Journals
2011 EN
Liping Hou · Christopher Phillips · Marco A. Azaro
+2 more
Background Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA “barcoding” to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies. Principal Findings Empirical performance in classification of relative types for any two given DNA samples (e.g., full siblings, parental, etc) indicated that for outbred populations the panel performs sufficiently to classify relationship in extended families and therefore also for smaller structures such as trios and for twin zygosity testing. Additionally, familial relationships do not significantly diminish the (mean match) probability of sharing SNP genotypes in pedigrees, further indicating the uniqueness of the “barcode.” Simulation using these SNPs for an African American case-control disease association study demonstrated that population stratification, even in complex admixed samples, can be adequately corrected under a range of disease models using the SNP panel. Conclusion The panel has been validated for use in a variety of human disease genetics research tasks including sample barcoding, relationship verification, population substructure detection and statistical correction. Given the ease of genotyping our specific assay contained herein, this panel represents a useful and economical panel for human geneticists.
Public Library of Science
Journals
2011 EN
Qunfeng Dong · David E. Nelson · Evelyn Toh
+4 more
Urine is the CDC-recommended specimen for STI testing. It was unknown if the bacterial communities (microbiomes) in urine reflected those in the distal male urethra. We compared microbiomes of 32 paired urine and urethral swab specimens obtained from adult men attending an STD clinic, by 16S rRNA PCR and deep pyrosequencing. Microbiomes of urine and swabs were remarkably similar, regardless of STI status of the subjects. Thus, urine can be used to characterize urethral microbiomes when swabs are undesirable, such as in population-based studies of the urethral microbiome or where multiple sampling of participants is required.
Public Library of Science
Journals
2011 EN
Sheena E Ramsay · Peter H. Whincup · Sarah Hardoon
+3 more
Background Coronary heart disease (CHD) mortality in the UK since the late 1970s has declined more markedly among higher socioeconomic groups. However, little is known about changes in coronary risk factors in different socioeconomic groups. This study examined whether changes in established coronary risk factors in Britain over 20 years between 1978–80 and 1998–2000 differed between socioeconomic groups. Methods and Findings A socioeconomically representative cohort of 7735 British men aged 40–59 years was followed-up from 1978–80 to 1998–2000; data on blood pressure (BP), cholesterol, body mass index (BMI) and cigarette smoking were collected at both points in 4252 survivors. Social class was based on longest-held occupation in middle-age. Compared with men in non-manual occupations, men in manual occupations experienced a greater increase in BMI (mean difference = 0.33 kg/m 2 ; 95%CI 0.14–0.53; p for interaction = 0.001), a smaller decline in non-HDL cholesterol (difference in mean change = 0.18 mmol/l; 95%CI 0.11–0.25, p for interaction≤0.0001) and a smaller increase in HDL cholesterol (difference in mean change = 0.04 mmol/l; 95%CI 0.02–0.06, p for interaction≤0.0001). However, mean systolic BP declined more in manual than non-manual groups (difference in mean change = 3.6; 95%CI 2.1–5.1, p for interaction≤0.0001). The odds of being a current smoker in 1978–80 and 1998–2000 did not differ between non-manual and manual social classes (p for interaction = 0.51). Conclusion Several key risk factors for CHD and type 2 diabetes showed less favourable changes in men in manual occupations. Continuing priority is needed to improve adverse cardiovascular risk profiles in socially disadvantaged groups in the UK.
Public Library of Science
Journals
2011 EN
Rebecca Nalloor · Kristopher M. Bunting · Almira Vazdarjanova
Background Emotionally traumatic experiences can lead to debilitating anxiety disorders, such as phobias and Post-Traumatic Stress Disorder (PTSD). Exposure to such experiences, however, is not sufficient to induce pathology, as only up to one quarter of people exposed to such events develop PTSD. These statistics, combined with findings that smaller hippocampal size prior to the trauma is associated with higher risk of developing PTSD, suggest that there are pre-disposing factors for such pathology. Because prospective studies in humans are limited and costly, investigating such pre-dispositions, and thus advancing understanding of the genesis of such pathologies, requires the use of animal models where predispositions are identified before the emotional trauma. Most existing animal models are retrospective: they classify subjects as those with or without a PTSD-like phenotype long after experiencing a traumatic event. Attempts to create prospective animal models have been largely unsuccessful. Methodology/Principal Findings Here we report that individual predispositions to a PTSD-like phenotype, consisting of impaired rate and magnitude of extinction of an emotionally traumatic event coupled with long-lasting elevation of acoustic startle responses, can be revealed following exposure to a mild stressor, but before experiencing emotional trauma. We compare, in rats, the utility of several classification criteria and report that a combination of criteria based on acoustic startle responses and behavior in an anxiogenic environment is a reliable predictor of a PTSD-like phenotype. Conclusions/Significance There are individual predispositions to developing impaired extinction and elevated acoustic startle that can be identified after exposure to a mildly stressful event, which by itself does not induce such a behavioral phenotype. The model presented here is a valuable tool for studying the etiology and pathophysiology of anxiety disorders and provides a platform for testing behavioral and pharmacological interventions that can reduce the probability of developing pathologic behaviors associated with such disorders.
Public Library of Science
Journals
2011 EN
Jianbo Lu · Lin Jiang · Lin Yu
+1 more
Despite the recent popularity of the metacommunity concept, ecologists have not evaluated the applicability of different metacommunity frameworks to insular organisms. We surveyed 50 closely spaced islands in the Thousand-Island Lake of China to examine the role of local (environmental) and regional (dispersal) factors in structuring woody plant assemblages (tree and shrub species) on these islands. By partitioning the variation in plant community structure into local and regional causes, we showed that local environmental conditions, specifically island morphometric characteristics, accounted for the majority of the variation in plant community structure among the studied islands. Spatial variables, representing the potential importance of species dispersal, explained little variation. We conclude that one metacommunity framework–species sorting–best characterizes these plant communities. This result reinforces the idea that the traditional approach of emphasizing the local perspective when studying ecological communities continues to hold its value.
Public Library of Science
Journals
2011 EN
Karen Banai · Rachel Yifat
Background Recent studies suggest that human auditory perception follows a prolonged developmental trajectory, sometimes continuing well into adolescence. Whereas both sensory and cognitive accounts have been proposed, the development of the ability to base current perceptual decisions on prior information, an ability that strongly benefits adult perception, has not been directly explored. Here we ask whether the auditory frequency discrimination of preschool children also improves when given the opportunity to use previously presented standard stimuli as perceptual anchors, and whether the magnitude of this anchoring effect undergoes developmental changes. Methodology/Principal Findings Frequency discrimination was tested using two adaptive same/different protocols. In one protocol ( with-reference ), a repeated 1-kHz standard tone was presented repeatedly across trials. In the other ( no-reference ), no such repetitions occurred. Verbal memory and early reading skills were also evaluated to determine if the pattern of correlations between frequency discrimination, memory and literacy is similar to that previously reported in older children and adults. Preschool children were significantly more sensitive in the with-reference than in the no-reference condition, but the magnitude of this anchoring effect was smaller than that observed in adults. The pattern of correlations among discrimination thresholds, memory and literacy replicated previous reports in older children. Conclusions/Significance The processes allowing the use of context to form perceptual anchors are already functional among preschool children, albeit to a lesser extent than in adults. Nevertheless, immature anchoring cannot fully account for the poorer frequency discrimination abilities of young children. That anchoring is present among the majority of typically developing preschool children suggests that the anchoring deficits observed among individuals with dyslexia represent a true deficit rather than a developmental delay.
Public Library of Science
Journals
2011 EN
Maurizio Gentilucci · Giovanna Cristina Campione
The present study aimed at determining whether, in healthy humans, postures assumed by distal effectors affect the control of the successive grasp executed with other distal effectors. In experiments 1 and 2, participants reached different objects with their head and grasped them with their mouth, after assuming different hand postures. The postures could be implicitly associated with interactions with large or small objects. The kinematics of lip shaping during grasp varied congruently with the hand posture, i.e. it was larger or smaller when it could be associated with the grasping of large or small objects, respectively. In experiments 3 and 4, participants reached and grasped different objects with their hand, after assuming the postures of mouth aperture or closure (experiment 3) and the postures of toe extension or flexion (experiment 4). The mouth postures affected the kinematics of finger shaping during grasp, that is larger finger shaping corresponded with opened mouth and smaller finger shaping with closed mouth. In contrast, the foot postures did not influence the hand grasp kinematics. Finally, in experiment 5 participants reached-grasped different objects with their hand while pronouncing opened and closed vowels, as verified by the analysis of their vocal spectra. Open and closed vowels induced larger and smaller finger shaping, respectively. In all experiments postures of the distal effectors induced no effect, or only unspecific effects on the kinematics of the reach proximal/axial component. The data from the present study support the hypothesis that there exists a system involved in establishing interactions between movements and postures of hand and mouth. This system might have been used to transfer a repertoire of hand gestures to mouth articulation postures during language evolution and, in modern humans, it may have evolved a system controlling the interactions existing between speech and gestures.
Public Library of Science
Journals
2011 EN
Giuseppe Donati · Kristina Kesch · Kelard Ndremifidy
+4 more
Background Frugivorous primates are known to encounter many problems to cope with habitat degradation, due to the fluctuating spatial and temporal distribution of their food resources. Since lemur communities evolved strategies to deal with periods of food scarcity, these primates are expected to be naturally adapted to fluctuating ecological conditions and to tolerate a certain degree of habitat changes. However, behavioral and ecological strategies adopted by frugivorous lemurs to survive in secondary habitats have been little investigated. Here, we compared the behavioral ecology of collared lemurs ( Eulemur collaris ) in a degraded fragment of littoral forest of south-east Madagascar, Mandena, with that of their conspecifics in a more intact habitat, Sainte Luce. Methodology/Principal Findings Lemur groups in Mandena and in Sainte Luce were censused in 2004/2007 and in 2000, respectively. Data were collected via instantaneous sampling on five lemur groups totaling 1,698 observation hours. The Shannon index was used to determine dietary diversity and nutritional analyses were conducted to assess food quality. All feeding trees were identified and measured, and ranging areas determined via the minimum convex polygon. In the degraded area lemurs were able to modify several aspects of their feeding strategies by decreasing group size and by increasing feeding time, ranging areas, and number of feeding trees. The above strategies were apparently able to counteract a clear reduction in both food quality and size of feeding trees. Conclusions/Significance Our findings indicate that collared lemurs in littoral forest fragments modified their behavior to cope with the pressures of fluctuating resource availability. The observed flexibility is likely to be an adaptation to Malagasy rainforests, which are known to undergo periods of fruit scarcity and low productivity. These results should be carefully considered when relocating lemurs or when selecting suitable areas for their conservation.
Public Library of Science
Journals
2011 EN
Gustav Paulay · John Starmer
Most oceanic islands harbor unusual and vulnerable biotas as a result of isolation. As many groups, including dominant competitors and predators, have not naturally reached remote islands, others were less constrained to evolve novel adaptations and invade adaptive zones occupied by other taxa on continents. Land crabs are an excellent example of such ecological release, and some crab lineages made the macro-evolutionary transition from sea to land on islands. Numerous land crabs are restricted to, although widespread among, oceanic islands, where they can be keystone species in coastal forests, occupying guilds filled by vertebrates on continents. In the remote Hawaiian Islands, land crabs are strikingly absent. Here we show that absence of land crabs in the Hawaiian Islands is the result of extinction, rather than dispersal limitation. Analysis of fossil remains from all major islands show that an endemic Geograpsus was abundant before human colonization, grew larger than any congener, and extended further inland and to higher elevation than other land crabs in Oceania. Land crabs are major predators of nesting sea birds, invertebrates and plants, affect seed dispersal, control litter decomposition, and are important in nutrient cycling; their removal can lead to large-scale shifts in ecological communities. Although the importance of land crabs is obvious on remote and relatively undisturbed islands, it is less apparent on others, likely because they are decimated by humans and introduced biota. The loss of Geograpsus and potentially other land crabs likely had profound consequences for Hawaiian ecosystems.
Public Library of Science
Journals
2011 EN
KoonKiu Yan · Mark Gerstein
The presence of web-based communities is a distinctive signature of Web 2.0. The web-based feature means that information propagation within each community is highly facilitated, promoting complex collective dynamics in view of information exchange. In this work, we focus on a community of scientists and study, in particular, how the awareness of a scientific paper is spread. Our work is based on the web usage statistics obtained from the PLoS Article Level Metrics dataset compiled by PLoS. The cumulative number of HTML views was found to follow a long tail distribution which is reasonably well-fitted by a lognormal one. We modeled the diffusion of information by a random multiplicative process, and thus extracted the rates of information spread at different stages after the publication of a paper. We found that the spread of information displays two distinct decay regimes: a rapid downfall in the first month after publication, and a gradual power law decay afterwards. We identified these two regimes with two distinct driving processes: a short-term behavior driven by the fame of a paper, and a long-term behavior consistent with citation statistics. The patterns of information spread were found to be remarkably similar in data from different journals, but there are intrinsic differences for different types of web usage (HTML views and PDF downloads versus XML). These similarities and differences shed light on the theoretical understanding of different complex systems, as well as a better design of the corresponding web applications that is of high potential marketing impact.
Public Library of Science