Correction
23 Dec 2015: The PLOS ONE Staff (2015) Correction: Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders. PLOS ONE 10(12): e0145899. https://doi.org/10.1371/journal.pone.0145899
The dynamics of the Min-protein system help Escherichia coli regulate the process of cell division by identifying the center of the cell. While this system exhibits robust bipolar oscillations in wild-type cell shapes, recent experiments have shown that when the cells are mechanically deformed into wide, flattened out, irregular shapes,...
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data...
We present a study of the metabolism of the Mycobacterium tuberculosis after exposure to antibiotics using proteomics data and flux balance analysis (FBA). The use of FBA to study prokaryotic organisms is well-established and allows insights into the metabolic pathways chosen by the organisms under different environmental conditions. To apply...
While most biological materials are insulating in nature, efficient extracellular electron transfer is a critical property of biofilms associated with microbial electrochemical systems and several microorganisms are capable of establishing conductive aggregates and biofilms. Though construction of these conductive microbial networks is an intriguing and important phenomenon in both natural...
The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
Background:
Nonalcoholic fatty liver disease (NAFLD) is a major public health burden in western societies. The progressive form of NAFLD, nonalcoholic steatohepatitis (NASH), is characterized by hepatosteatosis, inflammation, oxidative stress, and hepatic damage that can progress to fibrosis and cirrhosis; risk factors for hepatocellular carcinoma. Given the scope of NASH,...
Understanding seasonal migration and localized persistence of populations is critical for effective species harvest and conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, and distribution during annual assessments of proposed fisheries impacts. Most models, however, fail to account for the influence of biophysical factors on year-to-year...
With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an...
A small number of cetaceans have adapted to an entirely freshwater environment, having colonized rivers in Asia and South America from an ancestral origin in the marine environment. This includes the 'river dolphins', early divergence from the odontocete lineage, and two species of true dolphins (Family Delphinidae). Successful adaptation to...
Cattle grazing and invasion by non-native plant species are globally-ubiquitous changes occurring to plant communities that are likely to reverberate through whole food webs. We used a manipulative field experiment to quantify how arthropod community structure differed in native and non-native California grassland communities in the presence and absence of...
Natural habitats have the ability to protect coastal communities against the impacts of waves and storms, yet it is unclear how different habitats complement each other to reduce those impacts. Here, we investigate the individual and combined coastal protection services supplied by live corals on reefs, seagrass meadows, and mangrove...
Wildfire greatly impacts the composition and quantity of organic carbon stocks within watersheds. Most methods used to measure the contributions of fire altered organic carbon–i.e. pyrogenic organic carbon (Py-OC) in natural samples are designed to quantify specific fractions such as black carbon or polyaromatic hydrocarbons. In contrast, the CuO oxidation...
While there is a persistent inverse relationship between latitude and species diversity across many taxa and ecosystems, deviations from this norm offer an opportunity to understand the conditions that contribute to large-scale diversity patterns. Marine systems, in particular, provide such an opportunity, as marine diversity does not always follow a...
Black men who have sex with men (BMSM) experience among the highest rates of HIV infection in the United States. We conducted a community-based ethnography in New York City to identify the structural and environmental factors that influence BMSMs vulnerability to HIV and their engagement with HIV prevention services. Methods...
Land use and climate change occur simultaneously around the globe. Fully understanding their separate and combined effects requires a mechanistic understanding at the local scale where their effects are ultimately realized. Here we applied an individual-based model of fish population dynamics to evaluate the role of local stream variability in...
Using genetic approaches, particle image velocimetry and an inert tracer of cytoplasmic streaming, we have made a mechanistic connection between the motor proteins (myosins XI), cargo transported by these motors (distinct endomembrane compartment defined by membrane-anchored MyoB receptors) and the process of cytoplasmic streaming in plant cells. It is shown...
A promising new drug target for the development of novel broad-spectrum antibiotics is the highly conserved small GTPase Obg (YhbZ, CgtA), a protein essential for the survival of all bacteria including Neisseria gonorrhoeae (GC). GC is the agent of gonorrhea, a prevalent sexually transmitted disease resulting in serious consequences on...
Juvenile survival and recruitment can be more sensitive to environmental, ecological and anthropogenic factors than adult survival, influencing population-level processes like recruitment and growth rate in long-lived, iteroparous species such as southern right whales. Conventionally, Southern right whales are individually identified using callosity patterns, which do not stabilise until 6–12...
Volunteers are increasingly being recruited into citizen science projects to collect observations for scientific studies. An additional goal of these projects is to engage and educate these volunteers. Thus, there are few barriers to participation resulting in volunteer observers with varying ability to complete the project’s tasks. To improve the...
Pursuit of the triple bottom line of economic, community and ecological sustainability has increased the complexity of fishery management; fisheries assessments require new types of data and analysis to guide science-based policy in addition to traditional biological information and modeling. We introduce the Fishery Performance Indicators (FPIs), a broadly applicable...
Motivation:
Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of...
We report the sequence and characterization of the genomes of 21 isolates of Rhodococcus. Next generation sequencing technology was used to generate genome sequences. The reads for each genome were de novo assembled. The contigs were re-ordered, using the genome sequence of A44a as a reference. The program, Prokka, was...
We report the sequence and characterization of the genomes of 21 isolates of Rhodococcus. Next generation sequencing technology was used to generate genome sequences. The reads for each genome were de novo assembled. The contigs were re-ordered, using the genome sequence of A44a as a reference. The program, Prokka, was...
We report the sequence and characterization of the genomes of 21 isolates of Rhodococcus. Next generation sequencing technology was used to generate genome sequences. The reads for each genome were de novo assembled. The contigs were re-ordered, using the genome sequence of A44a as a reference. The program, Prokka, was...
In this dataset we present the environmental effect of solar panels. We had two weather stations, one in a control area and one in an area with solar panels. The weather stations collected wind speed, temperature, solar radiation and relative humidity. We also measured soil moisture in different shaded zones...
Individuals within populations often differ substantially in habitat use, the ecological consequences of which can be far reaching. Stable isotope analysis provides a convenient and often cost effective means of indirectly assessing the habitat use of individuals that can yield valuable insights into the spatiotemporal distribution of foraging specialisations within...
Full Text:
role in inshore and off-
shore habitat use.
PLOS ONE | DOI:10.1371/journal.pone.0157394 June 15, 2016
29 Dec 2015: Rosales SM, Vega Thurber R (2015) Correction: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLOS ONE 10(12): e0146208. https://doi.org/10.1371/journal.pone.0146208
Correction
25 Aug 2014: The PLOS ONE Staff (2014) Correction: Histopathologic Alterations Associated with Global Gene Expression Due to Chronic Dietary TCDD Exposure in Juvenile Zebrafish. PLOS ONE 9(8): e106605. https://doi.org/10.1371/journal.pone.0106605
OBJECTIVE: The 75% of older adults with multiple chronic conditions are at risk of therapeutic competition (i.e. treatment for
one condition may adversely affect a coexisting condition). The objective was to determine the prevalence of potential
therapeutic competition in community-living older adults.
METHODS: Cross-sectional descriptive study of a representative sample...
Correction:
21 Jan 2015: The PLOS ONE Staff (2015) Correction: Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages. PLOS ONE 10(1): e0117735. https://doi.org/10.1371/journal.pone.0117735
Correction: 7 Mar 2016: The PLOS ONE Staff (2016) Correction: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLOS ONE 11(3): e0151124. https://doi.org/10.1371/journal.pone.0151124
The data is a JSON format file containing the position, velocity, and fish identifier data for 300 golden shiners in a shallow (depth of 4.5 to 5 cm) rectangular water tank (2.1 by 1.2 meters). There are 5000 individual frames (samples of position and velocity) corresponding to video taken at...
Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology...
Full Text:
. doi:10.1371/journal.pone.0142903 PMID: 26619010
PLOS ONE | DOI:10.1371/journal.pone.0145899 December
Carbonate communities:The activity of anaerobic methane oxidizing microbes facilitates
precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate
the significant role of carbonate rocks in promoting diversity by providing unique habitat
and food resources for macrofaunal assemblages at seeps on the Costa Rica margin
(400–1850 m)....
Full Text:
/journal.pone.0136129.g001
PLOSONE | DOI:10.1371/journal.pone.0136129 August 14, 2015 2 / 5
Fig 11 is
Corrections
18 Mar 2010: Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M (2010) Correction: Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States. PLOS Biology 8(3): 10.1371/annotation/35686514-b7a9-4f65-9663-7baefc0d63c0.
15 Mar 2010: Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M (2010) Correction: Absolute Humidity...
Marine diseases are becoming more frequent, and tools for identifying pathogens and disease
reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics
provides insights into disease etiology by cataloguing and comparing sequences from suspected
pathogens. This method is a powerful approach to simultaneously evaluate both the
viral and bacterial...
Full Text:
the corrected
Table 1 here.
PLOSONE | DOI:10.1371/journal.pone.0146208 December 29, 2015 1 / 2
OPEN
Salmonid fish raised in hatcheries often have lower fitness (number of returning adult offspring) than wild fish when both spawn in the wild. Body size at release from hatcheries is positively correlated with survival at sea. So one explanation for reduced fitness is that hatcheries inadvertently select for trait values...
Plasma biochemistry and hematology reference intervals are integral health assessment tools in all medical fields, including aquatic animal health. As sablefish (Anoplopoma fimbria) are becoming aquaculturally and economically more important, this manuscript provides essential reference intervals (RI) for their plasma biochemistry and hematology along with reference photomicrographs of blood cells...
Plasmid transformation of chlamydiae has created new opportunities to investigate host–microbe interactions during chlamydial infections; however, there are still limitations. Plasmid transformation requires a replicon derived from the native Chlamydia plasmid, and these transformations are species-specific. We explored the utility of a broad host-range plasmid, pBBR1MCS-4, to transform chlamydiae, with...
The intensity and scale of wildfires has increased throughout the Pacific Northwest in recent decades, especially within the last decade, destroying vast amounts of valuable resources and assets. This trend is predicted to remain or even magnify due climate change, growing population, increased housing density. Furthermore, the associated stress of...
Mechanisms promoting coexistence between closely related species are fundamental for maintaining species diversity. Mechanisms of niche differentiation include allochrony which offsets the peak timing of resource utilisation between species. Many studies focus on spatial and temporal niche partitioning during the breeding season, few have investigated the role allochrony plays in...
Sea star wasting disease (SSWD) first appeared in Oregon in April 2014, and by June had spread to most of the coast. Although delayed compared to areas to the north and south, SSWD was initially most intense in north and central Oregon and spread southward. Up to 90% of individuals...
Full Text:
text below.
PLOSONE | DOI:10.1371/journal.pone.0157302 June 3, 2016 1 / 2
a11111
OPEN ACCESS
An important issue in the cellular industry is the rising energy cost and carbon footprint due to the rapid expansion of the cellular infrastructure. Greening cellular networks has thus attracted attention. Among the promising green cellular network techniques, the renewable energy-powered cellular network has drawn increasing attention as a critical...
Trust is a key variable for successful natural resource management and is commonly the focus of conceptual and methodological development. Distrust, on the other hand, is frequently cited as an obstacle to management, but appears to be rarely defined, conceptually underdeveloped, and inconsistently examined. This systematic review protocol (OSF preregistration...
Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013,...
Full Text:
infestans in the Northeastern United States and Canada. PLoS ONE, 9(12),
e116354. doi:10.1371/journal.pone
This paper sought to understand the extent to which, and how individuals use personal or collective language when asked to articulate sense of place from a collective perspective. Understanding a collective sense of place could illuminate place-based connections in natural resource industries, where it is as groups or as institutions...
Physical activity is important for health. However, there is a lack of literature related to the physical activity levels of adults living in urban villagers, which is a vulnerable population in China. The aim of this study is to compare the physical activity and sedentary behavior engagements between urban villagers...
Background
In the weeks following the first imported case of Ebola in the U. S. on September 29, 2014, coverage of the very limited outbreak dominated the news media, in a manner quite disproportionate to the actual threat to national public health; by the end of October, 2014, there were...
Full Text:
contagion of fear: the case of
ebola in America. PLoS ONE, 10(6), e0129179.
doi:10.1371/journal.pone
For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monitoring is both essential and challenging. Only recently have widespread monitoring programs been implemented for salmon habitat in the Pacific Northwest. Remote sensing data, such as Landsat images, are therefore a useful way to evaluate trends prior...
Spatial climate datasets of 1981–2010 long-term mean monthly average dew point and minimum and maximum vapor pressure deficit were developed for the conterminous United States at 30-arcsec (~800m) resolution. Interpolation of long-term averages (twelve monthly values per variable) was performed using PRISM (Parameter-elevation Relationships on Independent Slopes Model). Surface stations...
Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology...
Full Text:
of Plethodontid Salamanders. PLoS ONE, 10(11), e0142903.
doi:10.1371/journal.pone.0142903
10.1371
Carbonate communities:The activity of anaerobic methane oxidizing microbes facilitates
precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate
the significant role of carbonate rocks in promoting diversity by providing unique habitat
and food resources for macrofaunal assemblages at seeps on the Costa Rica margin
(400–1850 m)....
Full Text:
Carbonate at Costa Rica Methane Seeps. PLoS ONE, 10(7),
e0131080. doi:10.1371/journal.pone.0131080
10.1371
Captive rearing programs (hatcheries) are often used in conservation and management efforts
for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments
that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the...
Full Text:
Enrichment during
Juvenile Rearing. PLoS ONE, 10(3), e0118378.
doi:10.1371/journal.pone.0118378
10.1371
Testosterone plays an essential role in sexual differentiation of the male sheep brain. The ovine sexually dimorphic nucleus (oSDN), is 2 to 3 times larger in males than in females, and this sex difference is under the control of testosterone. The effect of testosterone on oSDN volume may result from...
Background:
Previous studies of compatibility of calcium chloride (CaCl₂) and phosphates have not included particle counts in the range specified by the United States Pharmacopeia. Micro-flow imaging techniques have been shown to be comparable to light obscuration when determining particle count and size in pharmaceutical solutions.
Objective:
The purpose of...
Full Text:
Using
Laser and Micro-Flow Imaging Methodology. PLoS ONE, 10(8), e0136894.
doi:10.1371/journal.pone
Correction
17 Oct 2012: Eng D, Ma HY, Xu J, Shih HP, Gross MK, et al. (2012) Correction: Loss of Abdominal Muscle in Pitx2 Mutants Associated with Altered Axial Specification of Lateral Plate Mesoderm. PLOS ONE 7(10): 10.1371/annotation/c980d5a1-1899-4d30-af7b-573d4049cf4b
Correction
5 Mar 2013: Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, et al. (2013) Correction: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi. PLOS Pathogens 9(3): 10.1371/annotation/fcca88ac-d684-46e0-a483-62af67e777bd
The cotton bollworm, Helicoverpa armigera (Hubner) is one of the most serious insect pest species to evolve resistance against many insecticides from different chemical classes. This species has evolved resistance to the pyrethroid insecticides across its native range and is becoming a truly global pest after establishing in South America...
Water is a limiting factor for plant growth and vegetation dynamics in alpine sandy land of the Tibetan Plateau, especially with the increasing frequency of extreme precipitation events and drought caused by climate change. Therefore, a relatively stable water source from either deeper soil profiles or ground water is necessary...
Full Text:
:10.1371/journal.pone.0156586 May 31, 2016 1 / 18
a11111
OPEN ACCESS
Citation: Zhu Y, Wang G, Li R (2016
Mycobacterium avium subsp. hominissuis is an opportunistic pathogen that is associated with biofilm-related infections of the respiratory tract and is difficult to treat. In recent years, extracellular DNA (eDNA) has been found to be a major component of bacterial biofilms, including many pathogens involved in biofilm-associated infections. To date, eDNA...
Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry.
Several methods for gene synthesis have been introduced in the growing area of genomics.
In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer) oligo fragments
from a library were assembled through successive...
Full Text:
- established 4-step process, which elongates a chain of nucleotide from the
PLOSONE | DOI:10.1371/journal.pone
Ocean acidification (OA) is altering the chemistry of the world’s oceans at rates unparalleled in the past roughly 1 million years. Understanding the impacts of this rapid change in baseline carbonate chemistry on marine organisms needs a precise, mechanistic understanding of physiological responses to carbonate chemistry. Recent experimental work has...
Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a...
Full Text:
, 10(3), e0116605. doi:10.1371/journal.pone.0116605
10.1371/journal.pone.0116605
Public Library of
Sea star wasting disease (SSWD) first appeared in Oregon in April 2014, and by June had spread to most of the coast. Although delayed compared to areas to the north and south, SSWD was initially most intense in north and central Oregon and spread southward. Up to 90% of individuals...
Full Text:
effects of this outbreak.
PLOS ONE | DOI:10.1371/journal.pone.0153994 May 4, 2016 1 / 28
a11111
OPEN
We report here that (4R,9Z)-hexadec-9-en-4-olide [(R)-desmolactone] is a sex
attractant or sex pheromone for multiple species and subspecies in the cerambycid
genus Desmocerus. This compound was previously identified as a female-produced
sex attractant pheromone of Desmocerus californicus californicus.
Headspace volatiles from female Desmocerus aureipennis aureipennis contained
(R)-desmolactone, and the antennae...
Full Text:
). PLoS ONE, 9
(12), e115498. doi:10.1371/journal.pone.0115498
10.1371/journal.pone.0115498
Public
For marine mammals, the ability to tolerate apnea and make extended dives is a defining adaptive trait, facilitating the exploitation of marine food resources. Elevated levels of myoglobin within the muscles are a consistent hallmark of this trait, allowing oxygen collected at the surface to be stored in the muscles...
Full Text:
:10.1371/journal.pone.0145893
10.1371/journal.pone.0145893
Public Library of Science
Version of Record
Conservation of Neotropical game species must take into account the livelihood and food security needs of local human populations. Hunting management decisions should therefore rely on abundance and distribution data that are as representative as possible of true population sizes and dynamics. We simultaneously applied a commonly used encounter-based method...
Full Text:
method of monitoring hunted vertebrate populations that complements
PLOS ONE | DOI:10.1371/journal.pone
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
Full Text:
North Pacific gray whales,
PLOSONE | DOI:10.1371/journal.pone.0147304 January 22, 2016 1 / 18
OPEN
Anthropogenic and natural stressors often interact to affect organisms. Amphibian populations are undergoing unprecedented declines and extinctions with pesticides and emerging infectious diseases implicated as causal factors. Although these factors often co-occur, their effects on amphibians are usually examined in isolation. We hypothesized that exposure of larval and metamorphic amphibians...
Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This...
Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic...
Full Text:
. PloS ONE, 10
(3), e0118502. doi:10.1371/journal.pone.0118502
10.1371/journal.pone.0118502
Public
A steam distillation extraction kinetics experiment was conducted to estimate essential oil yield, composition, antimalarial, and antioxidant capacity of cumin (Cuminum cyminum L.) seed (fruits). Furthermore, regression models were developed to predict essential oil yield and composition for a given duration of the steam distillation time (DT). Ten DT durations...
Fungi in the genus Ascosphaera (Ascomycota: Eurotiomycetes: Ascosphaerales) cause chalkbrood disease in larvae of bees. Here, we report the first-ever detection of the fungus in adult bumble bees that were raised in captivity for studies on colony development. Wild queens of Bombus griseocollis, B. nevadensis and B. vosnesenskii were collected...
RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
Marine diseases are becoming more frequent, and tools for identifying pathogens and disease
reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics
provides insights into disease etiology by cataloguing and comparing sequences from suspected
pathogens. This method is a powerful approach to simultaneously evaluate both the
viral and bacterial...
Full Text:
Virome in a Stranding Event. PLoS
ONE, 10(12), e0143944. doi:10.1371/journal.pone.0143944
10.1371
Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph
centipedes. The Geophilomorpha is the most speciose order of centipedes with
over a 1000 species described. They are notable for their large number of appendage bearing
segments and are being used as a laboratory model to study...
Full Text:
/journal.pone.0121369
10.1371/journal.pone.0121369
Public Library of Science
Version of Record
http
To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of...
Identification and classification of behavior states in animal movement data can be complex, temporally biased, time-intensive, scale-dependent, and unstandardized across studies and taxa. Large movement datasets are increasingly common and there is a need for efficient methods of data exploration that adjust to the individual variability of each track. We...
Species distribution models (SDMs) are increasingly applied in conservation management
to predict suitable habitat for poorly known populations. High predictive performance of
SDMs is evident in validations performed within the model calibration area (interpolation),
but few studies have assessed SDM transferability to novel areas (extrapolation), particularly
across large spatial scales...
The abiotic environment has strong influences on the growth, survival, behavior, and ecology of aquatic organisms. Biotic interactions and species life histories interact with abiotic factors to structure the food web. One measure of food-web structure is food-chain length. Several hypotheses predict a linear relationship between one environmental variable (e.g.,...
Digestion of milk proteins in the premature infant stomach releases functional peptides; however, which peptides are present has not been reported. Premature infants are often fed a combination of human milk and bovine milk fortifiers, but the variety of functional peptides released from both human and bovine milk proteins remains...
Climate change is expected to change the distribution of species. For long-lived, sessile
species such as trees, tracking the warming climate depends on seedling colonization of
newly favorable areas. We compare the distribution of seedlings and mature trees for all but
the rarest tree species in California, Oregon and Washington,...
Full Text:
:10.1371/journal.pone.0118069
10.1371/journal.pone.0118069
Public Library of Science
Version of Record
Understanding how intra-specific differences in plant traits mediate vulnerability to herbivores of relevant habitat-forming plants is vital to attain a better knowledge on the drivers of the structure and functioning of ecosystems. Such studies, however, are rare in seagrass-mesograzer systems despite the increasingly recognized relevance of mesograzers as seagrass consumers....
Full Text:
defences against herbivory.
PLOS ONE | DOI:10.1371/journal.pone.0156848 June 3, 2016 1 / 19
a11111
OPEN
The differentiation of precursor cells into mature adipocytes (adipogenesis) has been an area of increased focus, spurred by a rise in obesity rates. Though our understanding of adipogenesis and its regulation at the cellular level is growing, many questions remain, especially regarding the regulation of the metabolome. The 3T3-L1 cell...
Full Text:
-resolved metabolomics.
PLOS ONE | DOI:10.1371/journal.pone.0157118 June 8, 2016 1 / 18
a11111
OPEN
A number of researchers have attempted to estimate salmonid smolt survival during outmigration through an estuary. However, it is currently unclear how the design of such studies influences the accuracy and precision of survival estimates. In this simulation study we consider four patterns of smolt survival probability in the estuary,...
Full Text:
: Simulating the Effect of Sample Design on Inference. PLoS ONE, 10(7),
e0132912. doi:10.1371/journal.pone
Two novel research approaches were developed to facilitate controlled access to, and long-term monitoring of, juvenile Steller sea lions for periods longer than typically afforded by traditional fieldwork. The Transient Juvenile Steller sea lion Project at the Alaska SeaLife Center facilitated nutritional, physiological, and behavioral studies on the platform of...
Our objective was to identify the biological response and the cross-talk between liver and mammary tissue after intramammary infection (IMI) with Escherichia coli (E. coli) using RNAseq technology. Sixteen cows were inoculated with live E. coli into one mammary quarter at ~4–6 weeks in lactation. For all cows, biopsies were...
Full Text:
mammary tissue.
PLOS ONE | DOI:10.1371/journal.pone.0157480 June 23, 2016 1 / 28
a11111
OPEN ACCESS
Marine microbes exhibit highly varied, often non-spherical shapes that have functional significance for essential processes, including nutrient acquisition and sinking rates. There is a surprising absence of data, however, on how cell shape affects grazing, which is crucial for predicting the fate of oceanic carbon. We used synthetic spherical and...
Hepatocellular carcinoma (HCC) is currently one of the top lethal cancers with an increasing
trend. Deregulation of MYC in HCC is frequently detected and always correlated with poor
prognosis. As the zebrafish genome contains two differentially expressed zebrafish myc
orthologs, myca and mycb, it remains unclear about the oncogenicity of...
Full Text:
Transgenic Zebrafish Can Regress in tp53 Null Mutation. PLoS ONE,
10(1), e0117249. doi:10.1371/journal.pone
Stream-dwelling species in the U.S. southern Appalachian Mountains region are particularly vulnerable to climate change and acidification. The objectives of this study were to quantify the spatial extent of contemporary suitable habitat for acid- and thermally sensitive aquatic species and to forecast future habitat loss resulting from expected temperature increases...
Full Text:
ONE, 10(8), e0134757. doi:10.1371/journal.pone.0134757
10.1371/journal.pone.0134757
Public Library
Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native...
Cymbopogon flexuosus, lemongrass, and C. martinii, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared...
This work is about assessing model adequacy for negative binomial (NB) regression, particularly
(1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness
of models for NB dispersion parameters. Tools for the first are appropriate for NB
regression generally; those for the second are primarily intended for...
Full Text:
, 10(3), e0119254. doi:10.1371/journal.pone.0119254
10.1371/journal.pone.0119254
Public Library of
Cells in three-dimensional (3D) environments exhibit very different biochemical and biophysical phenotypes compared to the behavior of cells in two-dimensional (2D) environments. As an important biomechanical measurement, 2D traction force microscopy can not be directly extended into 3D cases. In order to quantitatively characterize the contraction field, we have developed...
Full Text:
normal component and is truly 3D in nature [7, 17, 18].
PLOSONE | DOI:10.1371/journal.pone.0156797 June
Upriver movements were determined for Chinook salmon Oncorhynchus tshawytscha returning to the Yukon River, a large, virtually pristine river basin. These returns have declined dramatically since the late 1990s, and information is needed to better manage the run and facilitate conservation efforts. A total of 2,860 fish were radio tagged...
Hybridization has been identified as a significant factor in the evolution of plants as groups of interbreeding species retain their phenotypic integrity despite gene exchange among forms. Recent studies have identified similar interactions in animals; however, the role of hybridization in the evolution of animals has been contested. Here we...
Full Text:
Klamath Basin catostomids.
PLOS ONE | DOI:10.1371/journal.pone.0149884 March 9, 2016 1 / 27
OPEN ACCESS
Palm leaves represent one of the most important non-timber forest products in tropical and subtropical regions. Brahea aculeata is an endemic palm of northwest Mexico, whose leaves are intensively exploited for roof thatch and handcrafts. As part of a long-term defoliation experiment, we evaluated the effects of different leaf harvest...
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide...