Regular group exercise is associated with improved mood but not quality of life following stroke
Purpose. People with stroke living in the community have an increased prevalence of depression and lower quality of life than healthy older adults. This cross-sectional observational study investigated whether participation in regular exercise was associated with improved mood and quality of life. Methods. We recruited three groups of community dwelling participants: 13 healthy older adults, 17 adults post-stroke who regularly participated in group exercise at a community fitness facility and 10 adults post-stroke who did not regularly exercise. We measured mood using the Depression, Anxiety, Stress Scale (DASS) and quality of life using the Assessment of Quality of Life (AQoL) scale. Results. Levels of stress and depression were significantly greater in the people with stroke who did not undertake regular exercise (p = 0.004 and p = 0.004 respectively), although this group had more recent strokes (p < 0.001). Both stroke groups had lower quality of life scores (p = 0.04) than the healthy adults. Conclusions. This small, community-based study confirms that people following stroke report poorer quality of life than stroke-free individuals. However, those who exercise regularly have significantly lower stress and depression compared to stroke survivors who do not. Future research should focus on the precise type and amount of exercise capable of improving mood following stroke.
McDonnell et al. (2014) Regular group exercise is associated with improved mood but not quality of life following stroke. PeerJ 2:e331 https://doi.org/10.7717/peerj.331
Intuitive physics and intuitive psychology (“theory of mind”) in offspring of mothers with psychoses
Offspring of individuals with psychoses sometimes display an abnormal development of cognition, language, motor performance, social adaptation, and emotional functions. The aim of this study was to investigate the ability of children of mothers with schizophrenia (n = 28) and bipolar disorder (n = 23) to understand mental states of others using the Eyes Test (folk psychology or “theory of mind”) and physical causal interactions of inanimate objects (folk physics). Compared with healthy controls (n = 29), the children of mothers with schizophrenia displayed significantly impaired performances on the Eyes Test but not on the folk physics test when corrected for IQ. The children of mothers with bipolar disorder did not differ from the controls. The folk physics test showed a significant covariance with IQ, whereas the Eyes Test did not exhibit such covariance. These results suggest that the attribution of mental states, but not the interpretation of causal interaction of objects, is impaired in offspring of individuals with schizophrenia, which may contribute to social dysfunctions.
Maróthi et al. (2014) Intuitive physics and intuitive psychology (“theory of mind”) in offspring of mothers with psychoses. PeerJ 2:e330 https://doi.org/10.7717/peerj.330
Contribution of insect pollinators to crop yield and quality varies with agricultural intensification
Background. Up to 75% of crop species benefit at least to some degree from animal pollination for fruit or seed set and yield. However, basic information on the level of pollinator dependence and pollinator contribution to yield is lacking for many crops. Even less is known about how insect pollination affects crop quality. Given that habitat loss and agricultural intensification are known to decrease pollinator richness and abundance, there is a need to assess the consequences for different components of crop production. Methods. We used pollination exclusion on flowers or inflorescences on a whole plant basis to assess the contribution of insect pollination to crop yield and quality in four flowering crops (spring oilseed rape, field bean, strawberry, and buckwheat) located in four regions of Europe. For each crop, we recorded abundance and species richness of flower visiting insects in ten fields located along a gradient from simple to heterogeneous landscapes. Results. Insect pollination enhanced average crop yield between 18 and 71% depending on the crop. Yield quality was also enhanced in most crops. For instance, oilseed rape had higher oil and lower chlorophyll contents when adequately pollinated, the proportion of empty seeds decreased in buckwheat, and strawberries’ commercial grade improved; however, we did not find higher nitrogen content in open pollinated field beans. Complex landscapes had a higher overall species richness of wild pollinators across crops, but visitation rates were only higher in complex landscapes for some crops. On the contrary, the overall yield was consistently enhanced by higher visitation rates, but not by higher pollinator richness. Discussion. For the four crops in this study, there is clear benefit delivered by pollinators on yield quantity and/or quality, but it is not maximized under current agricultural intensification. Honeybees, the most abundant pollinator, might partially compensate the loss of wild pollinators in some areas, but our results suggest the need of landscape-scale actions to enhance wild pollinator populations.
Bartomeus et al. (2014) Contribution of insect pollinators to crop yield and quality varies with agricultural intensification. PeerJ 2:e328 https://doi.org/10.7717/peerj.328
Severity of chronic Lyme disease compared to other chronic conditions: a quality of life survey
Overview. The Centers for Disease Control and Prevention (CDC) health-related quality of life (HRQoL) indicators are widely used in the general population to determine the burden of disease, identify health needs, and direct public health policy. These indicators also allow the burden of illness to be compared across different diseases. Although Lyme disease has recently been acknowledged as a major health threat in the USA with more than 300,000 new cases per year, no comprehensive assessment of the health burden of this tickborne disease is available. This study assesses the HRQoL of patients with chronic Lyme disease (CLD) and compares the severity of CLD to other chronic conditions. Methods. Of 5,357 subjects who responded to an online survey, 3,090 were selected for the study. Respondents were characterized as having CLD if they were clinically diagnosed with Lyme disease and had persisting symptoms lasting more than 6 months following antibiotic treatment. HRQoL of CLD patients was assessed using the CDC 9-item metric. The HRQoL analysis for CLD was compared to published analyses for the general population and other chronic illnesses using standard statistical methods. Results. Compared to the general population and patients with other chronic diseases reviewed here, patients with CLD reported significantly lower health quality status, more bad mental and physical health days, a significant symptom disease burden, and greater activity limitations. They also reported impairment in their ability to work, increased utilization of healthcare services, and greater out of pocket medical costs. Conclusions. CLD patients have significantly impaired HRQoL and greater healthcare utilization compared to the general population and patients with other chronic diseases. The heavy burden of illness associated with CLD highlights the need for earlier diagnosis and innovative treatment approaches that may reduce the burden of illness and concomitant costs posed by this illness.
Johnson et al. (2014) Severity of chronic Lyme disease compared to other chronic conditions: a quality of life survey. PeerJ 2:e322 https://doi.org/10.7717/peerj.322
Manuka-type honeys can eradicate biofilms produced by Staphylococcus aureus strains with different biofilm-forming abilities
Chronic wounds are a major global health problem. Their management is difficult and costly, and the development of antibiotic resistance by both planktonic and biofilm-associated bacteria necessitates the use of alternative wound treatments. Honey is now being revisited as an alternative treatment due to its broad-spectrum antibacterial activity and the inability of bacteria to develop resistance to it. Many previous antibacterial studies have used honeys that are not well characterized, even in terms of quantifying the levels of the major antibacterial components present, making it difficult to build an evidence base for the efficacy of honey as an antibiofilm agent in chronic wound treatment. Here we show that a range of well-characterized New Zealand manuka-type honeys, in which two principle antibacterial components, methylglyoxal and hydrogen peroxide, were quantified, can eradicate biofilms of a range of Staphylococcus aureus strains that differ widely in their biofilm-forming abilities. Using crystal violet and viability assays, along with confocal laser scanning imaging, we demonstrate that in all S. aureus strains, including methicillin-resistant strains, the manuka-type honeys showed significantly higher anti-biofilm activity than clover honey and an isotonic sugar solution. We observed higher anti-biofilm activity as the proportion of manuka-derived honey, and thus methylglyoxal, in a honey blend increased. However, methylglyoxal on its own, or with sugar, was not able to effectively eradicate S. aureus biofilms. We also demonstrate that honey was able to penetrate through the biofilm matrix and kill the embedded cells in some cases. As has been reported for antibiotics, sub-inhibitory concentrations of honey improved biofilm formation by some S. aureus strains, however, biofilm cell suspensions recovered after honey treatment did not develop resistance towards manuka-type honeys. New Zealand manuka-type honeys, at the concentrations they can be applied in wound dressings are highly active in both preventing S. aureus biofilm formation and in their eradication, and do not result in bacteria becoming resistant. Methylglyoxal requires other components in manuka-type honeys for this anti-biofilm activity. Our findings support the use of well-defined manuka-type honeys as a topical anti-biofilm treatment for the effective management of wound healing.
Lu et al. (2014) Manuka-type honeys can eradicate biofilms produced by Staphylococcus aureus strains with different biofilm-forming abilities. PeerJ 2:e326 https://doi.org/10.7717/peerj.326
The Adult ADHD Self-Report Scale (ASRS): utility in college students with attention-deficit/hyperactivity disorder
Background. The number of students with Attention Deficit/Hyperactivity Disorder (ADHD) enrolled in colleges and universities has increased markedly over the past few decades, giving rise to questions about how best to document symptoms and impairment in the post-secondary setting. The aim of the present study was to investigate the utility and psychometric properties of a widely-used rating scale for adults with ADHD, the Adult ADHD Self-Report Scale (ASRS-V1.1), in a sample of post-secondary students with ADHD. Methods. A total of 135 college students (mean age = 24, 42% males) with ADHD were recruited from Student Disability Services in post-secondary institutions. We compared informant responses on the ASRS administered via different modalities. First, students’ self-report was ascertained using the ASRS Screener administered via telephone interview, in which they were asked to provide real-life examples of behavior for each of the six items. Next, students self-reported symptoms on the 18-item paper version of the ASRS Symptom Checklist administered about 1–2 weeks later, and a collateral report using an online version of the 18-item ASRS Symptom Checklist. Students also completed self-report measures of everyday cognitive failure (CFQ) and executive functioning (BDEFS). Results. Results revealed moderate to good congruency between the 18-item ASRS-Self and ASRS-Collateral reports (correlation = .47), and between student self-report on the 6-item telephone-based and paper versions of the ASRS, with the paper version administered two weeks later (correlation = .66). The full ASRS self-report was related to impairment, such as in executive functioning (correlation = .63) and everyday cognitive failure (correlation = .74). Executive functioning was the only significant predictor of ASRS total scores. Discussion. Current findings suggest that the ASRS provides an easy-to-use, reliable, and cost-effective approach for gathering information about current symptoms of ADHD in college and university students. Collateral reports were moderately related to self-reports, although we note the difficulty in obtaining informant reports for this population. Use of a telephone interview to elicit behavioral descriptions for each item may be useful in future research that is required to specifically test the utility of the ASRS in, for example, documenting and confirming current reports of impairment due to ADHD symptoms and its positive and negative predictive power for diagnosis.
Gray et al. (2014) The Adult ADHD Self-Report Scale (ASRS): utility in college students with attention-deficit/hyperactivity disorder. PeerJ 2:e324 https://doi.org/10.7717/peerj.324
Mapping the self-association domains of ataxin-1: identification of novel non overlapping motifs
The neurodegenerative disease spinocerebellar ataxia type 1 (SCA1) is caused by aggregation and misfolding of the ataxin-1 protein. While the pathology correlates with mutations that lead to expansion of a polyglutamine tract in the protein, other regions contribute to the aggregation process as also non-expanded ataxin-1 is intrinsically aggregation-prone and forms nuclear foci in cell. Here, we have used a combined approach based on FRET analysis, confocal microscopy and in vitro techniques to map aggregation-prone regions other than polyglutamine and to establish the importance of dimerization in self-association/foci formation. Identification of aggregation-prone regions other than polyglutamine could greatly help the development of SCA1 treatment more specific than that based on targeting the low complexity polyglutamine region.
Menon et al. (2014) Mapping the self-association domains of ataxin-1: identification of novel non overlapping motifs. PeerJ 2:e323 https://doi.org/10.7717/peerj.323
Fuelling in front of the barrier—are there age based behavioral differences in Garden Warblers Sylvia borin?
Garden Warblers Sylvia borin were studied during autumn stopover in Crete before crossing the barrier of the Mediterranean Sea and the Sahara Desert. Birds followed with transmitters show extensive stopover periods, which were longer in first-year birds, 16 days, compared with adult birds, 14 days. The distribution of body masses from birds trapped in fig trees were used to estimate the departure body mass and the results found indicate that both age categories on average depart with a fuel load close to 100% of lean body mass. The movement of transmitter birds shows differences between first-year and adult birds. Adult birds move further away from the release site and many also left the study area. Several were found settled outside the study area, up to 17 km away, indicating that they regularly make longer stopover movements. It is suggested that this might be a result of that they return to a place where they stayed during an earlier migration. It was shown that stopover site fidelity exists and nine garden warblers were recaptured in the area during a following autumn. The results found highlights the importance of stopover areas close to the Sahara Desert.
Barboutis et al. (2014) Fuelling in front of the barrier—are there age based behavioral differences in Garden Warblers Sylvia borin?. PeerJ 2:e319 https://doi.org/10.7717/peerj.319
Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths
The number of cervical vertebrae in mammals is highly conserved at seven. We have shown that changes of this number are selected against due to a coupling with major congenital abnormalities (pleiotropic effects). Here we show that the incidence of abnormal cervical vertebral numbers in Late Pleistocene mammoths from the North Sea is high (33.3%) and approximately 10 times higher than that of extant elephants (3.6%). Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, which we deduced from the presence of rib articulation facets on sixth (posterior side) and seventh (anterior side) cervical vertebrae. The incidence of abnormal cervical vertebral numbers in mammoths appears to be much higher than in other mammalian species, apart from exceptional sloths, manatees and dugongs and indicates a vulnerable condition. We argue that the increased incidence of cervical ribs in mammoths is probably caused by inbreeding and adverse conditions that impact early pregnancies in declining populations close to extinction in the Late Pleistocene.
Reumer et al. (2014) Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths. PeerJ 2:e318 https://doi.org/10.7717/peerj.318
Oocyte size, egg index, and body lipid content in relation to body size in the solitary bee Megachile rotundata
Females of solitary, nest-provisioning bees have relatively low fecundity, but produce large eggs as part of their overall strategy of investing substantially in each offspring. In intraspecific comparisons of several species of solitary, nest-provisioning bees and wasps, the size of the mature eggs produced increases with female body size. We further examined oocyte size–body size correlations in the solitary bee Megachile rotundata (F.), an important crop pollinator. We hypothesized that larger females carry larger basal oocytes (i.e., those next in line to be oviposited) but that body size–oocyte size correlations would be absent soon after emergence, before their first eggs fully matured. Because egg production is likely affected by the quantity of stored lipids carried over from the bees’ immature stages, we also tested the hypothesis that female body size is correlated with the body lipid content at adult emergence, the time during which oocyte growth accelerates. We found significant correlations of body size with oocyte size variables chosen to reflect: (1) the magnitude of the investment in the next egg to be laid (i.e., the length and volume of the basal oocyte) and (2) the longer term potential to produce mature oocytes (i.e., the summed lengths and volumes of the three largest oocytes in each female). Positive correlations existed throughout the nesting season, even during the first week following adult emergence. The ability to produce and carry larger oocytes may be linked to larger females starting the nesting season with greater lipid stores (which we document here) or to greater space within the abdomen of larger females. Compared to other species of solitary bees, M. rotundata appears to have (1) smaller oocytes than solitary nest-provisioning bees in general, (2) comparable oocyte sizes relative to congeners, and (3) larger oocytes than related brood parasitic megachilids.
O’Neill et al. (2014) Oocyte size, egg index, and body lipid content in relation to body size in the solitary bee Megachile rotundata. PeerJ 2:e314 https://doi.org/10.7717/peerj.314
Effect of 2H and 18O water isotopes in kinesin-1 gliding assay
We show for the first time the effects of heavy-hydrogen water (2H2O) and heavy-oxygen water (H218O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We also show that gliding microtubule speed returns to its original speed after being treated with heavy-hydrogen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for using heavy waters in biomolecular devices incorporating molecular motors.
Maloney et al. (2014) Effect of 2H and 18O water isotopes in kinesin-1 gliding assay. PeerJ 2:e284 https://doi.org/10.7717/peerj.284
Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater)
Brown-headed Cowbirds (Molothrus ater) are the most widespread avian brood parasite in North America, laying their eggs in the nests of approximately 250 host species that raise the cowbird nestlings as their own. It is currently unknown how these heterospecific hosts influence the cowbird gut microbiota relative to other factors, such as the local environment and genetics. We test a Nature Hypothesis (positing the importance of cowbird genetics) and a Nurture Hypothesis (where the host parents are most influential to cowbird gut microbiota) using the V6 region of 16S rRNA as a microbial fingerprint of the gut from 32 cowbird samples and 16 potential hosts from nine species. We test additional hypotheses regarding the influence of the local environment and age of the birds. We found no evidence for the Nature Hypothesis and little support for the Nurture Hypothesis. Cowbird gut microbiota did not form a clade, but neither did members of the host species. Rather, the physical location, diet and age of the bird, whether cowbird or host, were the most significant categorical variables. Thus, passerine gut microbiota may be most strongly influenced by environmental factors. To put this variation in a broader context, we compared the bird data to a fecal microbiota dataset of 38 mammal species and 22 insect species. Insects were always the most variable; on some axes, we found more variation within cowbirds than across all mammals. Taken together, passerine gut microbiota may be more variable and environmentally determined than other taxonomic groups examined to date.
Hird et al. (2014) Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater). PeerJ 2:e321 https://doi.org/10.7717/peerj.321
DoReMi: context-based prioritization of linear motif matches
Many protein domains bind to short peptide sequences, called linear motifs. Data on their sequence specificities is sparse, which is why biologists usually resort to basic pattern searches to identify new putative binding sites for experimental follow-up. Most motifs have poor specificity and prioritization of the matches is thus crucial when scanning a full proteome with a pattern. Here we present a generic method to prioritize motif occurrence predictions by using cellular contextual information. We take 2 parameters as input: the motif occurrences and one or more of the interacting domains. The potential hits are ranked based on how strongly the context network associates them with a protein containing one of the specified domains, which leads to an increased predictive performance. The method is available through a web interface at doremi.jensenlab.org, which allows for an easy application of the method. We show that this approach leads to improved predictions of binding partners for PDZ domains and the SUMO binding domain. This is consistent with the earlier observation that coupling sequence motifs with network information improves kinase-specific substrate predictions.
Horn et al. (2014) DoReMi: context-based prioritization of linear motif matches. PeerJ 2:e315 https://doi.org/10.7717/peerj.315
Obesity prevalence and associated risk factors in outdoor living domestic horses and ponies
Reasons for performing study. The prevalence of obesity in companion animals, including horses and ponies has risen drastically in recent years and risk factors have been little investigated. Horses are unique amongst companion animals in that many are outdoor-living and forage independently on pasture; they also have a dual utility and companionship role. The body condition of wild and free-living equines is known to vary seasonally, yet previous estimates of the prevalence of obesity and associated risk factors in domestic animals do not consider this. Most previous studies were conducted during the summer months when pasture quality is greater and obesity prevalence is likely to be highest. In addition, many previous estimates do not use validated body condition scoring methods and rely on owner reporting. Objectives. To examine the prevalence and risk factors predictive of equine obesity at both the end of winter and the end of summer, in a domestic population of leisure horses with daily access to pasture. Using validated body condition scoring methods and a single, trained observer. Methods. Body condition and belly girth measurements were taken at the end of winter and during the summer in a population of leisure horses (n = 96) with outdoor pasture access for ≥6 h per day. Risk factor information was obtained by two owner questionnaires and analysed statistically using a mixed effects logistic regression model. The dependent variable was obese (BCS ≥ 7/9) or non-obese (BCS < 7/9). Risk factors associated with seasonal change in belly girth were also explored using a mixed effects linear regression model. Results. Obesity prevalence rose significantly from 27.08% at the end of winter to 35.41% during summer (p < 0.001). Breed was the risk factor most strongly associated with obesity (p < 0.001). Supplementary feed was not a strong predictor and there was no association with low intensity structured exercise. As winter BCS increased, the percentage seasonal change in belly girth decreased. Conclusions. Obesity prevalence differed between winter and summer in domestic equines. Supplementary feed and low intensity structured exercise in equines living outdoors for ≥6 h per day had limited or no effect on obesity levels. Seasonal variation in body condition was lower in obese equines. Potential relevance. It is important to consider season when studying equine obesity and obesity-associated disorders. Risk factor analysis suggests preventative measures may need to be breed specific. The metabolic implications of a lessened seasonal change in body condition in obese animals, warrants investigation.
Giles et al. (2014) Obesity prevalence and associated risk factors in outdoor living domestic horses and ponies. PeerJ 2:e299 https://doi.org/10.7717/peerj.299
Schistosome tegumental ecto-apyrase (SmATPDase1) degrades exogenous pro-inflammatory and pro-thrombotic nucleotides
Schistosomes are parasitic worms that can survive in the hostile environment of the human bloodstream where they appear refractory to both immune elimination and thrombus formation. We hypothesize that parasite migration in the bloodstream can stress the vascular endothelium causing this tissue to release chemicals alerting responsive host cells to the stress. Such chemicals are called damage associated molecular patterns (DAMPs) and among the most potent is the proinflammatory mediator, adenosine triphosphate (ATP). Furthermore, the ATP derivative ADP is a pro-thrombotic molecule that acts as a strong activator of platelets. Schistosomes are reported to possess at their host interactive tegumental surface a series of enzymes that could, like their homologs in mammals, degrade extracellular ATP and ADP. These are alkaline phosphatase (SmAP), phosphodiesterase (SmNPP-5) and ATP diphosphohydrolase (SmATPDase1). In this work we employ RNAi to knock down expression of the genes encoding these enzymes in the intravascular life stages of the parasite. We then compare the abilities of these parasites to degrade exogenously added ATP and ADP. We find that only SmATPDase1-suppressed parasites are significantly impaired in their ability to degrade these nucleotides. Suppression of SmAP or SmNPP-5 does not appreciably affect the worms’ ability to catabolize ATP or ADP. These findings are confirmed by the functional characterization of the enzymatically active, full-length recombinant SmATPDase1 expressed in CHO-S cells. The enzyme is a true apyrase; SmATPDase1 degrades ATP and ADP in a cation dependent manner. Optimal activity is seen at alkaline pH. The Km of SmATPDase1 for ATP is 0.4 ± 0.02 mM and for ADP, 0.252 ± 0.02 mM. The results confirm the role of tegumental SmATPDase1 in the degradation of the exogenous pro-inflammatory and pro-thrombotic nucleotides ATP and ADP by live intravascular stages of the parasite. By degrading host inflammatory signals like ATP, and pro-thrombotic signals like ADP, these parasite enzymes may minimize host immune responses, inhibit blood coagulation and promote schistosome survival.
Da’dara et al. (2014) Schistosome tegumental ecto-apyrase (SmATPDase1) degrades exogenous pro-inflammatory and pro-thrombotic nucleotides. PeerJ 2:e316 https://doi.org/10.7717/peerj.316
TNR and conservation on a university campus: a political ecological perspective
How to manage the impact of free-ranging cats on native wildlife is a polarizing issue. Conservation biologists largely support domestic cat euthanasia to mitigate impacts of free-ranging cat predation on small animal populations. Above all else, animal welfare activists support the humane treatment of free-ranging cats, objecting to euthanasia. Clearly, this issue of how to control free-ranging cat predation on small animals is value laden, and both positions must be considered and comprehended to promote effective conservation. Here, two gaps in the free-ranging cat—small-animal conservation literature are addressed. First, the importance of understanding the processes of domestication and evolution and how each relates to felid behavioral ecology is discussed. The leading hypothesis to explain domestication of wildcats (Felis silvestris) relates to their behavioral ecology as a solitary predator, which made them suited for pest control in early agricultural villages of the Old World. The relationship humans once had with cats, however, has changed because today domesticated cats are usually household pets. As a result, concerns of conservation biologists may relate to cats as predators, but cat welfare proponents come from the position of assuming responsibility for free-ranging household pets (and their feral offspring). Thus, the perceptions of pet owners and other members of the general public provide an important context that frames the relationship between free-ranging cats and small animal conservation. The second part of this paper assesses the effects of an information-based conservation approach on shifting student’s perception of a local Trap–Neuter–Return (TNR) program in introductory core science classes at the University of North Texas (UNT). UNT students are (knowingly or unknowingly) regularly in close proximity to a TNR program on campus that supports cat houses and feeding stations. A survey design implementing a tailored-information approach was used to communicate what TNR programs are, their goals, and the “conservationist” view of TNR programs. We gauged favorability of student responses to the goals of TNR programs prior to and after exposure to tailored information on conservation concerns related to free-ranging cats. Although these results are from a preliminary study, we suggest that an information-based approach may only be marginally effective at shifting perceptions about the conservation implications of free-ranging cats. Our position is that small animal conservation in Western societies occurs in the context of pet ownership, thus broader approaches that promote ecological understanding via environmental education are more likely to be successful than information-based approaches.
Dombrosky et al. (2014) TNR and conservation on a university campus: a political ecological perspective. PeerJ 2:e312 https://doi.org/10.7717/peerj.312
Is coral richness related to community resistance to and recovery from disturbance?
More diverse communities are thought to be more stable—the diversity–stability hypothesis—due to increased resistance to and recovery from disturbances. For example, high diversity can make the presence of resilient or fast growing species and key facilitations among species more likely. How natural, geographic biodiversity patterns and changes in biodiversity due to human activities mediate community-level disturbance dynamics is largely unknown, especially in diverse systems. For example, few studies have explored the role of diversity in tropical marine communities, especially at large scales. We tested the diversity–stability hypothesis by asking whether coral richness is related to resistance to and recovery from disturbances including storms, predator outbreaks, and coral bleaching on tropical coral reefs. We synthesized the results of 41 field studies conducted on 82 reefs, documenting changes in coral cover due to disturbance, across a global gradient of coral richness. Our results indicate that coral reefs in more species-rich regions were marginally less resistant to disturbance and did not recover more quickly. Coral community resistance was also highly dependent on pre-disturbance coral cover, probably due in part to the sensitivity of fast-growing and often dominant plating acroporid corals to disturbance. Our results suggest that coral communities in biodiverse regions, such as the western Pacific, may not be more resistant and resilient to natural and anthropogenic disturbances. Further analyses controlling for disturbance intensity and other drivers of coral loss and recovery could improve our understanding of the influence of diversity on community stability in coral reef ecosystems.
Zhang et al. (2014) Is coral richness related to community resistance to and recovery from disturbance?. PeerJ 2:e308 https://doi.org/10.7717/peerj.308
Differential genotoxicity of diphenyl diselenide (PhSe)2 and diphenyl ditelluride (PhTe)2
Organoselenium compounds have been pointed out as therapeutic agents. In contrast, the potential therapeutic aspects of tellurides have not yet been demonstrated. The present study evaluated the comparative toxicological effects of diphenyl diselenide (PhSe)2 and diphenyl ditelluride (PhTe)2 in mice after in vivo administration. Genotoxicity (as determined by comet assay) and mutagenicicity were used as end-points of toxicity. Subcutaneous administration of high doses of (PhSe)2 or (PhTe)2 (500 µmol/kg) caused distinct genotoxicity in mice. (PhSe)2 significantly decreased the DNA damage index after 48 and 96 h of its injection (p < 0.05). In contrast, (PhTe) caused a significant increase in DNA damage (p < 0.05) after 48 and 96 h of intoxication. (PhSe)2 did not cause mutagenicity but (PhTe)2 increased the micronuclei frequency, indicating its mutagenic potential. The present study demonstrated that acute in vivo exposure to ditelluride caused genotoxicity in mice, which may be associated with pro-oxidant effects of diphenyl ditelluride. In addition, the use of this compound and possibly other related tellurides must be carefully controlled.
Meinerz et al. (2014) Differential genotoxicity of diphenyl diselenide (PhSe)2 and diphenyl ditelluride (PhTe)2. PeerJ 2:e290 https://doi.org/10.7717/peerj.290
Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors
The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system.
Fonin et al. (2014) Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors. PeerJ 2:e275 https://doi.org/10.7717/peerj.275
Religious attendance after elevated depressive symptoms: is selection bias at work?
In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group.
Balbuena et al. (2014) Religious attendance after elevated depressive symptoms: is selection bias at work?. PeerJ 2:e311 https://doi.org/10.7717/peerj.311
Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City
Severe fragmentation is a typical fate of native remnant habitats in cities, and urban wildlife with limited dispersal ability are predicted to lose genetic variation in isolated urban patches. However, little information exists on the characteristics of urban green spaces required to conserve genetic variation. In this study, we examine whether isolation in New York City (NYC) parks results in genetic bottlenecks in white-footed mice (Peromyscus leucopus), and test the hypotheses that park size and time since isolation are associated with genetic variability using nonlinear regression and information-theoretic model selection. White-footed mice have previously been documented to exhibit male-biased dispersal, which may create disparities in genetic variation between males and females in urban parks. We use genotypes of 18 neutral microsatellite data and four different statistical tests to assess this prediction. Given that sex-biased dispersal may create disparities between population genetic patterns inferred from bi- vs. uni-parentally inherited markers, we also sequenced a 324 bp segment of the mitochondrial D-loop for independent inferences of historical demography in urban P. leucopus. We report that isolation in urban parks does not necessarily result in genetic bottlenecks; only three out of 14 populations in NYC parks exhibited a signature of a recent bottleneck at 18 neutral microsatellite loci. Mouse populations in larger urban parks, or parks that have been isolated for shorter periods of time, also do not generally contain greater genetic variation than populations in smaller parks. These results suggest that even small networks of green spaces may be sufficient to maintain the evolutionary potential of native species with certain characteristics. We also found that isolation in urban parks results in weak to nonexistent sex-biased dispersal in a species known to exhibit male-biased dispersal in less fragmented environments. In contrast to nuclear loci, mitochondrial D-loop haplotypes exhibited a mutational pattern of demographic expansion after a recent bottleneck or selective sweep. Estimates of the timing of this expansion suggest that it occurred concurrent with urbanization of NYC over the last few dozens to hundreds of years. Given the general non-neutrality of mtDNA in many systems and evidence of selection on related coding sequences in urban P. leucopus, we argue that the P. leucopus mitochondrial genome experienced recent negative selection against haplotypes not favored in isolated urban parks. In general, rapid adaptive evolution driven by urbanization, global climate change, and other human-caused factors is underappreciated by evolutionary biologists, but many more cases will likely be documented in the near future.
Munshi-South et al. (2014) Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City. PeerJ 2:e310 https://doi.org/10.7717/peerj.310
Using a pacifier to decrease sudden infant death syndrome: an emergency department educational intervention
Background. Pacifier use decreases the risk of sudden infant death syndrome (SIDS). An emergency department (ED) visit may provide an opportunistic ‘teachable moment’ for parents. Objectives. To test the hypotheses (1) that caregivers were less familiar with the role of pacifiers in sudden infant death (SIDS) prevention than other recommendations, and (2) that an ED educational intervention would increase pacifier use in infants younger than six months, and (3) that otitis media would not occur more frequently in pacifier users. Methods. We did an intervention-group-only longitudinal study in a county hospital ED. We measured pacifier use infants and baseline knowledge of SIDs prevention recommendations in caregivers. We followed up three months later to determine pacifier use, and 12 months later to determine episodes of otitis media. Results. We analyzed data for 780 infants. Parents knew of advice against co-sleeping in 469/780 (60%), smoking in 660/776 (85%), and prone sleeping in 613/780 (79%). Only 268/777 (35%) knew the recommendation to offer a pacifier at bedtime. At enrollment 449/780 (58%) did not use a pacifier. Of 210/338 infants aged less than 6 months followed up 41/112 (37%) non-users had started using a pacifier at bedtime (NNT 3). Over the same period, 37/98 (38%) users had discontinued their pacifier. Otitis media did not differ between users and non-users at 12 months. Conclusion. Caregiver knowledge of the role of pacifiers in SIDS prevention was less than for other recommendations. Our educational intervention appeared to increase pacifier use. Pacifier use was not associated with increased otitis media.
Walsh et al. (2014) Using a pacifier to decrease sudden infant death syndrome: an emergency department educational intervention. PeerJ 2:e309 https://doi.org/10.7717/peerj.309
Evaluation of the effect of formalin fixation on skin specimens in dogs and cats
Skin and subcutaneous tissues are the origin of most common neoplasms affecting dogs, accounting for approximately one third of all tumors encountered in the species. Surgical excision is frequently the best chance for a cure; determining factors influencing the success of excision are vital for surgical management of cases. This work examined the shrinkage of skin of various lengths from three sites in formalin for both dogs and cats. Tissues were measured on the animal (initial measurement), at the time of excision (post-removal), and after formalin fixation (post-fixation). While shrinkage after tissue removal was found in samples from the thorax, abdomen, and rear leg in dogs and from the rear leg in cats, no significant shrinkage due to formalin fixation was detected in any sample except for the thoracic samples from the dog. Therefore, when determining where to make incisions to effect a surgical cure, initial measurements should take into account tissue shrinkage effects.
Miller et al. (2014) Evaluation of the effect of formalin fixation on skin specimens in dogs and cats. PeerJ 2:e307 https://doi.org/10.7717/peerj.307
Degree of adaptive response in urban tolerant birds shows influence of habitat-of-origin
Urban exploiters and adapters are often coalesced under a term of convenience as ‘urban tolerant’. This useful but simplistic characterisation masks a more nuanced interplay between and within assemblages of birds that are more or less well adapted to a range of urban habitats. I test the hypotheses that objectively-defined urban exploiter and suburban adapter assemblages within the broad urban tolerant grouping in Melbourne vary in their responses within the larger group to predictor variables, and that the most explanatory predictor variables vary between the two assemblages. A paired, partitioned analysis of exploiter and adapter preferences for points along the urban–rural gradient was undertaken to decompose the overall trend into diagnosable parts for each assemblage. In a similar way to that in which time since establishment has been found to be related to high urban densities of some bird species and biogeographic origin predictive of urban adaptation extent, habitat origins of members of bird assemblages influence the degree to which they become urban tolerant. Bird species that objectively classify as urban tolerant will further classify as either exploiters or adapters according to the degree of openness of their habitats-of-origin.
Conole (2014) Degree of adaptive response in urban tolerant birds shows influence of habitat-of-origin. PeerJ 2:e306 https://doi.org/10.7717/peerj.306
Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB)
The eukaryotic polypyrimidine tract binding protein (PTB) serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB) is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs). We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34) which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34). The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposite sides that face away from each other. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.
Joshi et al. (2014) Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB). PeerJ 2:e305 https://doi.org/10.7717/peerj.305
Description of the cascade of care and factors associated with attrition before and after initiating antiretroviral therapy of HIV infected children in a cohort study in India
In low- and middle-income countries, the attrition across the continuum of care of HIV infected children is not well known. The aim of this study was to investigate predictors of mortality and loss to follow up (LTFU) in HIV infected children from a cohort study in India and to describe the cascade of care from HIV diagnosis to virological suppression after antiretroviral therapy (ART) initiation. Multivariable analysis was performed using competing risk regression. The cumulative incidence of attrition due to mortality or LTFU after five year of follow-up was 16% from entry into care to ART initiation and 24.9% after ART initiation. Of all children diagnosed with HIV, it was estimated that 91.9% entered into care, 77.2% were retained until ART initiation, 58% stayed in care after ART initiation, and 43.4% achieved virological suppression on ART. Approximately half of the attrition occurred before ART initiation, and the other half after starting ART. Belonging to socially disadvantaged communities and living >90 min from the hospital were associated with a higher risk of attrition. Being >10 years old and having higher 12-month risk of AIDS (calculated using the absolute CD4 lymphocyte count and the age) were associated with an increased risk of mortality. These findings indicate that we should consider placing more emphasis on promoting research and implementing interventions to improve the engagement of HIV infected children in pre-ART care. The results of this study can be used by HIV programmes to design interventions aimed at reducing the attrition across the continuum of care of HIV infected children in India.
Alvarez-Uria (2014) Description of the cascade of care and factors associated with attrition before and after initiating antiretroviral therapy of HIV infected children in a cohort study in India. PeerJ 2:e304 https://doi.org/10.7717/peerj.304
Upward nitrate transport by phytoplankton in oceanic waters: balancing nutrient budgets in oligotrophic seas
In oceanic subtropical gyres, primary producers are numerically dominated by small (1–5 µm diameter) pro- and eukaryotic cells that primarily utilize recycled nutrients produced by rapid grazing turnover in a highly efficient microbial loop. Continuous losses of nitrogen (N) to depth by sinking, either as single cells, aggregates or fecal pellets, are balanced by both nitrate inputs at the base of the euphotic zone and N2-fixation. This input of new N to balance export losses (the biological pump) is a fundamental aspect of N cycling and central to understanding carbon fluxes in the ocean. In the Pacific Ocean, detailed N budgets at the time-series station HOT require upward transport of nitrate from the nutricline (80–100 m) into the surface layer (∼0–40 m) to balance productivity and export needs. However, concentration gradients are negligible and cannot support the fluxes. Physical processes can inject nitrate into the base of the euphotic zone, but the mechanisms for transporting this nitrate into the surface layer across many 10s of m in highly stratified systems are unknown. In these seas, vertical migration by the very largest (102–103 µm diameter) phytoplankton is common as a survival strategy to obtain N from sub-euphotic zone depths. This vertical migration is driven by buoyancy changes rather than by flagellated movement and can provide upward N transport as nitrate (mM concentrations) in the cells. However, the contribution of vertical migration to nitrate transport has been difficult to quantify over the required basin scales. In this study, we use towed optical systems and isotopic tracers to show that migrating diatom (Rhizosolenia) mats are widespread in the N. Pacific Ocean from 140°W to 175°E and together with other migrating phytoplankton (Ethmodiscus, Halosphaera, Pyrocystis, and solitary Rhizosolenia) can mediate time-averaged transport of N (235 µmol N m-2 d-1) equivalent to eddy nitrate injections (242 µmol NO3− m-2 d-1). This upward biotic transport can close N budgets in the upper 250 m of the central Pacific Ocean and together with diazotrophy creates a surface zone where biological nutrient inputs rather than physical processes dominate the new N flux. In addition to these numerically rare large migrators, there is evidence in the literature of ascending behavior in small phytoplankton that could contribute to upward flux as well. Although passive downward movement has dominated models of phytoplankton flux, there is now sufficient evidence to require a rethinking of this paradigm. Quantifying these fluxes is a challenge for the future and requires a reexamination of individual phytoplankton sinking rates as well as methods for capturing and enumerating ascending phytoplankton in the sea.
Villareal et al. (2014) Upward nitrate transport by phytoplankton in oceanic waters: balancing nutrient budgets in oligotrophic seas. PeerJ 2:e302 https://doi.org/10.7717/peerj.302
Brain size varies with temperature in vertebrates
The tremendous variation in brain size among vertebrates has long been thought to be related to differences in species’ metabolic rates. It is thought that species with higher metabolic rates can supply more energy to support the relatively high cost of brain tissue. And yet, while body temperature is known to be a major determinant of metabolic rate, the possible effects of temperature on brain size have scarcely been explored. Thus, here we explore the effects of temperature on brain size among diverse vertebrates (fishes, amphibians, reptiles, birds and mammals). We find that, after controlling for body size, brain size increases exponentially with temperature in much the same way as metabolic rate. These results suggest that temperature-dependent changes in aerobic capacity, which have long been known to affect physical performance, similarly affect brain size. The observed temperature-dependence of brain size may explain observed gradients in brain size among both ectotherms and endotherms across broad spatial and temporal scales.
Gillooly et al. (2014) Brain size varies with temperature in vertebrates. PeerJ 2:e301 https://doi.org/10.7717/peerj.301
Thirty years of coral reef change in relation to coastal construction and increased sedimentation at Pelekane Bay, Hawaiʻi
Coral reefs are being critically impacted by anthropogenic processes throughout the world. Long term monitoring is essential to the understanding of coral reef response to human impacts and the effectiveness of corrective management efforts. Here we reevaluated a valuable coral reef baseline established in Pelekane Bay, Hawaiʻi during 1976 and subsequently resurveyed in 1996. During this time interval substantial impacts occurred followed by extensive corrective measures. Coral and fish communities showed dramatic declines from 1977 to 1996 due to massive harbor construction and suboptimal land management practices on the watershed. More recently, corrective measures in the form of watershed stabilization and fishing regulations have been implemented. Consequently our 2012 survey reveals that coral cover since 1996 has increased slightly accompanied by a significant increase in fish abundance, diversity, and evenness. This improvement can be attributed to lower fishing pressure since 1996 due to reduced shoreline access, tighter fishing regulations and increased monitoring of legal and illegal fishing activities. Stabilization of the coral community can be attributed partially to reduced sedimentation resulting from watershed restoration that included installation of sediment check dams, control of feral ungulates, controlled grazing and replanting of native vegetation. Insights into the mechanism that removes sediment from reefs was provided by a major storm event and a tsunami that remobilized and flushed out sediment deposits. The increase in herbivorous fishes probably played a role in reducing algal competition in favor of corals. The data suggest that the precipitous reef decline in this area has been arrested and offers support for the corrective actions previously undertaken.
Stender et al. (2014) Thirty years of coral reef change in relation to coastal construction and increased sedimentation at Pelekane Bay, Hawaiʻi. PeerJ 2:e300 https://doi.org/10.7717/peerj.300
A review of the Zoogonidae (Digenea: Microphalloidea) from fishes of the waters around New Caledonia, with the description of Overstreetia cribbi n. sp.
New and published reports of zoogonid digeneans from New Caledonian waters are recorded, including a description of Overstreetia cribbi n. sp. from Atherinomorus lacunosus. This species differs from its congeners in the detail of its circum-oral spination and some metrical features. Other new records are of: Diphterostomum plectorhynchi Machida, Kamegai & Kuramochi, 2006 in Diagramma pictum; Parvipyrum acanthuri (Pritchard, 1963) in Acanthurus dussumieri; Zoogonoides viviparus (Olsson, 1868) in Lagocephalus sceleratus; Deretrema ? combesorum (Bray & Justine, 2008a; Bray & Justine, 2008b) early ovigerous forms in Parupeneus pleurostigma; D? acutum (Pritchard, 1963) in P. barberinus; and an unidentified immature zoogonid in P. multifasciatus. The newly reported specimens are illustrated and measurements given. The distribution of New Caledonian zoogonids is listed.
Bray et al. (2014) A review of the Zoogonidae (Digenea: Microphalloidea) from fishes of the waters around New Caledonia, with the description of Overstreetia cribbi n. sp.. PeerJ 2:e292 https://doi.org/10.7717/peerj.292
Evolutionary history determines how plant productivity responds to phylogenetic diversity and species richness
The relationship between biodiversity and ecosystem function has received a great deal of attention in ecological research and recent results, from re-analyses, suggest that ecosystem function improves with increases in phylogenetic diversity. However, many of these results have been generalized across a range of different species and clades, and plants with different evolutionary histories could display different relationships between biodiversity and ecosystem function. To experimentally test this hypothesis, we manipulated species richness and phylogenetic diversity using 26 species from two subgenera of the genus Eucalyptus (subgenus Eucalyptus and subgenus Symphyomyrtus). We found that plant biomass (a measurement of ecosystem function) sometimes, but not always, responded to increases in species richness and phylogenetic diversity. Specifically, Symphyomyrtus plants showed a positive response while no comparable effect was observed for Eucalyptus plants, showing that responses to biodiversity can vary across different phylogenetic groups. Our results show that the impacts of evolutionary history may complicate the relationship between the diversity of plant communities and plant biomass.
Genung et al. (2014) Evolutionary history determines how plant productivity responds to phylogenetic diversity and species richness. PeerJ 2:e288 https://doi.org/10.7717/peerj.288
Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software
State of the art high-throughput technologies allow comprehensive experimental studies of organism metabolism and induce the need for a convenient presentation of large heterogeneous datasets. Especially, the combined analysis and visualization of data from different high-throughput technologies remains a key challenge in bioinformatics. We present here the MarVis-Graph software for integrative analysis of metabolic and transcriptomic data. All experimental data is investigated in terms of the full metabolic network obtained from a reference database. The reactions of the network are scored based on the associated data, and sub-networks, according to connected high-scoring reactions, are identified. Finally, MarVis-Graph scores the detected sub-networks, evaluates them by means of a random permutation test and presents them as a ranked list. Furthermore, MarVis-Graph features an interactive network visualization that provides researchers with a convenient view on the results. The key advantage of MarVis-Graph is the analysis of reactions detached from their pathways so that it is possible to identify new pathways or to connect known pathways by previously unrelated reactions. The MarVis-Graph software is freely available for academic use and can be downloaded at: http://marvis.gobics.de/marvis-graph.
Landesfeind et al. (2014) Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PeerJ 2:e239 https://doi.org/10.7717/peerj.239
A happier and less sinister past, a more hedonistic and less fatalistic present and a more structured future: time perspective and well-being
Background. Previous studies have established a link between how people relate to their past, present, and future (i.e., time perspective) and subjective well-being (i.e., life satisfaction, positive and negative affect). Time perspective comprises five dimensions: Past Positive, Past Negative, Present Hedonistic, Present Fatalistic, and Future. Life satisfaction can also be evaluated in relation to different time frames. Moreover, approach related positive affect is associated to a different concept of well-being labeled psychological well-being. In the present study we extend previous findings by investigating the effect of time perspective on the time frame of evaluations of life satisfaction (past, present, future) and by investigating the relationship between time perspective and psychological well-being. Method. Questionnaires on time perspective (Zimbardo’s Time Perspective Inventory), temporal life satisfaction (Temporal Satisfaction with Life Scale), affect (Positive Affect and Negative Affect Schedule), and psychological well-being (Scales of Psychological Well-Being—short version) were answered by 453 individuals. Two different structural equation models were tested, one of the relationship between time perspective and temporal life satisfaction, and the other of the relationship between time perspective, affect and psychological well-being. Results. Time perspective affected life satisfaction depending on the time scale on which it was evaluated—memory of a negative past influenced life satisfaction in all time frames, and a positive view of the past influenced both past and future life satisfaction. Moreover, less rumination about past negative events (i.e., low score on Past Negative), the tendency to take risks in the present to achieve happy feelings and/or avoid boredom (i.e., high scores on Present Hedonistic), and a less hopeless and pessimistic view about the present (low scores on Present Fatalistic) were associated with higher levels of psychological well-being and positive affect. These same time perspective dimensions were associated with lower levels of negative affect. The Future time perspective dimension (i.e., approaching life with self-control, punctuality, and planning for the future) was associated with both psychological well-being and positive affect. Conclusions. High levels of both subjective and psychological well-being are related to a happier and a less sinister past, a more hedonistic and less fatalistic present, as well as to a more structured future.
Sailer et al. (2014) A happier and less sinister past, a more hedonistic and less fatalistic present and a more structured future: time perspective and well-being. PeerJ 2:e303 https://doi.org/10.7717/peerj.303
The role of transcriptional regulation in maintaining the availability of mycobacterial adenylate cyclases
Mycobacterium species have a complex cAMP regulatory network indicated by the high number of adenylate cyclases annotated in their genomes. However the need for a high level of redundancy in adenylate cyclase genes remains unknown. We have used semiquantitiative RT-PCR to examine the expression of eight Mycobacterium smegmatis cyclases with orthologs in the human pathogen Mycobacterium tuberculosis, where cAMP has recently been shown to be important for virulence. All eight cyclases were transcribed in all environments tested, and only four demonstrated environmental-mediated changes in transcription. M. smegmatis genes MSMEG_0545 and MSMEG_4279 were upregulated during starvation conditions while MSMEG_0545 and MSMEG_4924 were downregulated in H2O2 and MSMEG_3780 was downregulated in low pH and starvation. Promoter fusion constructs containing M. tuberculosis H37Rv promoters showed consistent regulation compared to their M. smegmatis orthologs. Overall our findings indicate that while low levels of transcriptional regulation occur, regulation at the mRNA level does not play a major role in controlling cellular cyclase availability in a given environment.
Casey et al. (2014) The role of transcriptional regulation in maintaining the availability of mycobacterial adenylate cyclases. PeerJ 2:e298 https://doi.org/10.7717/peerj.298
Ecological distribution of protosteloid amoebae in New Zealand
During the period of March 2004 to December 2007, samples of aerial litter (dead but still attached plant parts) and ground litter (dead plant material on the ground) were collected from 81 study sites representing a wide range of latitudes (34°S to 50°S) and a variety of different types of habitats throughout New Zealand (including Stewart Island and the Auckland Islands). The objective was to survey the assemblages of protosteloid amoebae present in this region of the world. Twenty-nine described species of protosteloid amoebae were recorded by making morphological identifications of protosteloid amoebae fruiting bodies on cultured substrates. Of the species observed, Protostelium mycophaga was by far the most abundant and was found in more than half of all samples. Most species were found in fewer than 10% of the samples collected. Seven abundant or common species were found to display significantly increased likelihood for detection in aerial litter or ground litter microhabitats. There was some evidence of a general correlation between environmental factors - annual precipitation, elevation, and distance from the equator (latitude) - and the abundance and richness of protosteloid amoebae. An increase in each of these three factors correlated with a decrease in both abundance and richness. This study provides a thorough survey of the protosteloid amoebae present in New Zealand and adds to a growing body of evidence which suggests several correlations between their broad distributional patterns and environmental factors.
Zahn et al. (2014) Ecological distribution of protosteloid amoebae in New Zealand. PeerJ 2:e296 https://doi.org/10.7717/peerj.296
The avian fossil record in Insular Southeast Asia and its implications for avian biogeography and palaeoecology
Excavations and studies of existing collections during the last decades have significantly increased the abundance as well as the diversity of the avian fossil record for Insular Southeast Asia. The avian fossil record covers the Eocene through the Holocene, with the majority of bird fossils Pleistocene in age. Fossil bird skeletal remains represent at least 63 species in 54 genera and 27 families, and two ichnospecies are represented by fossil footprints. Birds of prey, owls and swiftlets are common elements. Extinctions seem to have been few, suggesting continuity of avian lineages since at least the Late Pleistocene, although some shifts in species ranges have occurred in response to climatic change. Similarities between the Late Pleistocene avifaunas of Flores and Java suggest a dispersal route across southern Sundaland. Late Pleistocene assemblages of Niah Cave (Borneo) and Liang Bua (Flores) support the rainforest refugium hypothesis in Southeast Asia as they indicate the persistence of forest cover, at least locally, throughout the Late Pleistocene and Holocene.
Meijer (2014) The avian fossil record in Insular Southeast Asia and its implications for avian biogeography and palaeoecology. PeerJ 2:e295 https://doi.org/10.7717/peerj.295
Happy software developers solve problems better: psychological measurements in empirical software engineering
For more than thirty years, it has been claimed that a way to improve software developers’ productivity and software quality is to focus on people and to provide incentives to make developers satisfied and happy. This claim has rarely been verified in software engineering research, which faces an additional challenge in comparison to more traditional engineering fields: software development is an intellectual activity and is dominated by often-neglected human factors (called human aspects in software engineering research). Among the many skills required for software development, developers must possess high analytical problem-solving skills and creativity for the software construction process. According to psychology research, affective states—emotions and moods—deeply influence the cognitive processing abilities and performance of workers, including creativity and analytical problem solving. Nonetheless, little research has investigated the correlation between the affective states, creativity, and analytical problem-solving performance of programmers. This article echoes the call to employ psychological measurements in software engineering research. We report a study with 42 participants to investigate the relationship between the affective states, creativity, and analytical problem-solving skills of software developers. The results offer support for the claim that happy developers are indeed better problem solvers in terms of their analytical abilities. The following contributions are made by this study: (1) providing a better understanding of the impact of affective states on the creativity and analytical problem-solving capacities of developers, (2) introducing and validating psychological measurements, theories, and concepts of affective states, creativity, and analytical-problem-solving skills in empirical software engineering, and (3) raising the need for studying the human factors of software engineering by employing a multidisciplinary viewpoint.
Graziotin et al. (2014) Happy software developers solve problems better: psychological measurements in empirical software engineering. PeerJ 2:e289 https://doi.org/10.7717/peerj.289
Ant-mediated seed dispersal in a warmed world
Climate change affects communities both directly and indirectly via changes in interspecific interactions. One such interaction that may be altered under climate change is the ant-plant seed dispersal mutualism common in deciduous forests of eastern North America. As climatic warming alters the abundance and activity levels of ants, the potential exists for shifts in rates of ant-mediated seed dispersal. We used an experimental temperature manipulation at two sites in the eastern US (Harvard Forest in Massachusetts and Duke Forest in North Carolina) to examine the potential impacts of climatic warming on overall rates of seed dispersal (using Asarum canadense seeds) as well as species-specific rates of seed dispersal at the Duke Forest site. We also examined the relationship between ant critical thermal maxima (CTmax) and the mean seed removal temperature for each ant species. We found that seed removal rates did not change as a result of experimental warming at either study site, nor were there any changes in species-specific rates of seed dispersal. There was, however, a positive relationship between CTmax and mean seed removal temperature, whereby species with higher CTmax removed more seeds at hotter temperatures. The temperature at which seeds were removed was influenced by experimental warming as well as diurnal and day-to-day fluctuations in temperature. Taken together, our results suggest that while temperature may play a role in regulating seed removal by ants, ant plant seed-dispersal mutualisms may be more robust to climate change than currently assumed.
Stuble et al. (2014) Ant-mediated seed dispersal in a warmed world. PeerJ 2:e286 https://doi.org/10.7717/peerj.286
Personality predicts the propensity for social learning in a wild primate
Social learning can play a critical role in the reproduction and survival of social animals. Individual differences in the propensity for social learning are therefore likely to have important fitness consequences. We asked whether personality might underpin such individual variation in a wild population of chacma baboons (Papio ursinus). We used two field experiments in which individuals had the opportunity to learn how to solve a task from an experienced conspecific demonstrator: exploitation of a novel food and a hidden item of known food. We investigated whether the (1) time spent watching a demonstrator and (2) changes in task-solving behaviour after watching a demonstrator were related to personality. We found that both boldness and anxiety influenced individual performance in social learning. Specifically, bolder and more anxious animals were more likely to show a greater improvement in task solving after watching a demonstrator. In addition, there was also evidence that the acquisition of social information was not always correlated with its use. These findings present new insights into the costs and benefits of different personality types, and have important implications for the evolution of social learning.
Carter et al. (2014) Personality predicts the propensity for social learning in a wild primate. PeerJ 2:e283 https://doi.org/10.7717/peerj.283
Occurrence of twin embryos in the eastern bluebird
We report the first record of presumed twinning in eastern bluebird (Sialia sialis) and provide a review of previously reported twinning events in wild birds. A nest containing twin eastern bluebird nestlings was monitored in 2013 in central Pennsylvania and reported to the Cornell Lab of Ornithology’s NestWatch program, a national program where volunteers submit data on wild nesting birds. A presumed double-yolked egg of a free-living eastern bluebird pair hatched successfully, and twin nestlings lived for 11 days in a nest box shared by three siblings. Due to the rarity of twinning in wild birds, engaging the public to monitor large numbers of nests is the most likely approach to documenting twinning in wild populations, and citizen science provides the infrastructure for individuals to share observations.
Bailey et al. (2014) Occurrence of twin embryos in the eastern bluebird. PeerJ 2:e273 https://doi.org/10.7717/peerj.273
Disturbance and climatic effects on red spruce community dynamics at its southern continuous range margin
Red spruce (Picea rubens) populations experienced a synchronous rangewide decline in growth and vigor starting in the 1960s, likely caused by climate change and a combination of environmental disturbances. However, it is not yet known if populations continue to decline or have recovered. Red spruce growing near its southern range margin in Massachusetts is a species of concern, in light of the vulnerability to climate change. This study uses population data from 17 permanent plots coupled with tree-ring data to examine radial growth rates, determine the growth-climate relationship, and document disturbance events. Red spruce at these plots ranged from 90 to 184 years old, and comprised 15 to 29 m2/ha basal area. Red spruce seedlings and saplings were common at plots with previously high overstory spruce abundance, indicating it could return to a more dominant position under favorable growing conditions. However, permanent plot measures over a 50 year time span did not indicate any consistent trends for changes in basal area or density for red spruce or other woody species. Climate data show that mean annual minimum, maximum, and summer temperatures have increased over the last 100 years. Dendroclimatological analyses indicated that red spruce growth was sensitive to both temperature and precipitation. Prior to the 1960s, spruce at these sites showed a positive response to precipitation; however after a multi-year drought in the 1960s showed an increasingly negative correlation with precipitation. There has been a negative growth response to regional warming, as spruce radial growth was mostly constrained by increasing temperatures, potentially coupled with the associated increasing drought-dress. I suggest the change in climate response is potentially due to a physiological threshold response to increasing temperatures, which may cause spruce to continue to decline or be lost from the lower elevation sites, while the high elevation sites has a persistent spruce population.
Ribbons (2014) Disturbance and climatic effects on red spruce community dynamics at its southern continuous range margin. PeerJ 2:e293 https://doi.org/10.7717/peerj.293
‘Mystery big cats’ in the Peruvian Amazon: morphometrics solve a cryptozoological mystery
Two big cat skulls procured from hunters of Yanachaga National Park, Peru, were reported as those of cats informally dubbed the ‘striped tiger’ and ‘anomalous jaguar’. Observations suggested that both skulls were distinct from those of jaguars, associated descriptions of integument did not conform to this species, and it has been implied that both represent members of one or two novel species. We sought to resolve the identity of the skulls using morphometrics. DNA could not be retrieved since both had been boiled as part of the defleshing process. We took 36 cranial and 13 mandibular measurements and added them to a database incorporating nearly 300 specimens of over 30 felid species. Linear discriminant analysis resolved both specimens as part of Panthera onca with high probabilities for cranial and mandibular datasets. Furthermore, the specimens exhibit characters typical of jaguars. If the descriptions of their patterning and pigmentation are accurate, we assume that both individuals were aberrant.
Naish et al. (2014) ‘Mystery big cats’ in the Peruvian Amazon: morphometrics solve a cryptozoological mystery. PeerJ 2:e291 https://doi.org/10.7717/peerj.291
Gamma-H2AX biodosimetry for use in large scale radiation incidents: comparison of a rapid ‘96 well lyse/fix’ protocol with a routine method
Following a radiation incident, preliminary dose estimates made by γ-H2AX foci analysis can supplement the early triage of casualties based on clinical symptoms. Sample processing time is important when many individuals need to be rapidly assessed. A protocol was therefore developed for high sample throughput that requires less than 0.1 ml blood, thus potentially enabling finger prick sampling. The technique combines red blood cell lysis and leukocyte fixation in one step on a 96 well plate, in contrast to the routine protocol, where lymphocytes in larger blood volumes are typically separated by Ficoll density gradient centrifugation with subsequent washing and fixation steps. The rapid ‘96 well lyse/fix’ method reduced the estimated sample processing time for 96 samples to about 4 h compared to 15 h using the routine protocol. However, scoring 20 cells in 96 samples prepared by the rapid protocol took longer than for the routine method (3.1 versus 1.5 h at zero dose; 7.0 versus 6.1 h for irradiated samples). Similar foci yields were scored for both protocols and consistent dose estimates were obtained for samples exposed to 0, 0.2, 0.6, 1.1, 1.2, 2.1 and 4.3 Gy of 250 kVp X-rays at 0.5 Gy/min and incubated for 2 h. Linear regression coefficients were 0.87 ± 0.06 (R2 = 97.6%) and 0.85 ± 0.05 (R2 = 98.3%) for estimated versus actual doses for the routine and lyse/fix method, respectively. The lyse/fix protocol can therefore facilitate high throughput processing for γ-H2AX biodosimetry for use in large scale radiation incidents, at the cost of somewhat longer foci scoring times.
Moquet et al. (2014) Gamma-H2AX biodosimetry for use in large scale radiation incidents: comparison of a rapid ‘96 well lyse/fix’ protocol with a routine method. PeerJ 2:e282 https://doi.org/10.7717/peerj.282
Artificial light and nocturnal activity in gammarids
Artificial light is gaining attention as a potential stressor to aquatic ecosystems. Artificial lights located near streams increase light levels experienced by stream invertebrates and we hypothesized light would depress night drift rates. We also hypothesized that the effect of light on drift rates would decrease over time as the invertebrates acclimated to the new light level over the course of one month’s exposure. These hypotheses were tested by placing Gammarus spp. in eight, 75 m × 1 m artificial flumes. One flume was exposed to strong (416 lx) artificial light at night. This strong light created a gradient between 4.19 and 0.04 lx over the neighboring six artificial flumes, while a control flume was completely covered with black plastic at night. Night-time light measurements taken in the Berlin area confirm that half the flumes were at light levels experienced by urban aquatic invertebrates. Surprisingly, no light treatment affected gammarid drift rates. In contrast, physical activity measurements of in situ individually caged G. roeseli showed they increased short-term activity levels in nights of complete darkness and decreased activity levels in brightly lit flumes. Both nocturnal and diurnal drift increased, and day drift rates were unexpectadly higher than nocturnal drift.
Perkin et al. (2014) Artificial light and nocturnal activity in gammarids. PeerJ 2:e279 https://doi.org/10.7717/peerj.279
Success rate of IR midazolam sedation in combination with C-CLAD in pediatric dental patients—a prospective observational study
Objective. To evaluate the success rate of intra-rectal (IR) midazolam in combination with nitrous oxide/oxygen (N2O) sedation in young uncooperative dental patients when the local anesthesia is delivered by a computerized controlled local anesthetic delivery (C-CLAD). Study Design. This observational study consisted of 219 uncooperative children (age: 4.3 ± 1.69 y) who received IR midazolam (0.4 mg/kg) and N2O to complete their dental treatment. Measured variables included: child’s pain disruptive behavior during delivery of anesthesia by C-CLAD (CHEOP Scale), child behavior during treatment (Houpt scale), dental procedure performed, and side effects that appeared during treatment. Results. There was a high level of cooperation (mean score: 6.69 ± 2.1) during administration of local anesthesia. Good-to-excellent behavior was shown by 87% of the children during treatment. Planned treatment was completed by 184 (92%) patients. No statistically significant changes were noticed in the oxygen saturation levels before and after treatment. Children with side effects included 3 (1.3%) with nistagmus, 5 (2.3%) with diplopia, and 18 (8.2%) with hiccups. Three consecutive sedations decreased the overall behavior score by 5.7% compared to the first appointment (p < .05). Conclusions. IR midazolam-N2O sedation in combination with C-CLAD is very effective for delivery of dental treatment to young uncooperative children.
Ashkenazi et al. (2014) Success rate of IR midazolam sedation in combination with C-CLAD in pediatric dental patients—a prospective observational study. PeerJ 2:e254 https://doi.org/10.7717/peerj.254
The invasive New Guinea flatworm Platydemus manokwari in France, the first record for Europe: time for action is now
Non-indigenous terrestrial flatworms (Platyhelminthes) have been recorded in thirteen European countries. They include Bipalium kewense and Dolichoplana striata that are largely restricted to hothouses and may be regarded as non-invasive species. In addition there are species from the southern hemisphere such as the invasive New Zealand flatworm Arthurdendyus triangulatus in the United Kingdom, Eire and the Faroe Islands, the Australian flatworm Australoplana sanguinea alba in Eire and the United Kingdom, and the Australian Blue Garden flatworm Caenoplana coerulea in France, Menorca and the United Kingdom. The United Kingdom has some twelve or more non-indigenous species most of which are Australian and New Zealand species. These species may move to an invasive stage when optimum environmental and other conditions occur, and the flatworms then have the potential to cause economic or environmental harm. In this paper, we report the identification (from morphology and molecular analysis of COI sequences) of non-indigenous terrestrial flatworms found in a hothouse in Caen (France) as the New Guinea flatworm Platydemus manokwari de Beauchamp, 1963 (Platyhelminthes, Continenticola, Geoplanidae, Rhynchodeminae). Platydemus manokwari is among the “100 World’s Worst Invader Alien Species”. Lists of World geographic records, prey in the field and prey in laboratories of P. manokwari are provided. This species is considered a threat to native snails wherever it is introduced. The recent discovery of P. manokwari in France represents a significant extension of distribution of this Invasive Alien Species from the Indo-Pacific region to Europe. If it escaped the hothouse, the flatworm might survive winters and become established in temperate countries. The existence of this species in France requires an early warning of this incursion to State and European Union authorities, followed by the eradication of the flatworm in its locality, tightening of internal quarantine measures to prevent further spread of the flatworm to and from this site, identifying if possible the likely primary source of the flatworm, and tracing other possible incursions that may have resulted from accidental dispersal of plants and soil from the site.
Justine et al. (2014) The invasive New Guinea flatworm Platydemus manokwari in France, the first record for Europe: time for action is now. PeerJ 2:e297 https://doi.org/10.7717/peerj.297
Adult neurobehavioral outcome of hyperbilirubinemia in full term neonates—a 30 year prospective follow-up study
Background. Neonatal hyperbilirubinemia (HB) may cause severe neurological damage, but serious consequences are effectively controlled by phototherapy and blood exchange transfusion. HB is still a serious health problem in economically compromised parts of the world. The long term outcome has been regarded favorable based on epidemiological data, but has not been confirmed in prospective follow-up studies extending to adulthood. Methods. We studied the long term consequences of HB in a prospective birth cohort of 128 HB cases and 82 controls. The cases are part of a neonatal at-risk cohort (n = 1196) that has been followed up to 30 years of age. HB cases were newborns ≥ 2500 g birth weight and ≥ 37 weeks of gestation who had bilirubin concentrations > 340 µmol/l or required blood exchange transfusion. Subjects with HB were divided into subgroups based on the presence (affected HB) or absence (unaffected HB) of diagnosed neurobehavioral disorders in childhood, and compared with healthy controls. Subjects were seen at discharge, 5, 9 and 16 years of life and parent’s and teacher’s assessments were recorded. At 30 years they filled a questionnaire about academic and occupational achievement, life satisfaction, somatic and psychiatric symptoms including a ADHD self-rating score. Cognitive functioning was tested using ITPA, WISC, and reading and writing tests at 9 years of life. Results. Compared to controls, the odds for a child with HB having neurobehavioral symptoms at 9 years was elevated (OR = 4.68). Forty-five per cent of the HB group were affected by cognitive abnormalities in childhood and continued to experience problems in adulthood. This was apparent in academic achievement (p < 0.0001) and the ability to complete secondary (p < 0.0001) and tertiary (p < 0.004) education. Also, the subgroup of affected HB reported persisting cognitive complaints e.g., problems with reading, writing and mathematics. Childhood symptoms of hyperactivity/impulsivity (p < 0.0001) and inattention (p < 0.02) were more common in HB groups, but in adulthood the symptoms were equal. The affected HB had lower scores in parameters reflecting life satisfaction, less controlled drinking, but not increased substance abuse. Discussion. Our results indicate that neonatal HB has negative consequences in adult age. A prospectively collected cohort with strict inclusion criteria enables to control most of the bias factors involved with retrospective data. The control and HB groups were remarkably similar at birth in terms of medical data, and the growth environment of the children, as well as the parents’ social groups, education, size of family, type of housing at birth and at 9 years of age. Our findings bear resemblance to disorders of the fronto-striatal network, and also symptoms of the ADHD spectrum were frequent in the HB group suggesting a link of HB to other neurodevelopmental disorders.
Hokkanen et al. (2014) Adult neurobehavioral outcome of hyperbilirubinemia in full term neonates—a 30 year prospective follow-up study. PeerJ 2:e294 https://doi.org/10.7717/peerj.294
Disorder affects judgements about a neighbourhood: police presence does not
Many police forces operate a policy of high visibility in disordered neighbourhoods with high crime. However, little is known about whether increased police presence influences people’s beliefs about a neighbourhood’s social environment or their fear of crime. Three experimental studies compared people’s perceptions of social capital and fear of crime in disordered and ordered neighbourhoods, either with a police presence or no police presence. In all studies, neighbourhood disorder lowered perceptions of social capital, resulting in a higher fear of crime. Police presence or absence had no significant effect. The pervasive effects of disorder above other environmental cues are discussed.
Hill et al. (2014) Disorder affects judgements about a neighbourhood: police presence does not. PeerJ 2:e287 https://doi.org/10.7717/peerj.287
Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions
Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was “too low” in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be focused on quantitative disciplines, which is likely higher than for most existing programs. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require dedicated, quantitative classes for ecology-related degrees that contain good mathematical and statistical practice.
Barraquand et al. (2014) Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions. PeerJ 2:e285 https://doi.org/10.7717/peerj.285
Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.
Kamvar et al. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281 https://doi.org/10.7717/peerj.281
Expression profiles of the immune genes CD4, CD8β, IFNγ, IL-4, IL-6 and IL-10 in mitogen-stimulated koala lymphocytes (Phascolarctos cinereus) by qRT-PCR
Investigation of the immune response of the koala (Phascolarctos cinereus) is needed urgently, but has been limited by scarcity of species-specific reagents and methods for this unique and divergent marsupial. Infectious disease is an important threat to wild populations of koalas; the most widespread and important of these is Chlamydial disease, caused by Chlamydia pecorum and Chlamydia pneumoniae. In addition, koala retrovirus (KoRV), which is of 100% prevalence in northern Australia, has been proposed as an important agent of immune suppression that could explain the koala’s susceptibility to disease. The correct balance of T regulatory, T helper 1 (Th1) and Th2 lymphocyte responses are important to an individual’s susceptibility or resistance to chlamydial infection. The ability to study chlamydial or KoRV pathogenesis, effects of environmental stressors on immunity, and the response of koalas to vaccines under development, by examining the koala’s adaptive response to natural infection or in-vitro stimulation, has been limited to date by a paucity of species- specific reagents. In this study we have used cytokine sequences from four marsupial genomes to identify mRNA sequences for key T regulatory, Th1 and Th2 cytokines interleukin 4 (IL-4), interleukin 6 (IL-6), interleukin 10 (IL-10) and interferon gamma (IFNγ) along with CD4 and CD8β. The koala sequences used for primer design showed >58% homology with grey short-tailed opossum, >71% with tammar wallaby and 78% with Tasmanian devil amino acid sequences. We report the development of real-time RT-PCR assays to measure the expression of these genes in unstimulated cells and after three common mitogen stimulation protocols (phorbol myristate acetate/ionomycin, phorbol myristate acetate/phytohemagglutinin and concanavalin A). Phorbol myristate acetate/ionomycin was found to be the most effective mitogen to up-regulate the production of IL-4, IL-10 and IFNγ. IL-6 production was not consistently up-regulated by any of the protocols. Expression of CD4 and CD8β was down-regulated by mitogen stimulation. We found that the reference genes GAPDH and 28s are valid for normalising cytokine expression by koala lymphocytes after mitogen stimulation.
Maher et al. (2014) Expression profiles of the immune genes CD4, CD8β, IFNγ, IL-4, IL-6 and IL-10 in mitogen-stimulated koala lymphocytes (Phascolarctos cinereus) by qRT-PCR. PeerJ 2:e280 https://doi.org/10.7717/peerj.280
FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models
We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.
Christensen et al. (2014) FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models. PeerJ 2:e277 https://doi.org/10.7717/peerj.277
Morphological traits: predictable responses to macrohabitats across a 300 km scale
Species traits may provide a short-cut to predicting generalities in species turnover in response to environmental change, particularly for poorly known taxa. We ask if morphological traits of assemblages respond predictably to macrohabitats across a large scale. Ant assemblages were collected at nine paired pasture and remnant sites from within three areas along a 300 km distance. We measured ten functional morphological traits for replicate individuals of each species. We used a fourth corner model to test associations between microhabitat variables, macrohabitats (pastures and remnants) and traits. In addition, we tested the phylogenetic independence of traits, to determine if responses were likely to be due to filtering by morphology or phylogeny. Nine of ten traits were predicted by macrohabitat and the majority of these traits were independent of phylogeny. Surprisingly, microhabitat variables were not associated with morphological traits. Traits which were associated with macrohabitats were involved in locomotion, feeding behaviour and sensory ability. Ants in remnants had more maxillary palp segments, longer scapes and wider eyes, while having shorter femurs, smaller apical mandibular teeth and shorter Weber’s lengths. A clear relationship between traits and macrohabitats across a large scale suggests that species are filtered by coarse environmental differences. In contrast to the findings of previous studies, fine-scale filtering of morphological traits was not apparent. If such generalities in morphological trait responses to habitat hold across even larger scales, traits may prove critical in predicting the response of species assemblages to global change.
Yates et al. (2014) Morphological traits: predictable responses to macrohabitats across a 300 km scale. PeerJ 2:e271 https://doi.org/10.7717/peerj.271