, Klaus Butterbach-Bahl, David E Pelster, Mariana C Rufino
African tropical montane forests are facing fast and dynamic changes in land use. However, the impacts of these changes on stream water quality are understudied. This paper aims at assessing the effect of land use and physical catchment characteristics on stream water concentrations of dissolved organic carbon (DOC), total dissolved nitrogen (TDN), nitrate (NO3-N) and dissolved organic nitrogen (DON) in the Mau Forest, the largest tropical montane forest in Kenya. We conducted five synoptic stream water sampling campaigns at the outlets of 13-16 catchments dominated by either natural forest, smallholder agriculture or commercial tea and tree plantations...
June 20, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28645028/lipid-homeostasis-and-regulated-cell-death
#9
REVIEW
Eran Agmon, Brent R Stockwell
Modern lipidomics analysis paints a dynamic picture of membrane organizations, as changing and adapting lipid assemblies that play an active role in cellular function. This article highlights how the lipid composition of membranes determines specific organelle functions, how homeostatic mechanisms maintain these functions by regulating physical properties of membranes, and how cells disrupt lipid homeostasis to bring about regulated cell death (RCD). These are broad phenomena, and representative examples are reviewed here...
June 20, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28645004/amplified-detection-of-hepatitis-b-virus-using-an-electrochemical-dna-biosensor-on-a-nanoporous-gold-platform
#10
Laleh Enayati Ahangar, Masoud A Mehrgardi
In the present study, a nanoporous gold platform was applied for the amplified detection of Hepatitis B virus (HBV) by an electrochemical DNA biosensor. Ferrocene as a redox reporter was covalently attached to the DNA probe and its electrochemical signal was recorded as the biosensor response. For real samples, DNA was firstly extracted from blood of patients and then amplified by polymerase chain reaction (PCR) for 5cycles. Sensitivity of this biosensor was enhanced by using nanoporous gold electrode, therefore this sensor can discriminate the genome of HBV in real sample with low PCR cycles...
June 15, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28644986/designing-novel-inhibitors-against-histone-acetyltransferase-hat-%C3%A2-gcn5-of-plasmodium-falciparum
#11
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar
During active proliferation phase of intra-erythrocytic cycle, the genome of P. falciparum is regulated epigenetically and evolutionary conserved parasite-specific histone proteins are extensively acetylated. The reversible process of lysine acetylation, causing transcriptional activation and its deacetylation, causing transcriptional repression is regulated by balanced activities of HATs and HDACs. They are also known to regulate antigenic variations and gametocytic conversion in P. falciparum. These histone modifying enzymes have been identified as potential targets for development of anitmalarials in literature...
June 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28644980/making-power-visible-doing-theatre-based-status-work-with-nursing-students
#12
Steven S Taylor, Rosemary A Taylor
As part of a senior leadership class in an undergraduate baccalaureate nursing program in the northeastern United States, we conducted an experiential, theater-based workshop designed to increase student awareness of the micro-dynamics of power and the enactment of status in their day-to-day lives. These exercises allowed student participants to embody status and power and understand it in ways that they did not after simply completing assigned readings. At the conclusion of the workshop the participants were asked to reflect on their status habits and the consequences of these habits in a single hand-written page...
June 15, 2017: Nurse Education in Practice
https://www.readbyqxmd.com/read/28644970/overexpression-of-populus%C3%A3-canescens-isoprene-synthase-gene-in-camelina-sativa-leads-to-alterations-in-its-growth-and-metabolism
#13
Lorenzo Rossi, Monica Borghi, Jinfen Yang, De-Yu Xie
Isoprene (2-methyl-1,3-butadiene) is a hemiterpene molecule. It has been estimated that the plant kingdom emits 500-750 million tons of isoprene in the environment, half of which results from tropical broadleaf trees and the remainder from shrubs. Camelina (Camelina sativa (L.) Crantz) is an emerging bioenergy plant for biodiesel. In this study, we characterized isoprene formation following a diurnal/nocturnal cycle in wild-type Camelina plants. To understand the potential effects of isoprene emission on this herbaceous plant, a gray poplar Populus×canescens isoprene synthase gene (PcISPS) was overexpressed in Camelina...
June 13, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28644917/an-oxygen-isotope-chronometer-for-cellulose-deposition-the-successive-leaves-formed-by-tillers-of-a-c4-perennial-grass
#14
Hai Tao Liu, Fang Yang, Xiao Ying Gong, Rudi Schäufele, Hans Schnyder
Multiannual time series of (palaeo)hydrological information can be reconstructed from the oxygen isotope composition of cellulose (δ(18) OCel ) in biological archives, e.g. tree-rings, but our ability to temporally resolve information at subannual scale is limited. We capitalized on the short and predictable leaf appearance interval (2.4 d) of a perennial C4 grass (Cleistogenes squarrosa), to assess its potential for providing highly time-resolved δ(18) OCel records of vapor pressure deficit (VPD). Plants grown at low (0...
June 23, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28644912/biofilm-formation-and-disinfectant-resistance-of-salmonella-spp-in-mono-and-dual-species-with-pseudomonas-aeruginosa
#15
Xinyi Pang, Yishan Yang, Hyun-Gyun Yuk
AIMS: This study aimed to evaluate the biofilm formation and disinfectant resistance of Salmonella cells in mono- and dual-species biofilms with Pseudomonas aeruginosa, and to investigate the role of extracellular polymeric substances (EPS) in protection of biofilms against disinfection treatment. METHODS AND RESULTS: The populations of Salmonella in mono- or dual-species biofilms with P. aeruginosa on stainless steel (SS) coupons were determined before and after exposure to commercial disinfectant, 50 μg ml(-1) chlorine or 200 μg ml(-1) Ecolab(®) Whisper(™) V (a blend of four effective quaternary ammonium compounds)...
June 23, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28644911/interictal-oscillations-and-focal-epileptic-disorders
#16
Maxime Lévesque, Pariya Salami, Zahra Shiri, Massimo Avoli
Neuronal network oscillations represent a main feature of the brain activity recorded in the EEG under normal and pathological conditions such as epilepsy. Specific oscillations occur between seizures in patients and in animal models of focal epilepsy, and thus they are termed interictal. According to their shape and intrinsic signal frequency, interictal oscillations are classified as spikes and high frequency oscillations (HFOs). Interictal spikes are recorded in the "wideband" EEG signal and consist of large-amplitude events that usually last less than 1 s; HFOs, in contrast, are extracted by amplifying the appropriately filtered EEG signal, and are usually categorized as ripples (80-200 Hz) and fast ripples (250-500 Hz)...
June 23, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28644900/suppression-of-chikungunya-virus-replication-and-differential-innate-responses-of-human-peripheral-blood-mononuclear-cells-during-co-infection-with-dengue-virus
#17
Mariana Ruiz Silva, José A Aguilar Briseño, Vinit Upasani, Heidi van der Ende-Metselaar, Jolanda M Smit, Izabela A Rodenhuis-Zybert
Dengue and chikungunya are viral diseases transmitted to humans by infected Aedes spp. mosquitoes. With an estimated 390 million infected people per year dengue virus (DENV) currently causes the most prevalent arboviral disease. During the last decade chikungunya virus (CHIKV) has caused large outbreaks and has expanded its territory causing millions of cases in Asia, Africa and America. The viruses share a common mosquito vector and during the acute phase cause similar flu-like symptoms that can proceed to more severe or debilitating symptoms...
June 23, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28644888/fragmentation-of-the-mitochondrial-network-in-skin-in-vivo
#18
Daniel Mellem, Martin Sattler, Sonja Pagel-Wolff, Sören Jaspers, Horst Wenck, Michael Alexander Rübhausen, Frank Fischer
Mitochondria form dynamic networks which adapt to the environmental requirements of the cell. We investigated the aging process of these networks in human skin cells in vivo by multiphoton microscopy. A study on the age-dependency of the mitochondrial network in young and old volunteers revealed that keratinocytes in old skin establish a significantly more fragmented network with smaller and more compact mitochondrial clusters than keratinocytes in young skin. Furthermore, we investigated the mitochondrial network during differentiation processes of keratinocytes within the epidermis of volunteers...
2017: PloS One
https://www.readbyqxmd.com/read/28644860/time-dependent-genetic-analysis-links-field-and-controlled-environment-phenotypes-in-the-model-c4-grass-setaria
#19
Max J Feldman, Rachel E Paul, Darshi Banan, Jennifer F Barrett, Jose Sebastian, Muh-Ching Yee, Hui Jiang, Alexander E Lipka, Thomas P Brutnell, José R Dinneny, Andrew D B Leakey, Ivan Baxter
Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments...
June 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28644841/low-dimensional-spike-rate-models-derived-from-networks-of-adaptive-integrate-and-fire-neurons-comparison-and-implementation
#20
Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Planck equation. This approach, however, leads to a model with an infinite-dimensional state space and non-standard boundary conditions. Here we derive from that description four simple models for the spike rate dynamics in terms of low-dimensional ordinary differential equations using two different reduction techniques: one uses the spectral decomposition of the Fokker-Planck operator, the other is based on a cascade of two linear filters and a nonlinearity, which are determined from the Fokker-Planck equation and semi-analytically approximated...
June 23, 2017: PLoS Computational Biology
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