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https://www.readbyqxmd.com/read/28442429/woodland-features-determining-home-range-size-of-roe-deer
#1
Sandro Lovari, Giulia Serrao, Emiliano Mori
Use of ecotones by ungulates may be mediated by their movements between main feeding areas and woodland, where they locate their shelter. The roe deer Capreolus capreolus has been termed as a woodland species, although we suggest that it did not evolve as a forest ungulate, but depending on forest glades. Roe deer feed on a wide range of vegetal species, although their diet is mainly dominated by woody plants. Our study was carried out in a fragmented area covered with small forest patches of Mediterranean "macchia" scrubwood, interspersed in an agricultural matrix...
April 22, 2017: Behavioural Processes
https://www.readbyqxmd.com/read/28425825/reviewing-treatments-and-outcomes-in-the-evolving-landscape-of-ulcerative-colitis
#2
Marla C Dubinsky
Ulcerative colitis (UC) is a chronic inflammatory disease extending proximally from the rectum to varying lengths of the colon that is characterized by alternating cycles of relapse and remission. Therapeutic goals for patients with active UC include induction and maintenance of remission and improvement in quality of life, as well as mucosal healing, a clinical outcome recently recognized in treatment guidance as being equally important. Mucosal healing is associated with favorable long-term patient outcomes related to remission, surgery, hospitalization, and quality of life...
April 20, 2017: Postgraduate Medicine
https://www.readbyqxmd.com/read/28423062/filamentous-fungal-carbon-catabolite-repression-supports-metabolic-plasticity-and-stress-responses-essential-for-disease-progression
#3
Sarah R Beattie, Kenneth M K Mark, Arsa Thammahong, Laure Nicolas Annick Ries, Sourabh Dhingra, Alayna K Caffrey-Carr, Chao Cheng, Candice C Black, Paul Bowyer, Michael J Bromley, Joshua J Obar, Gustavo H Goldman, Robert A Cramer
Aspergillus fumigatus is responsible for a disproportionate number of invasive mycosis cases relative to other common filamentous fungi. While many fungal factors critical for infection establishment are known, genes essential for disease persistence and progression are ill defined. We propose that fungal factors that promote navigation of the rapidly changing nutrient and structural landscape characteristic of disease progression represent untapped clinically relevant therapeutic targets. To this end, we find that A...
April 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28419782/natural-resource-landscapes-of-a-marine-bacterium-reveal-distinct-fitness-determining-genes-across-the-genome
#4
Alison F Takemura, Christopher H Corzett, Fatima Hussain, Philip Arevalo, Manoshi Datta, Xiaoqian Yu, Frederique Le Roux, Martin F Polz
Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls...
April 17, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#5
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28408285/from-epigenetic-landscape-to-phenotypic-fitness-landscape-evolutionary-effect-of-pathogens-on-host-traits
#6
Mark Jayson V Cortez, Jomar F Rabajante, Jerrold M Tubay, Ariel L Babierra
The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection...
April 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28404780/environmental-modification-via-a-quorum-sensing-molecule-influences-the-social-landscape-of-siderophore-production
#7
Roman Popat, Freya Harrison, Ana C da Silva, Scott A S Easton, Luke McNally, Paul Williams, Stephen P Diggle
Bacteria produce a wide variety of exoproducts that favourably modify their environment and increase their fitness. These are often termed 'public goods' because they are costly for individuals to produce and can be exploited by non-producers (cheats). The outcome of conflict over public goods is dependent upon the prevailing environment and the phenotype of the individuals in competition. Many bacterial species use quorum sensing (QS) signalling molecules to regulate the production of public goods. QS, therefore, determines the cooperative phenotype of individuals, and influences conflict over public goods...
April 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28391616/variation-in-the-post-mating-fitness-landscape-in-fruitflies
#8
Claudia Fricke, Tracey Chapman
Sperm competition is pervasive and fundamental to determining a male's overall fitness. Sperm traits and seminal fluid proteins (Sfps) are key factors. However, studies of sperm competition may often exclude females that fail to remate during a defined period. Hence, the resulting datasets contain fewer data from the potentially fittest males that have most success in preventing female remating. It is also important to consider a male's reproductive success before entering sperm competition, which is a major contributor to fitness...
April 9, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28390314/trade-off-between-soil-organic-carbon-sequestration-and-nitrous-oxide-emissions-from-winter-wheat-summer-maize-rotations-implications-of-a-25-year-fertilization-experiment-in-northwestern-china
#9
Jiangxin Gu, Mengxuan Yuan, Jixuan Liu, Yaoxu Hao, Yingtian Zhou, Dong Qu, Xueyun Yang
The primary aims of this study were to (i) quantify the variations in nitrous oxide (N2O) emissions and soil organic carbon (SOC) sequestration rates under winter wheat-summer maize cropping systems in Guanzhong Plain and (ii) evaluate the impact of organic amendments on greenhouse gas mitigation over a long-term period. We measured N2O fluxes during the maize season in 2015 under four fertilizer regimes in a long-term fertilization experiment. Soil was treated with only synthetic fertilizers in the maize season and with synthetic fertilizers, synthetic fertilizers plus crop residues and synthetic fertilizers plus low and high levels of dairy manure in the winter wheat season from 1990...
April 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28386598/defining-rna-small-molecule-affinity-landscapes-enables-design-of-a-small-molecule-inhibitor-of-an-oncogenic-noncoding-rna
#10
Sai Pradeep Velagapudi, Yiling Luo, Tuan Tran, Hafeez S Haniff, Yoshio Nakai, Mohammad Fallahi, Gustavo J Martinez, Jessica L Childs-Disney, Matthew D Disney
RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners...
March 22, 2017: ACS Central Science
https://www.readbyqxmd.com/read/28372381/electrical-transport-measurements-of-thin-film-samples-under-high-hydrostatic-pressure
#11
J Zabaleta, S C Parks, B Baum, A Teker, K Syassen, J Mannhart
We present a method to perform electrical measurements of epitaxial films and heterostructures a few nanometers thick under high hydrostatic pressures in a diamond anvil cell (DAC). Hydrostatic pressure offers the possibility to tune the rich landscape of properties shown by epitaxial heterostructures, systems in which the combination of different materials, performed with atomic precision, can give rise to properties not present in their individual constituents. Measuring electrical conductivity under hydrostatic pressure in these systems requires a robust method that can address all the challenges: the preparation of the sample with side length and thickness that fits in the DAC setup, a contacting method compatible with liquid media, a gasket insulation that resists high forces, as well as an accurate procedure to place the sample in the pressure chamber...
March 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28371130/recommendations-on-the-implementation-of-genetic-algorithms-for-the-directed-evolution-of-enzymes-for-industrial-purposes
#12
Mark Howard Barley, Nicholas Turner, Roy Goodacre
Within Directed Evolution the assessment of candidate enzymes and their modification is essential. In this study we investigate Genetic Algorithms (GAs) within this context and conduct a systematic study of the behavior of GAs on 20 Fitness Landscapes (FLs) of varying complexity, which allowed the tuning of the GA to be explored. From this study recommendations for the best GA settings to use for a GA-directed High Throughput Experimental program (where populations and the number of generations is necessarily low) are reported...
March 29, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28368421/selected-mitochondrial-dna-landscapes-activate-the-sirt3-axis-of-the-upr-mt-to-promote-metastasis
#13
T C Kenny, P Hart, M Ragazzi, M Sersinghe, J Chipuk, M A K Sagar, K W Eliceiri, T LaFramboise, S Grandhi, J Santos, A K Riar, L Papa, M D'Aurello, G Manfredi, M G Bonini, D Germain
By causing mitochondrial DNA (mtDNA) mutations and oxidation of mitochondrial proteins, reactive oxygen species (ROS) leads to perturbations in mitochondrial proteostasis. Several studies have linked mtDNA mutations to metastasis of cancer cells but the nature of the mtDNA species involved remains unclear. Our data suggests that no common mtDNA mutation identifies metastatic cells; rather the metastatic potential of several ROS-generating mutations is largely determined by their mtDNA genomic landscapes, which can act either as an enhancer or repressor of metastasis...
April 3, 2017: Oncogene
https://www.readbyqxmd.com/read/28367548/energy-landscapes-for-machine-learning
#14
Andrew J Ballard, Ritankar Das, Stefano Martiniani, Dhagash Mehta, Levent Sagun, Jacob D Stevenson, David J Wales
Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can be applied to these machine learning landscapes to gain new insight into the solution space involved in training and the nature of the corresponding predictions. In particular, we can define quantities analogous to molecular structure, thermodynamics, and kinetics, and relate these emergent properties to the structure of the underlying landscape...
April 3, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28367380/the-adaptive-value-of-habitat-preferences-from-a-multi-scale-spatial-perspective-insights-from-marsh-nesting-avian-species
#15
Jan Jedlikowski, Mattia Brambilla
BACKGROUND: Habitat selection and its adaptive outcomes are crucial features for animal life-history strategies. Nevertheless, congruence between habitat preferences and breeding success has been rarely demonstrated, which may result from the single-scale evaluation of animal choices. As habitat selection is a complex multi-scale process in many groups of animal species, investigating adaptiveness of habitat selection in a multi-scale framework is crucial. In this study, we explore whether habitat preferences acting at different spatial scales enhance the fitness of bird species, and check the appropriateness of single vs...
2017: PeerJ
https://www.readbyqxmd.com/read/28362551/the-double-life-of-the-ribosome-when-its-protein-folding-activity-supports-prion-propagation
#16
Cécile Voisset, Marc Blondel, Gary W Jones, Gaëlle Friocourt, Guillaume Stahl, Stéphane Chédin, Vincent Béringue, Reynald Gillet
It is no longer necessary to demonstrate that ribosome is the central machinery of protein synthesis. But it is less known that it is also key player of the protein folding process through another conserved function: the protein folding activity of the ribosome (PFAR). This ribozyme activity, discovered more than 2 decades ago, depends upon the domain V of the large rRNA within the large subunit of the ribosome. Surprisingly, we discovered that anti-prion compounds are also potent PFAR inhibitors, highlighting an unexpected link between PFAR and prion propagation...
March 4, 2017: Prion
https://www.readbyqxmd.com/read/28350864/codon-level-co-occurrences-of-germline-variants-and-somatic-mutations-in-cancer-are-rare-but-often-lead-to-incorrect-variant-annotation-and-underestimated-impact-prediction
#17
Amanda Koire, Young Won Kim, Jarey Wang, Panagiotis Katsonis, Haijing Jin, Olivier Lichtarge
Cancer cells explore a broad mutational landscape, bringing the possibility that tumor-specific somatic mutations could fall in the same codons as germline SNVs and leverage their presence to produce substitutions with a larger impact on protein function. While multiple, temporally consecutive mutations to the same codon have in the past been detected in the germline, this phenomenon has not yet been explored in the context of germline-somatic variant co-occurrences during cancer development. We examined germline context at somatic mutation sites for 1395 patients across four cancer cohorts (breast, skin, colon, and head and neck) and found 392 codon-level co-occurrences between germline and somatic variants, including over a dozen in well-known cancer genes...
2017: PloS One
https://www.readbyqxmd.com/read/28348931/basal-tolerance-to-heat-and-cold-exposure-of-the-spotted-wing-drosophila-drosophila-suzukii
#18
Thomas Enriquez, Hervé Colinet
The spotted wing Drosophila, Drosophila suzukii, is a new pest in Europe and America which causes severe damages, mostly to stone fruit crops. Temperature and humidity are among the most important abiotic factors governing insect development and fitness. In many situations, temperature can become stressful thus compromising survival. The ability to cope with thermal stress depends on basal level of thermal tolerance. Basic knowledge on temperature-dependent mortality of D. suzukii is essential to facilitate management of this pest...
2017: PeerJ
https://www.readbyqxmd.com/read/28347270/inclusion-of-the-fitness-sharing-technique-in-an-evolutionary-algorithm-to-analyze-the-fitness-landscape-of-the-genetic-code-adaptability
#19
José Santos, Ángel Monteagudo
BACKGROUND: The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution...
March 27, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28338672/posttransplant-maintenance-therapy-in-multiple-myeloma-the-changing-landscape
#20
REVIEW
S Sengsayadeth, F Malard, B N Savani, L Garderet, M Mohty
Transplant-eligible patients with multiple myeloma (MM) now have extended survival after diagnosis owing to effective modern treatment strategies that include new agents in induction therapy, autologous stem cell transplant (ASCT), consolidation therapy and posttransplant maintenance therapy. Standard of care for newly diagnosed, fit patients includes ASCT and, often nowadays, posttransplant maintenance. Several large studies have shown the efficacy of maintenance with thalidomide, lenalidomide and bortezomib in the treatment scheme of MM with regards to prolonging progression-free survival and, to a lesser degree, overall survival...
March 24, 2017: Blood Cancer Journal
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