title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1928
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Variation in phenology of hibernation and reproduction in the endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus)
link: https://peerj.com/articles/1138
last-modified: 2015-08-06
description: Hibernation is a key life history feature that can impact many other crucial aspects of a species’ biology, such as its survival and reproduction. I examined the timing of hibernation and reproduction in the federally endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus), which occurs across a broad range of latitudes and elevations in the American Southwest. Data from museum specimens and field studies supported predictions for later emergence and shorter active intervals in montane populations relative to lower elevation valley populations. A low-elevation population located at Bosque del Apache National Wildlife Refuge (BANWR) in the Rio Grande valley was most similar to other subspecies of Z. hudsonius: the first emergence date was in mid-May and there was an active interval of 162 days. In montane populations of Z. h. luteus, the date of first emergence was delayed until mid-June and the active interval was reduced to ca 124–135 days, similar to some populations of the western jumping mouse (Z. princeps). Last date of immergence into hibernation occurred at about the same time in all populations (mid to late October). In montane populations pregnant females are known from July to late August and evidence suggests that they have a single litter per year. At BANWR two peaks in reproduction were expected based on similarity of active season to Z. h. preblei. However, only one peak was clearly evident, possibly due to later first reproduction and possible torpor during late summer. At BANWR pregnant females are known from June and July. Due to the short activity season and geographic variation in phenology of key life history events of Z. h. luteus, recommendations are made for the appropriate timing for surveys for this endangered species.
creator: Jennifer K. Frey
uri: https://doi.org/10.7717/peerj.1138
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Frey

title: Space-use, movement and dispersal of sub-adult cougars in a geographically isolated population
link: https://peerj.com/articles/1118
last-modified: 2015-08-06
description: Cougar (Puma concolor) observations have increased in Midwest North America, with breeding populations re-establishing in several regions east of their contemporary range. The Cypress Hills Uplands, located in southwest Saskatchewan and southeast Alberta, was recently re-colonized by cougars and now supports the easternmost confirmed breeding population of cougars in Canada. A number of factors contribute to this cougar range expansion, but it is dispersal that provides the mechanism for re-colonization of historic range. We used GPS-collar data to examine space-use and movement behavior of sub-adult cougars, the age class associated with dispersal, in the Cypress Hills. Conditional logistic regression and a two-stage modeling approach were used to estimate resource selection functions (RSF) of sub-adult cougars during two distinct ranging behaviors: transient movements (i.e., dispersal and exploratory forays) and localizing movements (i.e., temporary home ranges). Linear regression was used to model movement rates, measured as the distance between consecutive 3-h GPS-relocations, of sub-adult cougars relative to different habitats, times of day and between transient and localizing behavior. All individual sub-adult cougars displayed bouts of transient and localizing behavior. All male cougars dispersed from their natal ranges and travelled considerably farther distances than female cougars. One male dispersed over 750 km eastward through the agricultural belt of northern Montana and southern Saskatchewan. Males occupied temporary home ranges in more open habitats on the fringes of the insular Cypress Hills, while females appeared to be recruited into the adult population, occupying treed habitat that provided more suitable cover. During both ranging behaviors, sub-adult cougars selected for rugged terrain and proximity to hydrological features (likely supporting riparian habitats) and avoided open cover types. Differences in habitat selection between ranging behaviors were observed in response to open water, roads and elevation. Although certain habitat characteristics were preferred, transient and localizing cougars used fast-paced nocturnal movements and shortened daytime movements when traversing open habitats to effectively limit their residency and exposure in less-suitable landscapes. Additionally, cougars moved greater distances at night during transient behavior compared to localizing behavior indicating cougars used cover of darkness to traverse novel terrain. In doing so, sub-adult cougars can successfully disperse several hundred kilometres across a matrix of open habitat in search of resources and mates.
creator: Carl D. Morrison
creator: Mark S. Boyce
creator: Scott E. Nielsen
uri: https://doi.org/10.7717/peerj.1118
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Morrison et al.

title: Whole genome sequencing enables the characterization of BurI, a LuxI homologue of Burkholderia cepacia strain GG4
link: https://peerj.com/articles/1117
last-modified: 2015-08-06
description: Quorum sensing is a mechanism for regulating proteobacterial gene expression in response to changes in cell population. In proteobacteria, N-acyl homoserine lactone (AHL) appears to be the most widely used signalling molecules in mediating, among others, the production of extracellular virulence factors for survival. In this work, the genome of B. cepacia strain GG4, a plasmid-free strain capable of AHL synthesis was explored. In silico analysis of the 6.6 Mb complete genome revealed the presence of a LuxI homologue which correspond to Type I quorum sensing. Here, we report the molecular cloning and characterization of this LuxI homologue, designated as BurI. This 609 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was approximately 25 kDa and is highly similar to several autoinducer proteins of the LuxI family among Burkholderia species. To verify the AHL synthesis activity of this protein, high resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-hexanoylhomoserine lactone, N-octanoylhomoserine lactone and 3-hydroxy-octanoylhomoserine lactone from induced E. coli BL21 harboring the recombinant BurI. Our data show, for the first time, the cloning and characterization of the LuxI homologue from B. cepacia strain GG4 and confirmation of its AHL synthesis activity.
creator: Kah Yan How
creator: Kar Wai Hong
creator: Kok-Gan Chan
uri: https://doi.org/10.7717/peerj.1117
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 How et al.

title: Allantoin ameliorates chemically-induced pancreatic β-cell damage through activation of the imidazoline I3 receptors
link: https://peerj.com/articles/1105
last-modified: 2015-08-06
description: Objective. Allantoin is the primary active compound in yams (Dioscorea spp.). Recently, allantoin has been demonstrated to activate imidazoline 3 (I3) receptors located in pancreatic tissues. Thus, the present study aimed to investigate the role of allantoin in the effect to improve damage induced in pancreatic β-cells by streptozotocin (STZ) via the I3 receptors.Research Design and Methods. The effect of allantoin on STZ-induced apoptosis in pancreatic β-cells was examined using the ApoTox-Glo triplex assay, live/dead cell double staining assay, flow cytometric analysis, and Western blottings. The potential mechanism was investigated using KU14R: an I3 receptor antagonist, and U73122: a phospholipase C (PLC) inhibitor. The effects of allantoin on serum glucose and insulin secretion were measured in STZ-treated rats.Results. Allantoin attenuated apoptosis and cytotoxicity and increased the viability of STZ-induced β-cells in a dose-dependent manner; this effect was suppressed by KU14R and U73112. Allantoin decreased the level of caspase-3 and increased the level of phosphorylated B-cell lymphoma 2 (Bcl-2) expression detected by Western blotting. The improvement in β-cells viability was confirmed using flow cytometry analysis. Daily injection of allantoin for 8 days in STZ-treated rats significantly lowered plasma glucose and increased plasma insulin levels. This action was inhibited by treatment with KU14R.Conclusion. Allantoin ameliorates the damage of β-cells induced by STZ. The blockade by pharmacological inhibitors indicated that allantoin can activate the I3 receptors through a PLC-related pathway to decrease this damage. Therefore, allantoin and related analogs may be effective in the therapy for β-cell damage.
creator: Marie Amitani
creator: Kai-Chun Cheng
creator: Akihiro Asakawa
creator: Haruka Amitani
creator: Timothy Sean Kairupan
creator: Nanami Sameshima
creator: Toshiaki Shimizu
creator: Teruto Hashiguchi
creator: Akio Inui
uri: https://doi.org/10.7717/peerj.1105
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Amitani et al.

title: Correlates of condom use among female sex workers in The Gambia: results of a cross-sectional survey
link: https://peerj.com/articles/1076
last-modified: 2015-08-06
description: Objectives. This study examined correlates of condom use among 248 female sex workers (FSW) in The Gambia.Methods. Between July and August 2011, FSW in The Gambia who were older than 16 years of age, the age of consent in The Gambia, were recruited for the study using venue-based sampling and snowball sampling, beginning with seeds who were established clients with the Network of AIDS Services Organizations. To be eligible, FSW must have reported selling sex for money, favors, or goods in the past 12 months. Bivariate and multivariate logistic regressions were used to determine associations and the relative odds of the independent variables with condom use. Four different condom use dependent variables were used: consistent condom use in the past six months during vaginal or anal sex with all clients and partners; consistent condom use in the past month during vaginal sex with new clients; consistent condom use in the past month during vaginal sex with nonpaying partners (including boyfriends, husbands, or casual sexual partners); and condom use at last vaginal or anal sex with a nonpaying partner.Results. Many FSW (67.34%, n = 167) reported it was not at all difficult to negotiate condom use with clients in all applicable situations, and these FSW were more likely to report consistent condom use with all clients and partners in the past 6 months (aOR 3.47, 95% CI [1.70–7.07]) compared to those perceiving any difficulty in condom negotiation. In addition, FSW were more likely to report using condoms in the past month with new clients (aOR 8.04, 95% CI [2.11–30.65]) and in the past month with nonpaying partners (aOR 2.93, 95% CI [1.09–7.89]) if they had been tested for HIV in the past year. Women who bought all their condoms were less likely than those who received all of their condoms for free (aOR 0.38, 95% CI [0.15–0.97]) to have used a condom at last vaginal or anal sex with a nonpaying partner.Conclusions. HIV and sexually transmitted infection (STI) prevention interventions for FSW should aim to improve condom negotiation self-efficacy since women who report less difficulty negotiating condom use are more likely to use condoms with clients. Interventions should also be aimed at structural issues such as increasing access to free condoms and HIV testing since these were positively associated with condom use among FSW.
creator: Ashley L. Grosso
creator: Esther L. Lei
creator: Sosthenes C. Ketende
creator: Sarah Peitzmeier
creator: Krystal Mason
creator: Nuha Ceesay
creator: Daouda Diouf
creator: Fatou Maria Drame
creator: Jaegan Loum
creator: Erin Papworth
creator: Stefan Baral
uri: https://doi.org/10.7717/peerj.1076
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Grosso et al.

title: Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
link: https://peerj.com/articles/1066
last-modified: 2015-08-06
description: Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.
creator: Nagesh A. Kuravadi
creator: Vijay Yenagi
creator: Kannan Rangiah
creator: HB Mahesh
creator: Anantharamanan Rajamani
creator: Meghana D. Shirke
creator: Heikham Russiachand
creator: Ramya Malarini Loganathan
creator: Chandana Shankara Lingu
creator: Shilpa Siddappa
creator: Aishwarya Ramamurthy
creator: BN Sathyanarayana
creator: Malali Gowda
uri: https://doi.org/10.7717/peerj.1066
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kuravadi et al.

title: Functional flexibility in wild bonobo vocal behaviour
link: https://peerj.com/articles/1124
last-modified: 2015-08-04
description: A shared principle in the evolution of language and the development of speech is the emergence of functional flexibility, the capacity of vocal signals to express a range of emotional states independently of context and biological function. Functional flexibility has recently been demonstrated in the vocalisations of pre-linguistic human infants, which has been contrasted to the functionally fixed vocal behaviour of non-human primates. Here, we revisited the presumed chasm in functional flexibility between human and non-human primate vocal behaviour, with a study on our closest living primate relatives, the bonobo (Pan paniscus). We found that wild bonobos use a specific call type (the “peep”) across a range of contexts that cover the full valence range (positive-neutral-negative) in much of their daily activities, including feeding, travel, rest, aggression, alarm, nesting and grooming. Peeps were produced in functionally flexible ways in some contexts, but not others. Crucially, calls did not vary acoustically between neutral and positive contexts, suggesting that recipients take pragmatic information into account to make inferences about call meaning. In comparison, peeps during negative contexts were acoustically distinct. Our data suggest that the capacity for functional flexibility has evolutionary roots that predate the evolution of human speech. We interpret this evidence as an example of an evolutionary early transition away from fixed vocal signalling towards functional flexibility.
creator: Zanna Clay
creator: Jahmaira Archbold
creator: Klaus Zuberbühler
uri: https://doi.org/10.7717/peerj.1124
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Clay et al.

title: Awake fMRI reveals a specialized region in dog temporal cortex for face processing
link: https://peerj.com/articles/1115
last-modified: 2015-08-04
description: Recent behavioral evidence suggests that dogs, like humans and monkeys, are capable of visual face recognition. But do dogs also exhibit specialized cortical face regions similar to humans and monkeys? Using functional magnetic resonance imaging (fMRI) in six dogs trained to remain motionless during scanning without restraint or sedation, we found a region in the canine temporal lobe that responded significantly more to movies of human faces than to movies of everyday objects. Next, using a new stimulus set to investigate face selectivity in this predefined candidate dog face area, we found that this region responded similarly to images of human faces and dog faces, yet significantly more to both human and dog faces than to images of objects. Such face selectivity was not found in dog primary visual cortex. Taken together, these findings: (1) provide the first evidence for a face-selective region in the temporal cortex of dogs, which cannot be explained by simple low-level visual feature extraction; (2) reveal that neural machinery dedicated to face processing is not unique to primates; and (3) may help explain dogs’ exquisite sensitivity to human social cues.
creator: Daniel D. Dilks
creator: Peter Cook
creator: Samuel K. Weiller
creator: Helen P. Berns
creator: Mark Spivak
creator: Gregory S. Berns
uri: https://doi.org/10.7717/peerj.1115
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Dilks et al.

title: Differential use of salmon by vertebrate consumers: implications for conservation
link: https://peerj.com/articles/1157
last-modified: 2015-08-04
description: Salmon and other anadromous fish are consumed by vertebrates with distinct life history strategies to capitalize on this ephemeral pulse of resource availability. Depending on the timing of salmon arrival, this resource may be in surplus to the needs of vertebrate consumers if, for instance, their populations are limited by food availability during other times of year. However, the life history of some consumers enables more efficient exploitation of these ephemeral resources. Bears can deposit fat and then hibernate to avoid winter food scarcity, and highly mobile consumers such as eagles, gulls, and other birds can migrate to access asynchronous pulses of salmon availability. We used camera traps on pink, chum, and sockeye salmon spawning grounds with various run times and stream morphologies, and on individual salmon carcasses, to discern potentially different use patterns among consumers. Wildlife use of salmon was highly heterogeneous. Ravens were the only avian consumer that fed heavily on pink salmon in small streams. Eagles and gulls did not feed on early pink salmon runs in streams, and only moderately at early sockeye runs, but were the dominant consumers at late chum salmon runs, particularly on expansive river flats. Brown bears used all salmon resources far more than other terrestrial vertebrates. Notably, black bears were not observed on salmon spawning grounds despite being the most frequently observed vertebrate on roads and trails. From a conservation and management perspective, all salmon species and stream morphologies are used extensively by bears, but salmon spawning late in the year are disproportionately important to eagles and other highly mobile species that are seasonally limited by winter food availability.
creator: Taal Levi
creator: Rachel E. Wheat
creator: Jennifer M. Allen
creator: Christopher C. Wilmers
uri: https://doi.org/10.7717/peerj.1157
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Levi et al.

title: Sixty years of change in avian communities of the Pacific Northwest
link: https://peerj.com/articles/1152
last-modified: 2015-08-04
description: Bird communities are influenced by local and regional processes. The degree to which communities are dynamic has implications for projecting responses in community composition as birds track geographic shifts of their habitats. Historic datasets offer a legacy of information that can be used to quantify changes over time in avian community composition. A rare, highly-detailed avian survey of multiple habitat types in the Willamette Valley, Oregon, was conducted in 1952. We resurveyed the same sites in 2013 and evaluated whether observed results agreed with theoretical patterns of community change. We compared alpha, beta, and gamma diversity between survey periods and evaluated shifts in categorical abundances of species. Most patterns of change were consistent with community turnover. Nearly 50% of species were replaced over six decades, with increased species richness and decreased evenness at local and regional spatial extents. Patterns of regional species turnover reflected local turnover. Evidence that local shifts in habitat type drove bird community change were not strongly supported, although historic data on habitats within study plots were limited to macro-level aerial photographs. Thus, regional factors and structural changes likely played important roles determining species composition and abundance.
creator: Jenna R. Curtis
creator: W. Douglas Robinson
uri: https://doi.org/10.7717/peerj.1152
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Curtis and Robinson