title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1785 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A new species of Brachycephalus (Anura: Brachycephalidae) from Santa Catarina, southern Brazil link: https://peerj.com/articles/2629 last-modified: 2016-10-27 description: A new species of Brachycephalus (Anura: Brachycephalidae) is described from the Atlantic Forest of northeastern state of Santa Catarina, southern Brazil. Nine specimens (eight adults and a juvenile) were collected from the leaf litter of montane forests 790–835 m above sea level (a.s.l.). The new species is a member of the pernix group by its bufoniform shape and the absence of dermal co-ossification and is distinguished from all its congeners by a combination of its general coloration (dorsal region of head, dorsum, legs, arms, and flanks light, brownish green to dark, olive green, with darker region in the middle of the dorsum and a white line along the vertebral column in most specimens) and by its smooth dorsum. The geographical distribution of the new species is highly reduced (extent of occurrence estimated as 25.04 ha, or possibly 34.37 ha). In addition, its habitat has experienced some level of degradation, raising concerns about the future conservation of the species. Preliminary density estimates suggest one calling individual every 3–4 m2 at 815–835 m a.s.l. and every 100 m2 at 790 m a.s.l. Together with the recently described B. boticario and B. fuscolineatus, the new species is among the southernmost species of Brachycephalus known to date. creator: Marcos R. Bornschein creator: Luiz F. Ribeiro creator: David C. Blackburn creator: Edward L. Stanley creator: Marcio R. Pie uri: https://doi.org/10.7717/peerj.2629 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bornschein et al. title: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse) link: https://peerj.com/articles/2617 last-modified: 2016-10-27 description: Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens) of Peromyscus eremicus (Cactus mouse), a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse) and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss. creator: Lauren L. Kordonowy creator: Matthew D. MacManes uri: https://doi.org/10.7717/peerj.2617 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kordonowy and MacManes title: Synthetic lung surfactants containing SP-B and SP-C peptides plus novel phospholipase-resistant lipids or glycerophospholipids link: https://peerj.com/articles/2635 last-modified: 2016-10-27 description: BackgroundThis study examines the biophysical and preclinical pulmonary activity of synthetic lung surfactants containing novel phospholipase-resistant phosphonolipids or synthetic glycerophospholipids combined with Super Mini-B (S-MB) DATK and/or SP-Css ion-lock 1 peptides that replicate the functional biophysics of surfactant proteins (SP)-B and SP-C. Phospholipase-resistant phosphonolipids used in synthetic surfactants are DEPN-8 and PG-1, molecular analogs of dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG), while glycerophospholipids used are active lipid components of native surfactant (DPPC:POPC:POPG 5:3:2 by weight). The objective of the work is to test whether these novel lipid/peptide synthetic surfactants have favorable preclinical activity (biophysical, pulmonary) for therapeutic use in reversing surfactant deficiency or dysfunction in lung disease or injury.MethodsSurface activity of synthetic lipid/peptide surfactants was assessed in vitro at 37 °C by measuring adsorption in a stirred subphase apparatus and dynamic surface tension lowering in pulsating and captive bubble surfactometers. Shear viscosity was measured as a function of shear rate on a Wells-Brookfield micro-viscometer. In vivo pulmonary activity was determined by measuring lung function (arterial oxygenation, dynamic lung compliance) in ventilated rats and rabbits with surfactant deficiency/dysfunction induced by saline lavage to lower arterial PO2 to <100 mmHg, consistent with clinical acute respiratory distress syndrome (ARDS).ResultsSynthetic surfactants containing 5:3:2 DPPC:POPC:POPG or 9:1 DEPN-8:PG-1 combined with 3% (by wt) of S-MB DATK, 3% SP-Css ion-lock 1, or 1.5% each of both peptides all adsorbed rapidly to low equilibrium surface tensions and also reduced surface tension to ≤1 mN/m under dynamic compression at 37 °C. However, dual-peptide surfactants containing 1.5% S-MB DATK + 1.5% SP-Css ion-lock 1 combined with 9:1 DEPN-8:PG-1 or 5:3:2 DPPC:POPC:POPG had the greatest in vivo activity in improving arterial oxygenation and dynamic lung compliance in ventilated animals with ARDS. Saline dispersions of these dual-peptide synthetic surfactants were also found to have shear viscosities comparable to or below those of current animal-derived surfactant drugs, supporting their potential ease of deliverability by instillation in future clinical applications.DiscussionOur findings support the potential of dual-peptide synthetic lipid/peptide surfactants containing S-MB DATK + SP-Css ion-lock 1 for treating diseases of surfactant deficiency or dysfunction. Moreover, phospholipase-resistant dual-peptide surfactants containing DEPN-8/PG-1 may have particular applications in treating direct forms of ARDS where endogenous phospholipases are present in the lungs. creator: Robert H. Notter creator: Rohun Gupta creator: Adrian L. Schwan creator: Zhengdong Wang creator: Mohanad Gh Shkoor creator: Frans J. Walther uri: https://doi.org/10.7717/peerj.2635 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Notter et al. title: Risk and clinical predictors of osteoporotic fracture in East Asian patients with chronic obstructive pulmonary disease: a population-based cohort study link: https://peerj.com/articles/2634 last-modified: 2016-10-27 description: IntroductionOsteoporosis is becoming an impending epidemic in the Asia-Pacific region. The association between risk of osteoporotic fracture (OTPF) and chronic obstructive pulmonary disease (COPD) in East Asian patients is yet to be fully examined. We conducted a nationwide population-based retrospective cohort study of 98,700 patients aged ≥50 years with or without COPD using a national administrative claims dataset.Materials and MethodsThe patients were divided into COPD and comparison groups comprising 19,740 and 78,960 patients, respectively. The groups were 1 to 4 matched for age, gender, index date, diabetes mellitus, pre-existing osteoporosis and chronic kidney disease. Information such as the geographic area where southern part represented more sunshine exposure, smoking-related diagnoses, alcohol use disorder, whether there was regular use of inhaled corticosteroids and oral corticosteroids, vitamin D prescriptions, Charlson-Deyo comorbidity index score, and other relevant medical comorbidities were extracted for analysis. They were followed up until OTPF or the end of the year 2013. The outcome measure was an osteoporotic vertebral fracture and other long-bone fractures. A multivariate Cox model was constructed to derive adjusted hazard ratios (aHR) for OTPF with corresponding 95% confidence intervals (CI) after controlling for age, sex, insurance premium category, vitamin D prescription, osteoporosis, and coronary heart disease (CHD). Kaplan–Meier curves of the probability of OTPF-free survival for each cohort were compared using the log-rank test. Patients with OTPF during the first follow-up year were excluded from the overall risk calculation. Contributing factors to the increased risk of OTPF in COPD patients were examined in a sensitivity analysis.ResultsAfter a total follow-up of 68,743 patient-years for the COPD group and 278,051 patient-years for the matched comparison group, the HR for OTPF was 1.24 (95% CI [1.02–1.51]; P = 0.0322) in COPD patients. The aHR was increased by 30% for vertebral OTPF (aHR = 1.297, 95% CI [1.020–1.649]; P = 0.0339). Differential lag time sensitivity analysis revealed a progressively elevated risk up to 8-fold increase in women (aHR = 8.0 (95% CI [1.81–35.4]; P < 0.01)) during the fifth follow-up year. COPD patients with pre-existing osteoporosis or given vitamin D prescription harbor a sustained increased risk up to the 5th (aHR, 4.1; 95% CI [1.61–10.35]) and third (aHR, 2.97; 95% CI [1.48–5.97]) follow-up year, respectively.ConclusionsOur nationwide population-based cohort study demonstrates that East Asian COPD patients aged 50 and beyond do harbor a modestly increased risk for osteoporotic vertebral fractures particularly for those who are female, have pre-existing osteoporosis or require vitamin D prescription. creator: Ping-Hsueh Lee creator: Victor C. Kok creator: Po-Liang Chou creator: Ming-Chang Ku creator: Yu-Ching Chen creator: Jorng-Tzong Horng uri: https://doi.org/10.7717/peerj.2634 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lee et al. title: Alcohol consumption and risk of fatty liver disease: a meta-analysis link: https://peerj.com/articles/2633 last-modified: 2016-10-27 description: BackgroundObservational studies have shown inconsistent results regarding alcohol consumption and risk of fatty liver. We performed a meta-analysis of published literature to investigate the association between alcohol consumption and fatty liver disease (FLD).MethodsWe searched Medline, Embase, Web of Science, and several Chinese databases, identifying studies that reported an association between alcohol consumption and the risk of FLD.ResultsA total of 16 studies with 76,608 participants including 13 cross-sectional studies, two cross-sectional following longitudinal studies, and one cohort study met the inclusion criteria. For light to moderate alcohol consumption (LMAC), there was a 22.6% reduction in risk of FLD (odds ratio [OR] = 0.774, 95% confidence interval CI [0.695–0.862], P <0.001), and subgroup analysis showed that a greater reduction in risk of FLD was found in the female drinkers (30.2%) and the drinkers with BMI ≥25 kg/m2(31.3%) compared with the male drinkers (22.6%) and the drinkers with BMI <25 kg/m2(21.3%), respectively. For heavy alcohol consumption, there was no significant influence on risk of FLD (OR = 0.869, 95% CI [0.553–1.364], P = 0.541) in Japanese women, but there was a 33.7% reduction in risk of FLD (OR = 0.663, 95% CI [0.574–0.765], P < 0.001) in Japanese men and a significant increased risk of FLD (OR = 1.785, 95% CI [1.064–2.996], P = 0.028) in Germans.ConclusionLMAC is associated with a significant protective effect on FLD in the studied population, especially in the women and obese population. However, the effect of heavy alcohol consumption on FLD remains unclear due to limited studies and small sample sizes. creator: Guoli Cao creator: Tingzhuang Yi creator: Qianqian Liu creator: Min Wang creator: Shaohui Tang uri: https://doi.org/10.7717/peerj.2633 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cao et al. title: Social buffering and contact transmission: network connections have beneficial and detrimental effects on Shigella infection risk among captive rhesus macaques link: https://peerj.com/articles/2630 last-modified: 2016-10-27 description: In social animals, group living may impact the risk of infectious disease acquisition in two ways. On the one hand, social connectedness puts individuals at greater risk or susceptibility for acquiring enteric pathogens via contact-mediated transmission. Yet conversely, in strongly bonded societies like humans and some nonhuman primates, having close connections and strong social ties of support can also socially buffer individuals against susceptibility or transmissibility of infectious agents. Using social network analyses, we assessed the potentially competing roles of contact-mediated transmission and social buffering on the risk of infection from an enteric bacterial pathogen (Shigella flexneri) among captive groups of rhesus macaques (Macaca mulatta). Our results indicate that, within two macaque groups, individuals possessing more direct and especially indirect connections in their grooming and huddling social networks were less susceptible to infection. These results are in sharp contrast to several previous studies that indicate that increased (direct) contact-mediated transmission facilitates infectious disease transmission, including our own findings in a third macaque group in which individuals central in their huddling network and/or which initiated more fights were more likely to be infected. In summary, our findings reveal that an individual’s social connections may increase or decrease its chances of acquiring infectious agents. They extend the applicability of the social buffering hypothesis, beyond just stress and immune-function-related health benefits, to the additional health outcome of infectious disease resistance. Finally, we speculate that the circumstances under which social buffering versus contact-mediated transmission may occur could depend on multiple factors, such as living condition, pathogen-specific transmission routes, and/or an overall social context such as a group’s social stability. creator: Krishna Balasubramaniam creator: Brianne Beisner creator: Jessica Vandeleest creator: Edward Atwill creator: Brenda McCowan uri: https://doi.org/10.7717/peerj.2630 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Balasubramaniam et al. title: Palaeoamyda messeliana nov. comb. (Testudines, Pan-Trionychidae) from the Eocene Messel Pit and Geiseltal localities, Germany, taxonomic and phylogenetic insights link: https://peerj.com/articles/2647 last-modified: 2016-10-27 description: BackgroundAbundant pan-trionychid (soft-shell) turtles specimens have been found in Eocene sequences of central Europe, particularly from two localities in Germany, the Messel Pit (a UNESCO World Natural Heritage Site) and Geiseltal, traditionally attributed to Trionyx messelianus or Rafetoides austriacus. Over the last two decades new specimens of this taxon from these two localities have been discovered and fully prepared. However, they have remained unstudied, as well as their phylogenetic position inside Pan-Trionychidae is unknown.ResultsFive new specimens of Palaeoamyda messeliana nov. comb. from Messel Pit and Geiseltal localities are fully described here. A revised diagnosis for the species is also presented here, together with its inclusion in a phylogenetic analysis of Pan-Trionychidae that shows that this species is sister to the extant Amyda cartilaginea, one of the most abundant pan-trionychid (soft-shell) turtles from Asia, both members of the clade Chitrini. The specimens described in here are among the best and most complete fossil pan-trionychid skeletons so far known. creator: Edwin Cadena uri: https://doi.org/10.7717/peerj.2647 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cadena title: Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast link: https://peerj.com/articles/2628 last-modified: 2016-10-27 description: Human-derived environmental pollutants and nutrients that reach the aquatic environment through sewage effluents, agricultural and industrial processes are constantly contributing to environmental changes that serve as drivers for adaptive responses and evolutionary changes in many taxa. In this study, we examined how two types of point sources of aquatic environmental pollution, harbors and sewage treatment plants, affect gene diversity and genetic differentiation in the blue mussel in the Baltic Sea area and off the Swedish west coast (Skagerrak). Reference sites (REF) were geographically paired with sites from sewage treatments plant (STP) and harbors (HAR) with a nested sampling scheme, and genetic differentiation was evaluated using a high-resolution marker amplified fragment length polymorphism (AFLP). This study showed that genetic composition in the Baltic Sea blue mussel was associated with exposure to sewage treatment plant effluents. In addition, mussel populations from harbors were genetically divergent, in contrast to the sewage treatment plant populations, suggesting that there is an effect of pollution from harbors but that the direction is divergent and site specific, while the pollution effect from sewage treatment plants on the genetic composition of blue mussel populations acts in the same direction in the investigated sites. creator: Josefine Larsson creator: Mikael Lönn creator: Emma E. Lind creator: Justyna Świeżak creator: Katarzyna Smolarz creator: Mats Grahn uri: https://doi.org/10.7717/peerj.2628 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Larsson et al. title: Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows link: https://peerj.com/articles/2622 last-modified: 2016-10-27 description: Ephemeral rivers act as linear oases in drylands providing key resources to people and wildlife. However, not much is known about these rivers’ sensitivities to human activities. We investigated the landscape-level determinants of riparian tree dieback along the Swakop River, a dammed ephemeral river in Namibia, focusing on the native ana tree (Faidherbia albida) and the invasive mesquite (Prosopis spp.). We surveyed over 1,900 individual trees distributed across 24 sites along a 250 km stretch of the river. General linear mixed models were used to test five hypotheses relating to three anthropogenic threats: river flow disruption from damming, human settlement and invasive species. We found widespread dieback in both tree populations: 51% mortality in ana tree, with surviving trees exhibiting 18% canopy death (median); and 26% mortality in mesquite, with surviving trees exhibiting 10% canopy death. Dieback in the ana tree was most severe where trees grew on drier stretches of the river, where tributary flow was absent and where mesquite grew more abundantly. Dieback in the mesquite, a more drought-tolerant taxon, did not show any such patterns. Our findings suggest that dieback in the ana tree is primarily driven by changes in river flow resulting from upstream dam creation and that tributary flows provide a local buffer against this loss of main channel flow. The hypothesis that the invasive mesquite may contribute to ana tree dieback was also supported. Our findings suggest that large dams along the main channels of ephemeral rivers have the ability to cause widespread mortality in downstream riparian trees. To mitigate such impacts, management might focus on the maintenance of natural tributary flows to buffer local tree populations from the disruption to main channel flow. creator: Caitlin M. S. Douglas creator: Mark Mulligan creator: Xavier A. Harrison creator: Joh R. Henschel creator: Nathalie Pettorelli creator: Guy Cowlishaw uri: https://doi.org/10.7717/peerj.2622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Douglas et al. title: Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses link: https://peerj.com/articles/2620 last-modified: 2016-10-27 description: The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. One PeTIFY belongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively. Two equivocal gene models were re-predicted and a putative retrotransposition event was found in a ZML protein. The distribution and conservation of domain or motif, and gene structure were also analyzed. Phylogenetic analysis with TIFY proteins of Arabidopsis and Oryza sativa indicated that JAZ subfamily could be further divided to four groups. Evolutionary analysis revealed intragenomic duplication and orthologous relationship between P. edulis, O. sativa, and B. distachyon. Calculation of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that the duplication of PeTIFY may have occurred around 16.7 million years ago (MYA), the divergence time of TIFY family among the P. edulis-O. sativa, P. edulis-B. distachyon, and O. sativa-B. distachyon was approximately 39 MYA, 39 MYA, and 45 MYA, respectively. They appear to have undergone extensive purifying selection during evolution. Transcriptome sequencing revealed that more than 50% of PeTIFY genes could be up-regulated by cold and dehydration stresses, and some PeTIFYs also share homology to know TIFYs involved in abiotic stress tolerance. Our results made insights into TIFY family of Moso bamboo, an economically important non-timber forest resource, and provided candidates for further identification of genes involved in regulating responses to abiotic stress. creator: Zhuo Huang creator: Si-Han Jin creator: Han-Du Guo creator: Xiao-Juan Zhong creator: Jiao He creator: Xi Li creator: Ming-Yan Jiang creator: Xiao-Fang Yu creator: Hai Long creator: Ming-Dong Ma creator: Qi-Bing Chen uri: https://doi.org/10.7717/peerj.2620 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huang et al.