PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Alcohol consumption and risk of fatty liver disease: a meta-analysis
items: Social buffering and contact transmission: network connections have beneficial and detrimental effects on Shigella infection risk among captive rhesus macaques
items: Palaeoamyda messeliana nov. comb. (Testudines, Pan-Trionychidae) from the Eocene Messel Pit and Geiseltal localities, Germany, taxonomic and phylogenetic insights
items: Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast
items: Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows
items: Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses
items: The PARA-suite: PAR-CLIP specific sequence read simulation and processing
items: Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status
items: Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning
items: Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae)

Alcohol consumption and risk of fatty liver disease: a meta-analysis
type: item
type: AcademicArticle
description: Background Observational 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). Methods We searched Medline, Embase, Web of Science, and several Chinese databases, identifying studies that reported an association between alcohol consumption and the risk of FLD. Results A 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. Conclusion LMAC 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.
format: application/pdf
format: text/html
creator: Guoli Cao
creator: Tingzhuang Yi
creator: Qianqian Liu
creator: Min Wang
creator: Shaohui Tang
subject: Evidence Based Medicine
subject: Gastroenterology and Hepatology
subject: Public Health
description: doi:10.7717/peerj.2633
publisher: PeerJ Inc.
rights: © 2016 Cao et al.
abstract: Background Observational 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). Methods We searched Medline, Embase, Web of Science, and several Chinese databases, identifying studies that reported an association between alcohol consumption and the risk of FLD. Results A 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. Conclusion LMAC 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.
bibliographic citation: Cao et al. (2016) Alcohol consumption and risk of fatty liver disease: a meta-analysis. PeerJ 4:e2633 https://doi.org/10.7717/peerj.2633
date submitted: 2016-08-09
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Guoli
author list: Agent
  family name: Yi
  given name: Tingzhuang
author list: Agent
  family name: Liu
  given name: Qianqian
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Tang
  given name: Shaohui
doi: 10.7717/peerj.2633
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Cao et al.
attribution name: Cao et al.

Social buffering and contact transmission: network connections have beneficial and detrimental effects on Shigella infection risk among captive rhesus macaques
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Krishna Balasubramaniam
creator: Brianne Beisner
creator: Jessica Vandeleest
creator: Edward Atwill
creator: Brenda McCowan
subject: Animal Behavior
subject: Infectious Diseases
description: doi:10.7717/peerj.2630
publisher: PeerJ Inc.
rights: © 2016 Balasubramaniam et al.
abstract: 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.
bibliographic citation: Balasubramaniam et al. (2016) Social buffering and contact transmission: network connections have beneficial and detrimental effects on Shigella infection risk among captive rhesus macaques. PeerJ 4:e2630 https://doi.org/10.7717/peerj.2630
date submitted: 2016-06-15
date accepted: 2016-09-29
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Balasubramaniam
  given name: Krishna
author list: Agent
  family name: Beisner
  given name: Brianne
author list: Agent
  family name: Vandeleest
  given name: Jessica
author list: Agent
  family name: Atwill
  given name: Edward
author list: Agent
  family name: McCowan
  given name: Brenda
doi: 10.7717/peerj.2630
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Balasubramaniam et al.
attribution name: Balasubramaniam et al.

Palaeoamyda messeliana nov. comb. (Testudines, Pan-Trionychidae) from the Eocene Messel Pit and Geiseltal localities, Germany, taxonomic and phylogenetic insights
type: item
type: AcademicArticle
description: Background Abundant 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. Results Five 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.
format: application/pdf
format: text/html
creator: Edwin Cadena
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2647
publisher: PeerJ Inc.
rights: © 2016 Cadena
abstract: Background Abundant 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. Results Five 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.
bibliographic citation: Cadena (2016) Palaeoamyda messeliana nov. comb. (Testudines, Pan-Trionychidae) from the Eocene Messel Pit and Geiseltal localities, Germany, taxonomic and phylogenetic insights. PeerJ 4:e2647 https://doi.org/10.7717/peerj.2647
date submitted: 2016-07-11
date accepted: 2016-10-03
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cadena
  given name: Edwin
doi: 10.7717/peerj.2647
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Cadena
attribution name: Cadena

Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Josefine Larsson
creator: Mikael Lönn
creator: Emma E. Lind
creator: Justyna Świeżak
creator: Katarzyna Smolarz
creator: Mats Grahn
subject: Ecology
subject: Environmental Sciences
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.2628
publisher: PeerJ Inc.
rights: © 2016 Larsson et al.
abstract: 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.
bibliographic citation: Larsson et al. (2016) Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast. PeerJ 4:e2628 https://doi.org/10.7717/peerj.2628
date submitted: 2016-03-17
date accepted: 2016-09-29
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Larsson
  given name: Josefine
author list: Agent
  family name: Lönn
  given name: Mikael
author list: Agent
  family name: Lind
  given name: Emma E.
author list: Agent
  family name: Świeżak
  given name: Justyna
author list: Agent
  family name: Smolarz
  given name: Katarzyna
author list: Agent
  family name: Grahn
  given name: Mats
doi: 10.7717/peerj.2628
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Larsson et al.
attribution name: Larsson et al.

Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Caitlin M. S. Douglas
creator: Mark Mulligan
creator: Xavier A. Harrison
creator: Joh R. Henschel
creator: Nathalie Pettorelli
creator: Guy Cowlishaw
subject: Biosphere Interactions
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.2622
publisher: PeerJ Inc.
rights: © 2016 Douglas et al.
abstract: 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.
bibliographic citation: Douglas et al. (2016) Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows. PeerJ 4:e2622 https://doi.org/10.7717/peerj.2622
date submitted: 2016-01-22
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Douglas
  given name: Caitlin M. S.
author list: Agent
  family name: Mulligan
  given name: Mark
author list: Agent
  family name: Harrison
  given name: Xavier A.
author list: Agent
  family name: Henschel
  given name: Joh R.
author list: Agent
  family name: Pettorelli
  given name: Nathalie
author list: Agent
  family name: Cowlishaw
  given name: Guy
doi: 10.7717/peerj.2622
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: © 2016 Douglas et al.
attribution name: Douglas et al.

Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.2620
publisher: PeerJ Inc.
rights: © 2016 Huang et al.
abstract: 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.
bibliographic citation: Huang et al. (2016) Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses. PeerJ 4:e2620 https://doi.org/10.7717/peerj.2620
date submitted: 2016-06-20
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Zhuo
author list: Agent
  family name: Jin
  given name: Si-Han
author list: Agent
  family name: Guo
  given name: Han-Du
author list: Agent
  family name: Zhong
  given name: Xiao-Juan
author list: Agent
  family name: He
  given name: Jiao
author list: Agent
  family name: Li
  given name: Xi
author list: Agent
  family name: Jiang
  given name: Ming-Yan
author list: Agent
  family name: Yu
  given name: Xiao-Fang
author list: Agent
  family name: Long
  given name: Hai
author list: Agent
  family name: Ma
  given name: Ming-Dong
author list: Agent
  family name: Chen
  given name: Qi-Bing
doi: 10.7717/peerj.2620
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Huang et al.
attribution name: Huang et al.

The PARA-suite: PAR-CLIP specific sequence read simulation and processing
type: item
type: AcademicArticle
description: Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, re…
format: application/pdf
format: text/html
creator: Andreas Kloetgen
creator: Arndt Borkhardt
creator: Jessica I. Hoell
creator: Alice C. McHardy
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.2619
publisher: PeerJ Inc.
rights: © 2016 Kloetgen et al.
abstract: Background Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth. Methods We here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection. Results We show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy. Availability The PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, re…
bibliographic citation: Kloetgen et al. (2016) The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ 4:e2619 https://doi.org/10.7717/peerj.2619
date submitted: 2016-05-25
date accepted: 2016-09-27
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kloetgen
  given name: Andreas
author list: Agent
  family name: Borkhardt
  given name: Arndt
author list: Agent
  family name: Hoell
  given name: Jessica I.
author list: Agent
  family name: McHardy
  given name: Alice C.
doi: 10.7717/peerj.2619
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Kloetgen et al.
attribution name: Kloetgen et al.

Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status
type: item
type: AcademicArticle
description: Altruism toward strangers is considered a defining feature of humans. However, manifestation of this behaviour is contingent on the costliness of the selfless act. The extent of altruistic tendencies also varies cross-culturally, being more common in societies with higher levels of market integration. However, the existence of local variation in selfless behaviour within populations has received relatively little empirical attention. Using a ‘lost letter’ design, we dropped 300 letters (half of them stamped, half of them unstamped) in 15 residential suburbs of the greater Perth area that differ markedly in socioeconomic status. The number of returned letters was used as evidence of altruistic behaviour. Costliness was assessed by comparing return rates for stamped vs. unstamped letters. We predicted that there is a positive association between suburb socioeconomic status and number of letters returned and that altruistic acts decrease in frequency when costs increase, even minimally. Both predictions were solidly supported and demonstrate that socioeconomic deprivation and elevated performance costs independently impinge on the universality of altruistic behaviour in humans.
format: application/pdf
format: text/html
creator: Cyril C. Grueter
creator: Jesse A. Ingram
creator: James W. Lewisson
creator: Olivia R. Bradford
creator: Melody Taba
creator: Rebecca E. Coetzee
creator: Michelle A. Sherwood
subject: Animal Behavior
subject: Anthropology
description: doi:10.7717/peerj.2610
publisher: PeerJ Inc.
rights: © 2016 Grueter et al.
abstract: Altruism toward strangers is considered a defining feature of humans. However, manifestation of this behaviour is contingent on the costliness of the selfless act. The extent of altruistic tendencies also varies cross-culturally, being more common in societies with higher levels of market integration. However, the existence of local variation in selfless behaviour within populations has received relatively little empirical attention. Using a ‘lost letter’ design, we dropped 300 letters (half of them stamped, half of them unstamped) in 15 residential suburbs of the greater Perth area that differ markedly in socioeconomic status. The number of returned letters was used as evidence of altruistic behaviour. Costliness was assessed by comparing return rates for stamped vs. unstamped letters. We predicted that there is a positive association between suburb socioeconomic status and number of letters returned and that altruistic acts decrease in frequency when costs increase, even minimally. Both predictions were solidly supported and demonstrate that socioeconomic deprivation and elevated performance costs independently impinge on the universality of altruistic behaviour in humans.
bibliographic citation: Grueter et al. (2016) Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status. PeerJ 4:e2610 https://doi.org/10.7717/peerj.2610
date submitted: 2016-08-02
date accepted: 2016-09-26
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grueter
  given name: Cyril C.
author list: Agent
  family name: Ingram
  given name: Jesse A.
author list: Agent
  family name: Lewisson
  given name: James W.
author list: Agent
  family name: Bradford
  given name: Olivia R.
author list: Agent
  family name: Taba
  given name: Melody
author list: Agent
  family name: Coetzee
  given name: Rebecca E.
author list: Agent
  family name: Sherwood
  given name: Michelle A.
doi: 10.7717/peerj.2610
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Grueter et al.
attribution name: Grueter et al.

Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning
type: item
type: AcademicArticle
description: Foraging specialization allows social insects to more efficiently exploit resources in their environment. Recent research on honeybees suggests that specialization on pollen or nectar among foragers is linked to reproductive physiology and sensory tuning (the Reproductive Ground-Plan Hypothesis; RGPH). However, our understanding of the underlying physiological relationships in non-Apis bees is still limited. Here we show that the bumblebee Bombus terrestris has specialist pollen and nectar foragers, and test whether foraging specialization in B. terrestris is linked to reproductive physiology, measured as ovarian activation. We show that neither ovary size, sensory sensitivity, measured through proboscis extension response (PER), or whole-body lipid stores differed between pollen foragers, nectar foragers, or generalist foragers. Body size also did not differ between any of these three forager groups. Non-foragers had significantly larger ovaries than foragers. This suggests that potentially reproductive individuals avoid foraging.
format: application/pdf
format: text/html
creator: Adam R. Smith
creator: Peter Graystock
creator: William O.H. Hughes
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.2599
publisher: PeerJ Inc.
rights: © 2016 Smith et al.
abstract: Foraging specialization allows social insects to more efficiently exploit resources in their environment. Recent research on honeybees suggests that specialization on pollen or nectar among foragers is linked to reproductive physiology and sensory tuning (the Reproductive Ground-Plan Hypothesis; RGPH). However, our understanding of the underlying physiological relationships in non-Apis bees is still limited. Here we show that the bumblebee Bombus terrestris has specialist pollen and nectar foragers, and test whether foraging specialization in B. terrestris is linked to reproductive physiology, measured as ovarian activation. We show that neither ovary size, sensory sensitivity, measured through proboscis extension response (PER), or whole-body lipid stores differed between pollen foragers, nectar foragers, or generalist foragers. Body size also did not differ between any of these three forager groups. Non-foragers had significantly larger ovaries than foragers. This suggests that potentially reproductive individuals avoid foraging.
bibliographic citation: Smith et al. (2016) Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning. PeerJ 4:e2599 https://doi.org/10.7717/peerj.2599
date submitted: 2016-07-14
date accepted: 2016-09-23
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Adam R.
author list: Agent
  family name: Graystock
  given name: Peter
author list: Agent
  family name: Hughes
  given name: William O.H.
doi: 10.7717/peerj.2599
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Smith et al.
attribution name: Smith et al.

Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae)
type: item
type: AcademicArticle
description: Background The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae). Closely related species in this family exhibit distinct larval feeding habits, most notably necro-saprophagy and obligate parasitism. Methods To understand the genetic and molecular bases underlying these habits, expression levels of eight candidate genes for feeding behavior—Cyp6g2, foraging, glutamate dehydrogenase, Jonah65aiv, Malvolio, PGRP-SC2, RPS6-p70-protein kinase, and smooth—were measured in four species using qPCR. Moreover we used expression values and sequence information to reconstruct the relationship among species and the dN/dS rate to infer possible sites under selection. Results For most candidate genes, no statistically significant differences were observed, indicating a high degree of conservation in expression. However, Malvolio was differentially expressed between habits. Evolutionary analyses based on transcript levels and nucleotide sequences of Malvolio coding region suggest that transcript levels were correlated to feeding habit preferences among species, although deviations under a strictly neutral model were also observed in statistical tests. Discussion Malvolio was the only gene demonstrating a possible connection to feeding habit. Differences in gene expression may be involved in (or be a result of) the genetic regulation of Calliphoridae feeding habit. Our results are the first steps towards understanding the genetic basis and evolution of feeding behavior in Calliphoridae using a functional approach.
format: application/pdf
format: text/html
creator: Gisele Antoniazzi Cardoso
creator: Marco Antonio Tonus Marinho
creator: Raquel Dietsche Monfardini
creator: Ana Maria Lima de Azeredo Espin
creator: Tatiana Teixeira Torres
subject: Entomology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.2598
publisher: PeerJ Inc.
rights: © 2016 Cardoso et al.
abstract: Background The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae). Closely related species in this family exhibit distinct larval feeding habits, most notably necro-saprophagy and obligate parasitism. Methods To understand the genetic and molecular bases underlying these habits, expression levels of eight candidate genes for feeding behavior—Cyp6g2, foraging, glutamate dehydrogenase, Jonah65aiv, Malvolio, PGRP-SC2, RPS6-p70-protein kinase, and smooth—were measured in four species using qPCR. Moreover we used expression values and sequence information to reconstruct the relationship among species and the dN/dS rate to infer possible sites under selection. Results For most candidate genes, no statistically significant differences were observed, indicating a high degree of conservation in expression. However, Malvolio was differentially expressed between habits. Evolutionary analyses based on transcript levels and nucleotide sequences of Malvolio coding region suggest that transcript levels were correlated to feeding habit preferences among species, although deviations under a strictly neutral model were also observed in statistical tests. Discussion Malvolio was the only gene demonstrating a possible connection to feeding habit. Differences in gene expression may be involved in (or be a result of) the genetic regulation of Calliphoridae feeding habit. Our results are the first steps towards understanding the genetic basis and evolution of feeding behavior in Calliphoridae using a functional approach.
bibliographic citation: Cardoso et al. (2016) Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae). PeerJ 4:e2598 https://doi.org/10.7717/peerj.2598
date submitted: 2016-06-20
date accepted: 2016-09-23
issued: 2016-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardoso
  given name: Gisele Antoniazzi
author list: Agent
  family name: Marinho
  given name: Marco Antonio Tonus
author list: Agent
  family name: Monfardini
  given name: Raquel Dietsche
author list: Agent
  family name: Espin
  given name: Ana Maria Lima de Azeredo
author list: Agent
  family name: Torres
  given name: Tatiana Teixeira
doi: 10.7717/peerj.2598
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-27
copyright: ©2016 Cardoso et al.
attribution name: Cardoso et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359