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https://www.readbyqxmd.com/read/27912915/modeling-sampling-strategies-for-determination-of-zooplankton-abundance-in-ballast-water
#1
Marco R Hernandez, Mattias L Johansson, Yanyu Xiao, Mark A Lewis, Hugh J MacIsaac
Ballast water has been a major source of non-indigenous species introductions. The International Maritime Organization has proposed performance standard that will establish an upper limit for viable organisms in discharged ballast. Here we test different sampling efforts for zooplankton in ballast water on a commercial vessel. We fit different probability density functions to find the most representative and evaluated sampling efforts necessary to achieve error rates (α, β) of <0.05. Our tests encompassed four seasonal trials and five sample volumes...
November 29, 2016: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/27912019/dynamic-n-occupancy-models-estimating-demographic-rates-and-local-abundance-from-detection-nondetection-data
#2
Sam Rossman, Charles B Yackulic, Sarah P Saunders, Janice Reid, Ray Davis, Elise F Zipkin
Occupancy modeling is a widely used analytical technique for assessing species distributions and range dynamics. However, occupancy analyses frequently ignore variation in abundance of occupied sites, even though site abundances affect many of the parameters being estimated (e.g., extinction, colonization, detection probability). We introduce a new model ("dynamic N-occupancy") capable of providing accurate estimates of local abundance, population gains (reproduction/immigration), and apparent survival probabilities while accounting for imperfect detection using only detection/nondetection data...
December 2016: Ecology
https://www.readbyqxmd.com/read/27909816/ecological-and-physical-barriers-shape-genetic-structure-of-the-alpine-porcini-boletus-reticuloceps
#3
Bang Feng, Jian Wei Liu, Jianping Xu, Kuan Zhao, Zai Wei Ge, Zhu L Yang
The Alpine porcini, Boletus reticuloceps, is an ectomycorrhizal mushroom distributed in subalpine areas of Southwest China, central China, and Taiwan Island. This distribution pattern makes it an ideal organism to infer how ectomycorrhizal fungi have reacted to historical tectonic and climatic changes, and to illustrate the mechanism for the disjunction of organisms between Southwest China and Taiwan. In this study, we explored the phylogeographic pattern of B. reticuloceps by microsatellite genotyping, DNA sequencing, ecological factor analysis, and species distribution modeling...
December 1, 2016: Mycorrhiza
https://www.readbyqxmd.com/read/27908425/copper-accumulation-in-rodent-brain-astrocytes-a-species-difference
#4
Brendan Sullivan, Gregory Robison, Yulia Pushkar, John K Young, Kebreten F Manaye
Changes in Cu homeostasis have been implicated in multiple neurodegenerative diseases. Factors controlling and regulating the distribution of Cu in the brain remain largely unknown. We have previously reported that a sub-set of astrocytes in the subventricular zone (SVZ) contain Cu-rich aggregates. Here we expand previous studies with detailed X-ray fluorescent imaging (XRF) analysis of the additional brain areas of hippocampus (HP) and rostral migratory stream (RMS). We also use conventional DAB (3,3'-diaminobenzidine) staining which accesses both peroxidase and pseudo-peroxidase activities...
January 2017: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/27907262/potential-breeding-distributions-of-u-s-birds-predicted-with-both-short-term-variability-and-long-term-average-climate-data
#5
Brooke L Bateman, Anna M Pidgeon, Volker C Radeloff, Curtis H Flather, Jeremy VanDerWal, H Resit Akçakaya, Wayne E Thogmartin, Thomas P Albright, Stephen J Vavrus, Patricia J Heglund
Climate conditions, such as temperature or precipitation, averaged over several decades strongly affect species distributions, as evidenced by experimental results and a plethora of models demonstrating statistical relations between species occurrences and long-term climate averages. However, long-term averages can conceal climate changes that have occurred in recent decades and may not capture actual species occurrence well because the distributions of species, especially at the edges of their range, are typically dynamic and may respond strongly to short-term climate variability...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907261/fitting-state-space-integral-projection-models-to-size-structured-time-series-data-to-estimate-unknown-parameters
#6
J Wilson White, Kerry J Nickols, Daniel Malone, Mark H Carr, Richard M Starr, Flora Cordoleani, Marissa L Baskett, Alan Hastings, Louis W Botsford
Integral projection models (IPMs) have a number of advantages over matrix-model approaches for analyzing size-structured population dynamics, because the latter require parameter estimates for each age or stage transition. However, IPMs still require appropriate data. Typically they are parameterized using individual-scale relationships between body size and demographic rates, but these are not always available. We present an alternative approach for estimating demographic parameters from time series of size-structured survey data using a Bayesian state-space IPM (SSIPM)...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907181/the-role-of-ocean-currents-in-the-temperature-selection-of-plankton-insights-from-an-individual-based-model
#7
Ferdi L Hellweger, Erik van Sebille, Benjamin C Calfee, Jeremy W Chandler, Erik R Zinser, Brandon K Swan, Neil D Fredrick
Biogeography studies that correlate the observed distribution of organisms to environmental variables are typically based on local conditions. However, in cases with substantial translocation, like planktonic organisms carried by ocean currents, selection may happen upstream and local environmental factors may not be representative of those that shaped the local population. Here we use an individual-based model of microbes in the global surface ocean to explore this effect for temperature. We simulate up to 25 million individual cells belonging to up to 50 species with different temperature optima...
2016: PloS One
https://www.readbyqxmd.com/read/27907017/the-farther-the-better-effects-of-multiple-environmental-variables-on-reef-fish-assemblages-along-a-distance-gradient-from-river-influences
#8
Leonardo M Neves, Tatiana P Teixeira-Neves, Guilherme H Pereira-Filho, Francisco G Araújo
The conservation and management of site-attached assemblages of coastal reefs are particularly challenging because of the tremendous environmental variation that exists at small spatial scales. In this sense, understanding the primary sources of variation in spatial patterns of the biota is fundamental for designing effective conservation policies. We investigated spatial variation in fish assemblages around the windward and leeward sides of coastal islands situated across a gradient of riverine influence (13 km in length)...
2016: PloS One
https://www.readbyqxmd.com/read/27906971/nullomers-and-high-order-nullomers-in-genomic-sequences
#9
Davide Vergni, Daniele Santoni
A nullomer is an oligomer that does not occur as a subsequence in a given DNA sequence, i.e. it is an absent word of that sequence. The importance of nullomers in several applications, from drug discovery to forensic practice, is now debated in the literature. Here, we investigated the nature of nullomers, whether their absence in genomes has just a statistical explanation or it is a peculiar feature of genomic sequences. We introduced an extension of the notion of nullomer, namely high order nullomers, which are nullomers whose mutated sequences are still nullomers...
2016: PloS One
https://www.readbyqxmd.com/read/27903876/handicap-principle-implies-emergence-of-dimorphic-ornaments
#10
Sara M Clifton, Rosemary I Braun, Daniel M Abrams
Species spanning the animal kingdom have evolved extravagant and costly ornaments to attract mating partners. Zahavi's handicap principle offers an elegant explanation for this: ornaments signal individual quality, and must be costly to ensure honest signalling, making mate selection more efficient. Here, we incorporate the assumptions of the handicap principle into a mathematical model and show that they are sufficient to explain the heretofore puzzling observation of bimodally distributed ornament sizes in a variety of species...
November 30, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27903870/sea-level-driven-glacial-age-refugia-and-post-glacial-mixing-on-subtropical-coasts-a-palaeohabitat-and-genetic-study
#11
Greer A Dolby, Ryan Hechinger, Ryan A Ellingson, Lloyd T Findley, Julio Lorda, David K Jacobs
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1000 km...
November 30, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27903064/modelling-of-the-distribution-of-biomphalaria-glabrata-and-biomphalaria-straminea-in-the-metropolitan-region-of-recife-pernambuco-brazil
#12
Verônica Santos Barbosa, Ricardo José de Paula Souza E Guimarães, Rodrigo Moraes Loyo, Constança Simões Barbosa
The occurrence of schistosomiasis is directly linked to the presence of its snail intermediate host Biomphalaria spp. Knowledge of geographical distribution, habitats and behaviour of these snails in relation to the climate is essential for guiding measures for disease prevention and control. This study aims to model the distribution of B. glabrata and B. straminea in schistosomiasis non-endemic areas of the metropolitan region of Recife (MRR) based on environmental data and estimates of snail distributions in endemic and neighbouring areas...
November 25, 2016: Geospatial Health
https://www.readbyqxmd.com/read/27902732/predictors-of-current-and-longer-term-patterns-of-abundance-of-american-pikas-ochotona-princeps-across-a-leading-edge-protected-area
#13
Lucas Moyer-Horner, Erik A Beever, Douglas H Johnson, Mark Biel, Jami Belt
American pikas (Ochotona princeps) have been heralded as indicators of montane-mammal response to contemporary climate change. Pikas no longer occupy the driest and lowest-elevation sites in numerous parts of their geographic range. Conversely, pikas have exhibited higher rates of occupancy and persistence in Rocky Mountain and Sierra Nevada montane 'mainlands'. Research and monitoring efforts on pikas across the western USA have collectively shown the nuance and complexity with which climate will often act on species in diverse topographic and climatic contexts...
2016: PloS One
https://www.readbyqxmd.com/read/27902336/characterization-of-the-banana-streak-virus-capsid-protein-and-mapping-of-the-immunodominant-continuous-b-cell-epitopes-to-the-surface-exposed-n-terminus
#14
Jenny Vo, Paul Campbell, Nur N Mahfuzc, Ras Ramli, Daniel Pagendam, Ross Barnard, Andrew Geering
This study identified the structural proteins of two badnavirus species, Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV), and mapped the distribution of continuous B-cell epitopes. Two different CP isoforms of about 44 and 40 kDa (CP1 and CP2) and the virion-associated protein (VAP) were consistently associated with purified virions. For both viral species, the N-terminus of CP2 was successfully sequenced by Edman degradation but that of CP1 was chemically blocked. De novo peptide sequencing of tryptic digests suggested that CP1 and CP2 derive from the same region of the P3 polyprotein but differ in the length of either the N- or C-terminus...
October 24, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901304/predicting-occurrence-of-juvenile-shark-habitat-to-improve-conservation-planning
#15
Beverly Z L Oh, Ana M M Sequeira, Mark G Meekan, Jonathan L W Ruppert, Jessica J Meeuwig
Fishing and habitat degradation have increased the extinction risk of sharks, and conservation strategies recognize that survival of juveniles is critical for the effective management of shark populations. Despite the rapid expansion of marine protected areas (MPAs) globally, the paucity of shark-monitoring data on large scales (100s-1000s km) means that the effectiveness of MPAs in halting shark declines remains unclear. Using data collected by baited remote underwater video systems (BRUVS) in northwestern Australia, we developed generalized linear models to elucidate the ecological drivers of the occurrence of juvenile shark habitat...
November 30, 2016: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/27899586/r-loopdb-a-database-for-r-loop-forming-sequences-rlfs-and-r-loops
#16
Piroon Jenjaroenpun, Thidathip Wongsurawat, Sawannee Sutheeworapong, Vladimir A Kuznetsov
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897236/recognition-of-mould-colony-on-unhulled-paddy-based-on-computer-vision-using-conventional-machine-learning-and-deep-learning-techniques
#17
Ke Sun, Zhengjie Wang, Kang Tu, Shaojin Wang, Leiqing Pan
To investigate the potential of conventional and deep learning techniques to recognize the species and distribution of mould in unhulled paddy, samples were inoculated and cultivated with five species of mould, and sample images were captured. The mould recognition methods were built using support vector machine (SVM), back-propagation neural network (BPNN), convolutional neural network (CNN), and deep belief network (DBN) models. An accuracy rate of 100% was achieved by using the DBN model to identify the mould species in the sample images based on selected colour-histogram parameters, followed by the SVM and BPNN models...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896732/species-tree-estimation-from-genome-wide-data-with-guenomu
#18
Leonardo de Oliveira Martins, David Posada
The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been developed to take this incongruence into account; these can be divided grossly into supertree and supermatrix approaches. Here we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program guenomu...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896583/use-of-ultra-high-spatial-resolution-aerial-imagery-in-the-estimation-of-chaparral-wildfire-fuel-loads
#19
Ian T Schmidt, John F O'Leary, Douglas A Stow, Kellie A Uyeda, Phillip J Riggan
Development of methods that more accurately estimate spatial distributions of fuel loads in shrublands allows for improved understanding of ecological processes such as wildfire behavior and postburn recovery. The goal of this study is to develop and test remote sensing methods to upscale field estimates of shrubland fuel to broader-scale biomass estimates using ultra-high spatial resolution imagery captured by a light-sport aircraft. The study is conducted on chaparral shrublands located in eastern San Diego County, CA, USA...
December 2016: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/27896558/h3k9ac-involved-in-the-decondensation-of-spermatozoal-nuclei-during-spermatogenesis-in-chinese-mitten-crab-eriocheir-sinensis
#20
Genliang Li, Xianjiang Kang, Shumei Mu, Mingshen Guo, Shiwen Huang, Qinna Chen, Song Nong, Xiaomin Huang, Hongliu Hu, Ke Sun
As a well-known crustacean model species, the Chinese mitten crab Eriocheir sinensis presents spermatozoa with decondensed DNA. Our aim was to analyze structural distribution of the histone H3 and its acetylated lysine 9 (H3K9ac) during spermatogenesis for the mechanistic understanding of the nuclear decondensation of the spermatozoa in E. sinensis. Using specific antibodies, we followed the structural distribution and acetylated lysine 9 of the histone H3 during spermatogenesis, especially spermiogenesis, of E...
November 28, 2016: Cytotechnology
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