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1.  Pragmatic Perspective on Conservation Genetics and Demographic History of the Last Surviving Population of Kashmir Red Deer (Cervus elaphus hanglu) in India 
PLoS ONE  2015;10(2):e0117069.
The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.
PMCID: PMC4324630  PMID: 25671567
2.  Characterization of a Novel Plasmid, pMAH135, from Mycobacterium avium Subsp. hominissuis 
PLoS ONE  2015;10(2):e0117797.
Mycobacterium avium complex (MAC) causes mainly two types of disease. The first is disseminated disease in immunocompromised hosts, such as individuals infected by human immunodeficiency virus (HIV). The second is pulmonary disease in individuals without systemic immunosuppression, and the incidence of this type is increasing worldwide. M. avium subsp. hominissuis, a component of MAC, causes infection in pigs as well as in humans. Many aspects of the different modes of M. avium infection and its host specificity remain unclear. Here, we report the characteristics and complete sequence of a novel plasmid, designated pMAH135, derived from M. avium strain TH135 in an HIV-negative patient with pulmonary MAC disease. The pMAH135 plasmid consists of 194,711 nucleotides with an average G + C content of 66.5% and encodes 164 coding sequences (CDSs). This plasmid was unique in terms of its homology to other mycobacterial plasmids. Interestingly, it contains CDSs with sequence homology to mycobactin biosynthesis proteins and type VII secretion system-related proteins, which are involved in the pathogenicity of mycobacteria. It also contains putative conserved domains of the multidrug efflux transporter. Screening of isolates from humans and pigs for genes located on pMAH135 revealed that the detection rate of these genes was higher in clinical isolates from pulmonary MAC disease patients than in those from HIV-positive patients, whereas the genes were almost entirely absent in isolates from pigs. Moreover, variable number tandem repeats typing analysis showed that isolates carrying pMAH135 genes are grouped in a specific cluster. Collectively, the pMAH135 plasmid contains genes associated with M. avium’s pathogenicity and resistance to antimicrobial agents. The results of this study suggest that pMAH135 influence not only the pathological manifestations of MAC disease, but also the host specificity of MAC infection.
PMCID: PMC4324632  PMID: 25671431
3.  A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields 
PLoS ONE  2015;10(2):e0117790.
Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal capabilities were not as important.
PMCID: PMC4324633  PMID: 25671322
4.  Bioprospecting the American Alligator (Alligator mississippiensis) Host Defense Peptidome 
PLoS ONE  2015;10(2):e0117394.
Cationic antimicrobial peptides and their therapeutic potential have garnered growing interest because of the proliferation of bacterial resistance. However, the discovery of new antimicrobial peptides from animals has proven challenging due to the limitations associated with conventional biochemical purification and difficulties in predicting active peptides from genomic sequences, if known. As an example, no antimicrobial peptides have been identified from the American alligator, Alligator mississippiensis, although their serum is antimicrobial. We have developed a novel approach for the discovery of new antimicrobial peptides from these animals, one that capitalizes on their fundamental and conserved physico-chemical properties. This sample-agnostic process employs custom-made functionalized hydrogel microparticles to harvest cationic peptides from biological samples, followed by de novo sequencing of captured peptides, eliminating the need to isolate individual peptides. After evaluation of the peptide sequences using a combination of rational and web-based bioinformatic analyses, forty-five potential antimicrobial peptides were identified, and eight of these peptides were selected to be chemically synthesized and evaluated. The successful identification of multiple novel peptides, exhibiting antibacterial properties, from Alligator mississippiensis plasma demonstrates the potential of this innovative discovery process in identifying potential new host defense peptides.
PMCID: PMC4324634  PMID: 25671663
5.  Prevalence and Correlates of Physical Inactivity in Community-Dwelling Older Adults in Ireland 
PLoS ONE  2015;10(2):e0118293.
The public health challenges associated with rapid population ageing are likely to be exacerbated by poor physical activity levels. The purpose of this study was to identify correlates of physical inactivity in a population-representative sample of older adults in Ireland. This paper reports a secondary analysis of data from 4892 adults aged 60+ from the Irish Longitudinal Study on Ageing (TILDA). TILDA includes an assessment of the mental and physical health, and social and financial circumstances of participants assessed in a home interview and self-completion questionnaire. Chi squared statistics and forced entry logistic regression were used to identify factors associated with physical inactivity. Females were over twice as likely to be inactive as their male counterparts (Odds Ratio 2.2). Increasing old age was associated with inactivity among males and females. Those who reported above secondary level education, no reported falls in the last year and no fear of falling were less likely to be physically inactive. While older adults who noted poor/fair self-reported health, that they did not look after grandchildren, did not own a car or did not attend a course were also more likely to be inactive than those who reported positively for these items. Gender displayed a strong but often contrasting influence on factors that affect physical activity among older adults. Among females, living alone or in a rural area, retirement, fair/poor emotional health and activity being limited by illness were all significantly associated with inactivity. While cohabiting, being employed and residing in an urban area were related to low levels of activity in males. Our findings identify specific groups of the older Irish population who may be at particular risk of physical inactivity and thereby the associated physiological and psychological hazards. These results can support the development of tailored interventions to promote healthy ageing.
PMCID: PMC4324635  PMID: 25671621
6.  Alteration of Histone Acetylation Pattern during Long-Term Serum-Free Culture Conditions of Human Fetal Placental Mesenchymal Stem Cells 
PLoS ONE  2015;10(2):e0117068.
Increasing evidence suggests that the mesenchymal stem cells (MSCs) derived from placenta of fetal origin (fPMSCs) are superior to MSCs of other sources for cell therapy. Since the initial number of isolated MSCs is limited, in vitro propagation is often required to reach sufficient numbers of cells for therapeutic applications, during which MSCs may undergo genetic and/or epigenetic alterations that subsequently increase the probability of spontaneous malignant transformation. Thus, factors that influence genomic and epigenetic stability of MSCs following long-term expansions need to be clarified before cultured MSCs are employed for clinical settings. To date, the genetic and epigenetic stability of fPMSCs after long-term in vitro expansion has not been fully investigated. In this report, alterations to histone acetylation and consequence on the expression pattern of fPMSCs following in vitro propagation under serum-free conditions were explored. The results show that fPMSCs maintain their MSC characteristics before they reached a senescent state. Furthermore, acetylation modification patterns were changed in fPMSCs along with gradually increased global histone deacetylase (HDAC) activity and expression of HDAC subtypes HDAC4, HDAC5 and HDAC6, as well as a down-regulated global histone H3/H4 acetylation during in vitro culturing. In line with the acetylation alterations, the expression of oncogenes Oct4, Sox2 and TERT were significantly decreased over the propagation period. Of note, the down-regulation of Oct4 was strongly associated with changes in acetylation. Intriguingly, telomere length in fPMSCs did not significantly change during the propagating process. These findings suggest that human fPMSCs may be a safe and reliable resource of MSCs and can be propagated under serum-free conditions with less risk of spontaneous malignancy, and warrants further validation in clinical settings.
PMCID: PMC4324636  PMID: 25671548
7.  High Prevalence of Respiratory Muscle Weakness in Hospitalized Acute Heart Failure Elderly Patients 
PLoS ONE  2015;10(2):e0118218.
Respiratory Muscle Weakness (RMW) has been defined when the maximum inspiratory pressure (MIP) is lower than 70% of the predictive value. The prevalence of RMW in chronic heart failure patients is 30 to 50%. So far there are no studies on the prevalence of RMW in acute heart failure (AHF) patients.
Evaluate the prevalence of RMW in patients admitted because of AHF and the condition of respiratory muscle strength on discharge from the hospital.
Sixty-three patients had their MIP measured on two occasions: at the beginning of the hospital stay, after they had reached respiratory, hemodynamic and clinical stability and before discharge from the hospital. The apparatus and technique to measure MIP were adapted because of age-related limitations of the patients. Data on cardiac ejection fraction, ECG, brain natriuretic peptide (BNP) levels and on the use of noninvasive ventilation (NIV) were collected.
The mean age of the 63 patients under study was 75 years. On admission the mean ejection fraction was 33% (95% CI: 31–35) and the BNP hormone median value was 726.5 pg/ml (range: 217 to 2283 pg/ml); 65% of the patients used NIV. The median value of MIP measured after clinical stabilization was -52.7 cmH2O (range: -20 to -120 cmH2O); 76% of the patients had MIP values below 70% of the predictive value. On discharge, after a median hospital stay of 11 days, the median MIP was -53.5 cmH2O (range:-20 to -150 cmH2O); 71% of the patients maintained their MIP values below 70% of the predictive value. The differences found were not statistically significant.
Elderly patients admitted with AHF may present a high prevalence of RMW on admission; this condition may be maintained at similar levels on discharge in a large percentage of these patients, even after clinical stabilization of the heart condition.
PMCID: PMC4324642  PMID: 25671566
8.  Characterization of Self-Assembled Virus-Like Particles of Merkel Cell Polyomavirus 
PLoS ONE  2015;10(2):e0115646.
In our recombinant baculovirus system, VP1 protein of merkel cell polyomavirus (MCPyV), which is implicated as a causative agent in Merkel cell carcinoma, was self-assembled into MCPyV-like particles (MCPyV-LP) with two different sizes in insect cells, followed by being released into the culture medium. DNA molecules of 1.5- to 5-kb, which were derived from host insect cells, were packaged in large, ~50-nm spherical particles but not in small, ~25-nm particles. Structure reconstruction using cryo-electron microscopy showed that large MCPyV-LPs are composed of 72 pentameric capsomeres arranged in a T = 7 icosahedral surface lattice and are 48 nm in diameter. The MCPyV-LPs did not share antigenic determinants with BK- and JC viruses (BKPyV and JCPyV). The VLP-based enzyme immunoassay was applied to investigate age-specific prevalence of MCPyV infection in the general Japanese population aged 1–70 years. While seroprevalence of MCPyV increased with age in children and young individuals, its seropositivity in each age group was lower compared with BKPyV and JCPyV.
PMCID: PMC4324643  PMID: 25671590
9.  Effects of Low Doses of Pioglitazone on Resting-State Functional Connectivity in Conscious Rat Brain 
PLoS ONE  2015;10(2):e0117973.
Pioglitazone (PIO) is a peroxisome proliferator-activated receptor-γ (PPARγ) agonist in clinical use for treatment of type 2 diabetes (T2DM). Accumulating evidence suggests PPARγ agonists may be useful for treating or delaying the onset of Alzheimer’s disease (AD), possibly via actions on mitochondria, and that dose strengths lower than those clinically used for T2DM may be efficacious. Our major objective was to determine if low doses of pioglitazone, administered orally, impacted brain activity. We measured blood-oxygenation-level dependent (BOLD) low-frequency fluctuations in conscious rats to map changes in brain resting-state functional connectivity due to daily, oral dosing with low-dose PIO. The connectivity in two neural circuits exhibited significant changes compared with vehicle after two days of treatment with PIO at 0.08 mg/kg/day. After 7 days of treatment with a range of PIO dose-strengths, connections between 17 pairs of brain regions were significantly affected. Functional connectivity with the CA1 region of the hippocampus, a region that is involved in memory and is affected early in the progression of AD, was specifically investigated in a seed-based analysis. This approach revealed that the spatial pattern of CA1 connectivity was consistent among all dose groups at baseline, prior to treatment with PIO, and in the control group imaged on day 7. Compared to baseline and controls, increased connectivity to CA1 was observed regionally in the hypothalamus and ventral thalamus in all PIO-treated groups, but was least pronounced in the group treated with the highest dose of PIO. These data support our hypothesis that PIO modulates neuronal and/or cerebrovascular function at dose strengths significantly lower than those used to treat T2DM and therefore may be a useful therapy for neurodegenerative diseases including AD.
PMCID: PMC4324644  PMID: 25671601
10.  Effects of Ethnic Attributes on the Quality of Family Planning Services in Lima, Peru: A Randomized Crossover Trial 
PLoS ONE  2015;10(2):e0115274.
Most studies reporting ethnic disparities in the quality of healthcare come from developed countries and rely on observational methods. We conducted the first experimental study to evaluate whether health providers in Peru provide differential quality of care for family planning services, based on the indigenous or mestizo (mixed ethnoracial ancestry) profile of the patient. In a crossover randomized controlled trial conducted in 2012, a sample of 351 out of the 408 public health establishments in Metropolitan Lima, Peru were randomly assigned to receive unannounced simulated patients enacting indigenous and mestizo profiles (sequence-1) or mestizo and then indigenous profiles (sequence-2), with a five week wash-out period. Both ethnic profiles used the same scripted scenario for seeking contraceptive advice but had distinctive cultural attributes such as clothing, styling of hair, make-up, accessories, posture and patterns of movement and speech. Our primary outcome measure of quality of care is the proportion of technical tasks performed by providers, as established by Peruvian family planning clinical guidelines. Providers and data analysts were kept blinded to the allocation. We found a non-significant mean difference of -0·7% (p = 0·23) between ethnic profiles in the percentage of technical tasks performed by providers. However we report large deficiencies in the compliance with quality standards of care for both profiles. Differential provider behaviour based on the patient's ethnic profiles compared in the study did not contribute to deficiencies in family planning outcomes observed. The study highlights the need to explore other determinants for poor compliance with quality standards, including demand and supply side factors, and calls for interventions to improve the quality of care for family planning services in Metropolitan Lima.
PMCID: PMC4324646  PMID: 25671664
11.  Unequally Distributed Psychological Assets: Are There Social Disparities in Optimism, Life Satisfaction, and Positive Affect? 
PLoS ONE  2015;10(2):e0118066.
Socioeconomic status is associated with health disparities, but underlying psychosocial mechanisms have not been fully identified. Dispositional optimism may be a psychosocial process linking socioeconomic status with health. We hypothesized that lower optimism would be associated with greater social disadvantage and poorer social mobility. We also investigated whether life satisfaction and positive affect showed similar patterns. Participants from the Midlife in the United States study self-reported their optimism, satisfaction, positive affect, and socioeconomic status (gender, race/ethnicity, education, occupational class and prestige, income). Social disparities in optimism were evident. Optimistic individuals tended to be white and highly educated, had an educated parent, belonged to higher occupational classes with more prestige, and had higher incomes. Findings were generally similar for satisfaction, but not positive affect. Greater optimism and satisfaction were also associated with educational achievement across generations. Optimism and life satisfaction are consistently linked with socioeconomic advantage and may be one conduit by which social disparities influence health.
PMCID: PMC4324648  PMID: 25671665
12.  Proliferation and Differentiation of Trypanosoma cruzi inside Its Vector Have a New Trigger: Redox Status 
PLoS ONE  2015;10(2):e0116712.
Trypanosoma cruzi proliferate and differentiate inside different compartments of triatomines gut that is the first environment encountered by T. cruzi. Due to its complex life cycle, the parasite is constantly exposed to reactive oxygen species (ROS). We tested the influence of the pro-oxidant molecules H2O2 and the superoxide generator, Paraquat, as well as, metabolism products of the vector, with distinct redox status, in the proliferation and metacyclogenesis. These molecules are heme, hemozoin and urate. We also tested the antioxidants NAC and GSH. Heme induced the proliferation of epimastigotes and impaired the metacyclogenesis. β-hematin, did not affect epimastigote proliferation but decreased parasite differentiation. Conversely, we show that urate, GSH and NAC dramatically impaired epimastigote proliferation and during metacyclogenesis, NAC and urate induced a significant increment of trypomastigotes and decreased the percentage of epimastigotes. We also quantified the parasite loads in the anterior and posterior midguts and in the rectum of the vector by qPCR. The treatment with the antioxidants increased the parasite loads in all midgut sections analyzed. In vivo, the group of vectors fed with reduced molecules showed an increment of trypomastigotes and decreased epimastigotes when analyzed by differential counting. Heme stimulated proliferation by increasing the cell number in the S and G2/M phases, whereas NAC arrested epimastigotes in G1 phase. NAC greatly increased the percentage of trypomastigotes. Taken together, these data show a shift in the triatomine gut microenvironment caused by the redox status may also influence T. cruzi biology inside the vector. In this scenario, oxidants act to turn on epimastigote proliferation while antioxidants seem to switch the cycle towards metacyclogenesis. This is a new insight that defines a key role for redox metabolism in governing the parasitic life cycle.
PMCID: PMC4324650  PMID: 25671543
13.  Differences in the Ovine HSP90AA1 Gene Expression Rates Caused by Two Linked Polymorphisms at Its Promoter Affect Rams Sperm DNA Fragmentation under Environmental Heat Stress Conditions 
PLoS ONE  2015;10(2):e0116360.
Heat shock (HS) is one of the best-studied exogenous cellular stresses. Almost all tissues, cell types, metabolic pathways and biochemical reactions are affected in greater or lesser extent by HS. However, there are some especially thermo sensible cellular types such as the mammalian male germ cells. The present study examined the role of three INDELs in conjunction with the -660G/C polymorphism located at the HSP90AA1 promoter region over the gene expression rate under HS. Specially, the -668insC INDEL, which is very close to the -660G/C transversion, is a good candidate to be implied in the transcriptional regulation of the gene by itself or in a cooperative way with this SNP. Animals carrying the genotype II-668 showed higher transcription rates than those with ID-668 (FC = 3.07) and DD-668 (FC = 3.40) genotypes for samples collected under HS. A linkage between gene expression and sperm DNA fragmentation was also found. When HS conditions were present along or in some stages of the spermatogenesis, alternative genotypes of the -668insC and -660G/C mutations are involved in the effect of HS over sperm DNA fragmentation. Thus, unfavorable genotypes in terms of gene expression induction (ID-668GC-660 and DD-668GG-660) do not produce enough mRNA (stored as messenger ribonucleoprotein particles) and Hsp90α protein to cope with future thermal stress which might occur in posterior stages when transcriptional activity is reduced and cell types and molecular processes are more sensible to heat (spermatocytes in pachytene and spermatids protamination). This would result in the impairment of DNA packaging and the consequent commitment of the events occurring shortly after fertilization and during embryonic development. In the short-term, the assessment of the relationship between sperm DNA fragmentation sensitivity and ram’s fertility will be of interest to a better understanding of the mechanisms of response to HS and its consequences on animal production and reproduction performance.
PMCID: PMC4324765  PMID: 25671615
14.  Simulating Fiction: Individual Differences in Literature Comprehension Revealed with fMRI 
PLoS ONE  2015;10(2):e0116492.
When we read literary fiction, we are transported to fictional places, and we feel and think along with the characters. Despite the importance of narrative in adult life and during development, the neurocognitive mechanisms underlying fiction comprehension are unclear. We used functional magnetic resonance imaging (fMRI) to investigate how individuals differently employ neural networks important for understanding others’ beliefs and intentions (mentalizing), and for sensori-motor simulation while listening to excerpts from literary novels. Localizer tasks were used to localize both the cortical motor network and the mentalizing network in participants after they listened to excerpts from literary novels. Results show that participants who had high activation in anterior medial prefrontal cortex (aMPFC; part of the mentalizing network) when listening to mentalizing content of literary fiction, had lower motor cortex activity when they listened to action-related content of the story, and vice versa. This qualifies how people differ in their engagement with fiction: some people are mostly drawn into a story by mentalizing about the thoughts and beliefs of others, whereas others engage in literature by simulating more concrete events such as actions. This study provides on-line neural evidence for the existence of qualitatively different styles of moving into literary worlds, and adds to a growing body of literature showing the potential to study narrative comprehension with neuroimaging methods.
PMCID: PMC4324766  PMID: 25671708
15.  Synergistic Interaction between Selective Drugs in Cell Populations Models 
PLoS ONE  2015;10(2):e0117558.
The design of selective drugs and combinatorial drug treatments are two of the main focuses in modern pharmacology. In this study we use a mathematical model of chimeric ligand-receptor interaction to show that the combination of selective drugs is synergistic in nature, providing a way to gain optimal selective potential at reduced doses compared to the same drugs when applied individually. We use a cell population model of proliferating cells expressing two different amounts of a target protein to show that both selectivity and synergism are robust against variability and heritability in the cell population. The reduction in the total drug administered due to the synergistic performance of the selective drugs can potentially result in reduced toxicity and off-target interactions, providing a mechanism to improve the treatment of cell-based diseases caused by aberrant gene overexpression, such as cancer and diabetes.
PMCID: PMC4324767  PMID: 25671700
16.  Early Olfactory Environment Influences Social Behaviour in Adult Octodon degus 
PLoS ONE  2015;10(2):e0118018.
We evaluated the extent to which manipulation of early olfactory environment can influence social behaviours in the South American Hystricognath rodent Octodon degus. The early olfactory environment of newborn degus was manipulated by scenting all litter members with eucalyptol during the first month of life. The social behaviour of sexually mature animals (5–7 months old) towards conspecifics was then assessed using a y-maze to compare the response of control (naïve) and treated animals to two different olfactory configurations (experiment 1): (i) a non-familiarized conspecific impregnated with eucalyptol (eucalyptol arm) presented against (ii) a non-familiarized unscented conspecific (control arm). In addition, in dyadic encounters, we assessed the behaviour of control and eucalyptol treated animals towards a non-familiarized conspecific scented with eucalyptol (experiment 2). We found that control subjects explored and spent significantly less time in the eucalyptol arm, indicating neophobic behaviours towards the artificially scented conspecific. Treated subjects explored and spent similar time in both arms of the maze, showing the same interest for both olfactory stimuli presented. During dyadic encounters in experiment 2, an interaction effect between early experience and sex was observed. Control males escaped and avoided their scented partner more frequently than eucalyptol treated male subjects and than females. Both groups did not differ in the exploration of their scented partners, suggesting that avoidance within agonistic context does not relate to neophobic behaviours. Our results suggest that the exposure to eucalyptol during early ontogeny decreases evasive behaviours within an agonistic context as a result of olfactory learning. Altogether, these results indicate that olfactory cues learned in early ontogeny can influence olfactory-guided behaviours in adult degus.
PMCID: PMC4324768  PMID: 25671542
17.  Performance of an In-House Human Immunodeficiency Virus Type 1 Genotyping System for Assessment of Drug Resistance in Cuba 
PLoS ONE  2015;10(2):e0117176.
As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.
PMCID: PMC4324769  PMID: 25671421
18.  Contrasting Effects of Different Mammalian Herbivores on Sagebrush Plant Communities 
PLoS ONE  2015;10(2):e0118016.
Herbivory by both grazing and browsing ungulates shapes the structure and functioning of terrestrial ecosystems worldwide, and both types of herbivory have been implicated in major ecosystem state changes. Despite the ecological consequences of differences in diets and feeding habits among herbivores, studies that experimentally distinguish effects of grazing from spatially co-occurring, but temporally segregated browsing are extremely rare. Here we use a set of long-term exclosures in northern Utah, USA, to determine how domestic grazers vs. wild ungulate herbivores (including browsers and mixed feeders) affect sagebrush-dominated plant communities that historically covered ~62 million ha in North America. We sampled plant community properties and found that after 22 years grazing and browsing elicited perceptible changes in overall plant community composition and distinct responses by individual plant species. In the woody layer of the plant community, release from winter and spring wild ungulate herbivory increased densities of larger Wyoming big sagebrush (Artemisia tridentata, ssp. wyomingensis) at the expense of small sagebrush, while disturbance associated with either cattle or wild ungulate activity alone was sufficient to increase bare ground and reduce cover of biological soil crusts. The perennial bunchgrass, bottlebrush squirretail (Elymus elymoides), responded positively to release from summer cattle grazing, and in turn appeared to competitively suppress another more grazing tolerant perennial grass, Sandberg’s blue grass (Poa secunda). Grazing by domestic cattle also was associated with increased non-native species biomass. Together, these results illustrate that ungulate herbivory has not caused sagebrush plant communities to undergo dramatic state shifts; however clear, herbivore-driven shifts are evident. In a dry, perennial-dominated system where plant community changes can occur very slowly, our results provide insights into potential long-term trajectories of these plant communities under different large herbivore regimes. Our results can be used to guide long-term management strategies for sagebrush systems and improve habitat for endemic wildlife species such as sage-grouse (Centrocercus spp.).
PMCID: PMC4324772  PMID: 25671428
19.  The Morphometrics of “Masculinity” in Human Faces 
PLoS ONE  2015;10(2):e0118374.
In studies of social inference and human mate preference, a wide but inconsistent array of tools for computing facial masculinity has been devised. Several of these approaches implicitly assumed that the individual expression of sexually dimorphic shape features, which we refer to as maleness, resembles facial shape features perceived as masculine. We outline a morphometric strategy for estimating separately the face shape patterns that underlie perceived masculinity and maleness, and for computing individual scores for these shape patterns. We further show how faces with different degrees of masculinity or maleness can be constructed in a geometric morphometric framework. In an application of these methods to a set of human facial photographs, we found that shape features typically perceived as masculine are wide faces with a wide inter-orbital distance, a wide nose, thin lips, and a large and massive lower face. The individual expressions of this combination of shape features—the masculinity shape scores—were the best predictor of rated masculinity among the compared methods (r = 0.5). The shape features perceived as masculine only partly resembled the average face shape difference between males and females (sexual dimorphism). Discriminant functions and Procrustes distances to the female mean shape were poor predictors of perceived masculinity.
PMCID: PMC4324773  PMID: 25671667
20.  Psychometric Properties of the Autoquestionnaire Qualité De Vie Enfant Imagé (AUQEI) Applied to Children with Cerebral Palsy 
PLoS ONE  2015;10(2):e0115643.
Quality of life (QL) assessments of children with incapacitating diseases, such as cerebral palsy (CP), have often been conducted with the help of the representatives of a child, making QL assessment more subjective. TheAutoquestionnaireQualité de Vie Enfant Imagé (AUQEI) is a QL assessment designed for children to self-report—it uses images to facilitate the reporting process.
evaluate the psychometric properties of AUQEI when responses are given by children with CP.
Children aged 4 to 12 years (45 with CP and 45 healthy children) gave responses to the questionnaire. The data quality, reliability and validity were assessed. The data loss rate ranged from 8.8% to 46.7%, and was highest for the “autonomy” factor. No floor or ceiling effect was detected. The success rate for reliability of the internal consistency of the items was less than 80% for the “autonomy” factor. Cronbach’s alpha coefficient was 0.71 for the instrument and less than 0.5 for the factors. All the factors had a success rate of greater than 80% for the discriminating validity of the items. The factors did not have correlations between each other, thus indicating adequate discriminating validity. Convergent validity was tested and a significant correlation was demonstrated only between the AUQEI “functioning” factor and the Child Health Questionnaire—50-Item (CHQ-PF50) physical summary score (r = 0.31, p = 0.042). The AUQEI scores did not have correlations with the gross motor function scores (p>0.05) as expected for divergent validity. Regarding construct validity, the total AUQEI score obtained by the CP group was lower (median: 47.3) than that of the healthy group (median: 51.0) (p<0.01).
The AUQEI was shown to be a reliable and valid instrument for assessing children with CP when the total score was used. Convergent validity should continue to be tested in future studies.
PMCID: PMC4324774  PMID: 25671523
21.  Synthesis and Evaluation of a Novel Adenosine-Ribose Probe for Global-Scale Profiling of Nucleoside and Nucleotide-Binding Proteins 
PLoS ONE  2015;10(2):e0115644.
Proteomics is a powerful approach used for investigating the complex molecular mechanisms of disease pathogenesis and progression. An important challenge in modern protein profiling approaches involves targeting of specific protein activities in order to identify altered molecular processes associated with disease pathophysiology. Adenosine-binding proteins represent an important subset of the proteome where aberrant expression or activity changes of these proteins have been implicated in numerous human diseases. Herein, we describe an affinity-based approach for the enrichment of adenosine-binding proteins from a complex cell proteome. A novel N6-biotinylated-8-azido-adenosine probe (AdoR probe) was synthesized, which contains a reactive group that forms a covalent bond with the target proteins, as well as a biotin tag for affinity enrichment using avidin chromatography. Probe specificity was confirmed with protein standards prior to further evaluation in a complex protein mixture consisting of a lysate derived from mouse neuroblastoma N18TG2 cells. Protein identification and relative quantitation using mass spectrometry allowed for the identification of small variations in abundance of nucleoside- and nucleotide-binding proteins in these samples where a significant enrichment of AdoR-binding proteins in the labeled proteome from the neuroblastoma cells was observed. The results from this study demonstrate the utility of this method to enrich for nucleoside- and nucleotide-binding proteins in a complex protein mixture, pointing towards a unique set of proteins that can be examined in the context of further understanding mechanisms of disease, or fundamental biological processes in general.
PMCID: PMC4324776  PMID: 25671571
22.  Self-Rated Health Status and Subjective Health Complaints Associated with Health-Promoting Lifestyles among Urban Chinese Women: A Cross-Sectional Study 
PLoS ONE  2015;10(2):e0117940.
This study aimed to investigate whether self-rated health status (SRH) and subjective health complaints (SHC) of urban Chinese women are associated with their health-promoting lifestyles (HPL).
We conducted a cross-sectional study on 8142 eligible Chinese participants between 2012 and 2013. Demographic and SHC data were collected. Each subject completed the SRH questionnaire and the Chinese version of the Health-Promoting Lifestyle Profile-II (HPLP-II). Correlation and binary regression analyses were performed to examine the associations of SRH and SHC with HPL.
Both SRH and HPL of urban Chinese women were moderate. The most common complaints were fatigue (1972, 24.2%), eye discomfort (1571, 19.3%), and insomnia (1542, 18.9%). Teachers, highly educated subjects and elderly women had lower SRH scores, while college students and married women had better HPL. All items of HPLP-II were positively correlated with SRH (r = 0.127-0.533, P = 0.000) and negatively correlated with SHC to a significant extent (odds ratio [OR] = 1.40-11.37).
Aspects of HPL, particularly stress management and spiritual growth, are associated with higher SRH and lower SHC ratings among urban Chinese women. Physical activity and health responsibility are additionally related to reduced fatigue and nervousness. We believe that these findings will be instrumental in encouraging researchers and urban women to adopt better health-promoting lifestyles with different priorities in their daily lives.
PMCID: PMC4324778  PMID: 25671578
23.  Larval Settlement: The Role of Surface Topography for Sessile Coral Reef Invertebrates 
PLoS ONE  2015;10(2):e0117675.
For sessile marine invertebrates with complex life cycles, habitat choice is directed by the larval phase. Defining which habitat-linked cues are implicated in sessile invertebrate larval settlement has largely concentrated on chemical cues which are thought to signal optimal habitat. There has been less effort establishing physical settlement cues, including the role of surface microtopography. This laboratory based study tested whether surface microtopography alone (without chemical cues) plays an important contributing role in the settlement of larvae of coral reef sessile invertebrates. We measured settlement to tiles, engineered with surface microtopography (holes) that closely matched the sizes (width) of larvae of a range of corals and sponges, in addition to surfaces with holes that were markedly larger than larvae. Larvae from two species of scleractinian corals (Acropora millepora and Ctenactis crassa) and three species of coral reef sponges (Luffariella variabilis, Carteriospongia foliascens and Ircinia sp.,) were used in experiments. L. variabilis, A. millepora and C. crassa showed markedly higher settlement to surface microtopography that closely matched their larval width. C. foliascens and Ircinia sp., showed no specificity to surface microtopography, settling just as often to microtopography as to flat surfaces. The findings of this study question the sole reliance on chemical based larval settlement cues, previously established for some coral and sponge species, and demonstrate that specific physical cues (surface complexity) can also play an important role in larval settlement of coral reef sessile invertebrates.
PMCID: PMC4324781  PMID: 25671562
24.  Modelling Associations between Public Understanding, Engagement and Forest Conditions in the Inland Northwest, USA 
PLoS ONE  2015;10(2):e0117975.
Opinions about public lands and the actions of private non-industrial forest owners in the western United States play important roles in forested landscape management as both public and private forests face increasing risks from large wildfires, pests and disease. This work presents the responses from two surveys, a random-sample telephone survey of more than 1500 residents and a mail survey targeting owners of parcels with 10 or more acres of forest. These surveys were conducted in three counties (Wallowa, Union, and Baker) in northeast Oregon, USA. We analyze these survey data using structural equation models in order to assess how individual characteristics and understanding of forest management issues affect perceptions about forest conditions and risks associated with declining forest health on public lands. We test whether forest understanding is informed by background, beliefs, and experiences, and whether as an intervening variable it is associated with views about forest conditions on publicly managed forests. Individual background characteristics such as age, gender and county of residence have significant direct or indirect effects on our measurement of understanding. Controlling for background factors, we found that forest owners with higher self-assessed understanding, and more education about forest management, tend to hold more pessimistic views about forest conditions. Based on our results we argue that self-assessed understanding, interest in learning, and willingness to engage in extension activities together have leverage to affect perceptions about the risks posed by declining forest conditions on public lands, influence land owner actions, and affect support for public policies. These results also have broader implications for management of forested landscapes on public and private lands amidst changing demographics in rural communities across the Inland Northwest where migration may significantly alter the composition of forest owner goals, understanding, and support for various management actions.
PMCID: PMC4324782  PMID: 25671619
25.  Methamphetamine Accelerates Cellular Senescence through Stimulation of De Novo Ceramide Biosynthesis 
PLoS ONE  2015;10(2):e0116961.
Methamphetamine is a highly addictive psychostimulant that causes profound damage to the brain and other body organs. Post mortem studies of human tissues have linked the use of this drug to diseases associated with aging, such as coronary atherosclerosis and pulmonary fibrosis, but the molecular mechanism underlying these findings remains unknown. Here we used functional lipidomics and transcriptomics experiments to study abnormalities in lipid metabolism in select regions of the brain and, to a greater extent, peripheral organs and tissues of rats that self-administered methamphetamine. Experiments in various cellular models (primary mouse fibroblasts and myotubes) allowed us to investigate the molecular mechanisms of systemic inflammation and cellular aging related to methamphetamine abuse. We report now that methamphetamine accelerates cellular senescence and activates transcription of genes involved in cell-cycle control and inflammation by stimulating production of the sphingolipid messenger ceramide. This pathogenic cascade is triggered by reactive oxygen species, likely generated through methamphetamine metabolism via cytochrome P450, and involves the recruitment of nuclear factor-κB (NF-κB) to induce expression of enzymes in the de novo pathway of ceramide biosynthesis. Inhibitors of NF-κB signaling and ceramide formation prevent methamphetamine-induced senescence and systemic inflammation in rats self-administering the drug, attenuating their health deterioration. The results suggest new therapeutic strategies to reduce the adverse consequences of methamphetamine abuse and improve effectiveness of abstinence treatments.
PMCID: PMC4324822  PMID: 25671639

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