PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Phalangeal joints kinematics during ostrich (Struthio camelus) locomotion
items: Diversity and distribution of the Caddisflies (Insecta: Trichoptera) of Ecuador
items: Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence
items: In vitro effect of direct current electrical stimulation on rat mesenchymal stem cells
items: Effects of grazing intensity and the use of veterinary medical products on dung beetle biodiversity in the sub-mountainous landscape of Central Italy
items: Optimizing the use of a sensor resource for opponent polarization coding
items: Handling stress may confound murine gut microbiota studies
items: Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter
items: Hepatic fibrosis and factors associated with liver stiffness in HIV mono-infected individuals
items: Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

Phalangeal joints kinematics during ostrich (Struthio camelus) locomotion
type: item
type: AcademicArticle
description: The ostrich is a highly cursorial bipedal land animal with a permanently elevated metatarsophalangeal joint supported by only two toes. Although locomotor kinematics in walking and running ostriches have been examined, these studies have been largely limited to above the metatarsophalangeal joint. In this study, kinematic data of all major toe joints were collected from gaits with double support (slow walking) to running during stance period in a semi-natural setup with two selected cooperative ostriches. Statistical analyses were conducted to investigate the effect of locomotor gait on toe joint kinematics. The MTP3 and MTP4 joints exhibit the largest range of motion whereas the first phalangeal joint of the 4th toe shows the largest motion variability. The interphalangeal joints of the 3rd and 4th toes present very similar motion patterns over stance phases of slow walking and running. However, the motion patterns of the MTP3 and MTP4 joints and the vertical displacement of the metatarsophalangeal joint are significantly different during running and slow walking. Because of the biomechanical requirements, osctriches are likely to select the inverted pendulum gait at low speeds and the bouncing gait at high speeds to improve movement performance and energy economy. Interestingly, the motions of the MTP3 and MTP4 joints are highly synchronized from slow to fast locomotion. This strongly suggests that the 3rd and 4th toes really work as an “integrated system” with the 3rd toe as the main load bearing element whilst the 4th toe as the complementary load sharing element with a primary role to ensure the lateral stability of the permanently elevated metatarsophalangeal joint.
format: application/pdf
format: text/html
creator: Rui Zhang
creator: Qiaoli Ji
creator: Gang Luo
creator: Shuliang Xue
creator: Songsong Ma
creator: Jianqiao Li
creator: Lei Ren
subject: Animal Behavior
subject: Bioengineering
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.2857
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: The ostrich is a highly cursorial bipedal land animal with a permanently elevated metatarsophalangeal joint supported by only two toes. Although locomotor kinematics in walking and running ostriches have been examined, these studies have been largely limited to above the metatarsophalangeal joint. In this study, kinematic data of all major toe joints were collected from gaits with double support (slow walking) to running during stance period in a semi-natural setup with two selected cooperative ostriches. Statistical analyses were conducted to investigate the effect of locomotor gait on toe joint kinematics. The MTP3 and MTP4 joints exhibit the largest range of motion whereas the first phalangeal joint of the 4th toe shows the largest motion variability. The interphalangeal joints of the 3rd and 4th toes present very similar motion patterns over stance phases of slow walking and running. However, the motion patterns of the MTP3 and MTP4 joints and the vertical displacement of the metatarsophalangeal joint are significantly different during running and slow walking. Because of the biomechanical requirements, osctriches are likely to select the inverted pendulum gait at low speeds and the bouncing gait at high speeds to improve movement performance and energy economy. Interestingly, the motions of the MTP3 and MTP4 joints are highly synchronized from slow to fast locomotion. This strongly suggests that the 3rd and 4th toes really work as an “integrated system” with the 3rd toe as the main load bearing element whilst the 4th toe as the complementary load sharing element with a primary role to ensure the lateral stability of the permanently elevated metatarsophalangeal joint.
bibliographic citation: Zhang et al. (2017) Phalangeal joints kinematics during ostrich (Struthio camelus) locomotion. PeerJ 5:e2857 https://doi.org/10.7717/peerj.2857
date submitted: 2016-07-29
date accepted: 2016-12-02
issued: 2017-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rui
author list: Agent
  family name: Ji
  given name: Qiaoli
author list: Agent
  family name: Luo
  given name: Gang
author list: Agent
  family name: Xue
  given name: Shuliang
author list: Agent
  family name: Ma
  given name: Songsong
author list: Agent
  family name: Li
  given name: Jianqiao
author list: Agent
  family name: Ren
  given name: Lei
doi: 10.7717/peerj.2857
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-12
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

Diversity and distribution of the Caddisflies (Insecta: Trichoptera) of Ecuador
type: item
type: AcademicArticle
description: Background Aquatic insects and other freshwater animals are some of the most threatened forms of life on Earth. Caddisflies (Trichoptera) are highly biodiverse in the Neotropics and occupy a wide variety of freshwater habitats. In Andean countries, including Ecuador, knowledge of the aquatic biota is limited, and there is a great need for baseline data on the species found in these countries. Here we present the first list of Trichoptera known from Ecuador, a country that harbors two global biodiversity “hotspots.” Methods We conducted a literature review of species previously reported from Ecuador and supplemented these data with material we collected during five recent field inventories from about 40 localities spanning both hotspots. Using species presence data for each Ecuadorian province, we calculated the CHAO 2 species estimator to obtain the minimum species richness for the country. Results We recorded 310 species, including 48 new records from our own field inventories for the country. CHAO 2 calculations showed that only 54% of the species have been found. Hydroptilidae and Hydropsychidae were the most species rich families. We report the family Xiphocentronidae for the first time from Ecuador as well as several new records of genera from different families. Discussion As in the neighboring Andean countries of Colombia and Peru, it is common to find undescribed species of caddisflies. There are vast areas of Ecuador and the northern Andes that are completely unexplored, and we expect that hundreds of new species are yet to be discovered.
format: application/pdf
format: text/html
creator: Blanca Ríos-Touma
creator: Ralph W. Holzenthal
creator: Jolanda Huisman
creator: Robin Thomson
creator: Ernesto Rázuri-Gonzales
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.2851
publisher: PeerJ Inc.
rights: © 2017 Ríos-Touma et al.
abstract: Background Aquatic insects and other freshwater animals are some of the most threatened forms of life on Earth. Caddisflies (Trichoptera) are highly biodiverse in the Neotropics and occupy a wide variety of freshwater habitats. In Andean countries, including Ecuador, knowledge of the aquatic biota is limited, and there is a great need for baseline data on the species found in these countries. Here we present the first list of Trichoptera known from Ecuador, a country that harbors two global biodiversity “hotspots.” Methods We conducted a literature review of species previously reported from Ecuador and supplemented these data with material we collected during five recent field inventories from about 40 localities spanning both hotspots. Using species presence data for each Ecuadorian province, we calculated the CHAO 2 species estimator to obtain the minimum species richness for the country. Results We recorded 310 species, including 48 new records from our own field inventories for the country. CHAO 2 calculations showed that only 54% of the species have been found. Hydroptilidae and Hydropsychidae were the most species rich families. We report the family Xiphocentronidae for the first time from Ecuador as well as several new records of genera from different families. Discussion As in the neighboring Andean countries of Colombia and Peru, it is common to find undescribed species of caddisflies. There are vast areas of Ecuador and the northern Andes that are completely unexplored, and we expect that hundreds of new species are yet to be discovered.
bibliographic citation: Ríos-Touma et al. (2017) Diversity and distribution of the Caddisflies (Insecta: Trichoptera) of Ecuador. PeerJ 5:e2851 https://doi.org/10.7717/peerj.2851
date submitted: 2016-09-07
date accepted: 2016-12-01
issued: 2017-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ríos-Touma
  given name: Blanca
author list: Agent
  family name: Holzenthal
  given name: Ralph W.
author list: Agent
  family name: Huisman
  given name: Jolanda
author list: Agent
  family name: Thomson
  given name: Robin
author list: Agent
  family name: Rázuri-Gonzales
  given name: Ernesto
doi: 10.7717/peerj.2851
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-12
copyright: ©2017 Ríos-Touma et al.
attribution name: Ríos-Touma et al.

Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence
type: item
type: AcademicArticle
description: Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models). In addition, we developed an ensemble forecast by averaging predicted probability of the above four models results. Commonly used model performance metrics (Area under ROC (AUC) and true skill statistic (TSS)) were employed to evaluate model accuracy. The latest satellite tracking data and compiled literature data were used as two independent testing datasets to confront model predictions. We found Random Forest demonstrated the best performance for the most assessment method, provided a better model fit to the testing data, and achieved better species range maps for each crane species in undersampled areas. Random Forest has been generally available for more than 20 years and has been known to perform extremely well in ecological predictions. However, while increasingly on the rise, its potential is still widely underused in conservation, (spatial) ecological applications and for inference. Our results show that it informs ecological and biogeographical theories as well as being suitable for conservation applications, specifically when the study area is undersampled. This method helps to save model-selection time and effort, and allows robust and rapid assessments and de…
format: application/pdf
format: text/html
creator: Chunrong Mi
creator: Falk Huettmann
creator: Yumin Guo
creator: Xuesong Han
creator: Lijia Wen
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2849
publisher: PeerJ Inc.
rights: © 2017 Mi et al.
abstract: Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models). In addition, we developed an ensemble forecast by averaging predicted probability of the above four models results. Commonly used model performance metrics (Area under ROC (AUC) and true skill statistic (TSS)) were employed to evaluate model accuracy. The latest satellite tracking data and compiled literature data were used as two independent testing datasets to confront model predictions. We found Random Forest demonstrated the best performance for the most assessment method, provided a better model fit to the testing data, and achieved better species range maps for each crane species in undersampled areas. Random Forest has been generally available for more than 20 years and has been known to perform extremely well in ecological predictions. However, while increasingly on the rise, its potential is still widely underused in conservation, (spatial) ecological applications and for inference. Our results show that it informs ecological and biogeographical theories as well as being suitable for conservation applications, specifically when the study area is undersampled. This method helps to save model-selection time and effort, and allows robust and rapid assessments and de…
bibliographic citation: Mi et al. (2017) Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence. PeerJ 5:e2849 https://doi.org/10.7717/peerj.2849
date submitted: 2016-10-10
date accepted: 2016-12-01
issued: 2017-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mi
  given name: Chunrong
author list: Agent
  family name: Huettmann
  given name: Falk
author list: Agent
  family name: Guo
  given name: Yumin
author list: Agent
  family name: Han
  given name: Xuesong
author list: Agent
  family name: Wen
  given name: Lijia
doi: 10.7717/peerj.2849
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-12
copyright: ©2017 Mi et al.
attribution name: Mi et al.

In vitro effect of direct current electrical stimulation on rat mesenchymal stem cells
type: item
type: AcademicArticle
description: Background Electrical stimulation (ES) has been successfully used to treat bone defects clinically. Recently, both cellular and molecular approaches have demonstrated that ES can change cell behavior such as migration, proliferation and differentiation. Methods In the present study we exposed rat bone marrow- (BM-) and adipose tissue- (AT-) derived mesenchymal stem cells (MSCs) to direct current electrical stimulation (DC ES) and assessed temporal changes in osteogenic differentiation. We applied 100 mV/mm of DC ES for 1 h per day for three, seven and 14 days to cells cultivated in osteogenic differentiation medium and assessed viability and calcium deposition at the different time points. In addition, expression of osteogenic genes, Runx2, Osteopontin, and Col1A2 was assessed in BM- and AT-derived MSCs at the different time points. Results Results showed that ES changed osteogenic gene expression patterns in both BM- and AT-MSCs, and these changes differed between the two groups. In BM-MSCs, ES caused a significant increase in mRNA levels of Runx2, Osteopontin and Col1A2 at day 7, while in AT-MSCs, the increase in Runx2 and Osteopontin expression were observed after 14 days of ES. Discussion This study shows that rat bone marrow- and adipose tissue-derived stem cells react differently to electrical stimuli, an observation that could be important for application of electrical stimulation in tissue engineering.
format: application/pdf
format: text/html
creator: Sahba Mobini
creator: Liudmila Leppik
creator: Vishnu Thottakkattumana Parameswaran
creator: John Howard Barker
subject: Bioengineering
subject: Cell Biology
subject: Orthopedics
description: doi:10.7717/peerj.2821
publisher: PeerJ Inc.
rights: © 2017 Mobini et al.
abstract: Background Electrical stimulation (ES) has been successfully used to treat bone defects clinically. Recently, both cellular and molecular approaches have demonstrated that ES can change cell behavior such as migration, proliferation and differentiation. Methods In the present study we exposed rat bone marrow- (BM-) and adipose tissue- (AT-) derived mesenchymal stem cells (MSCs) to direct current electrical stimulation (DC ES) and assessed temporal changes in osteogenic differentiation. We applied 100 mV/mm of DC ES for 1 h per day for three, seven and 14 days to cells cultivated in osteogenic differentiation medium and assessed viability and calcium deposition at the different time points. In addition, expression of osteogenic genes, Runx2, Osteopontin, and Col1A2 was assessed in BM- and AT-derived MSCs at the different time points. Results Results showed that ES changed osteogenic gene expression patterns in both BM- and AT-MSCs, and these changes differed between the two groups. In BM-MSCs, ES caused a significant increase in mRNA levels of Runx2, Osteopontin and Col1A2 at day 7, while in AT-MSCs, the increase in Runx2 and Osteopontin expression were observed after 14 days of ES. Discussion This study shows that rat bone marrow- and adipose tissue-derived stem cells react differently to electrical stimuli, an observation that could be important for application of electrical stimulation in tissue engineering.
bibliographic citation: Mobini et al. (2017) In vitro effect of direct current electrical stimulation on rat mesenchymal stem cells. PeerJ 5:e2821 https://doi.org/10.7717/peerj.2821
date submitted: 2016-07-12
date accepted: 2016-11-22
issued: 2017-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mobini
  given name: Sahba
author list: Agent
  family name: Leppik
  given name: Liudmila
author list: Agent
  family name: Thottakkattumana Parameswaran
  given name: Vishnu
author list: Agent
  family name: Barker
  given name: John Howard
doi: 10.7717/peerj.2821
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-12
copyright: ©2017 Mobini et al.
attribution name: Mobini et al.

Effects of grazing intensity and the use of veterinary medical products on dung beetle biodiversity in the sub-mountainous landscape of Central Italy
type: item
type: AcademicArticle
description: Grazing extensification and intensification are among the main problems affecting European grasslands. We analyze the impact of grazing intensity (low and moderate) and the use of veterinary medical products (VMPs) on the dung beetle community in the province of Pesaro-Urbino (Italy). Grazing intensity is a key factor in explaining the diversity of dung beetles. In the case of the alpha diversity component, sites with a low level of grazing activity—related in a previous step to the subsequent abandonment of traditional farming—is characterized by a loss of species richness (q = 0) and a reduction in alpha diversity at the levels q = 1 and q = 2. In the case of beta diversity, sites with a different grazing intensity show remarkable differences in terms of the composition of their species assemblages. The use of VMPs is another important factor in explaining changes in dung beetle diversity. In sites with a traditional use of VMPs, a significant loss of species richness and biomass is observed, as is a notable effect on beta diversity. In addition, the absence of indicator species in sites with a historical use of VMPs corroborates the hypothesis that these substances have a ubiquitous effect on dung beetles. However, the interaction between grazing activity and VMPs when it comes to explaining changes in dung beetle diversity is less significant (or is not significant) than the main effects (each factor separately) for alpha diversity, biomass and species composition. This may be explained if we consider that both factors affect the various species differently. In other words, the reduction in dung availability affects several larger species more than it does very small species, although this does not imply that the former are more susceptible to injury caused by the ingestion of dung contaminated with VMPs. Finally, in order to prevent negative consequences for dung beetle diversity, we propose the maintenance of a moderate grazing intensity and the rational use o…
format: application/pdf
format: text/html
creator: Mattia Tonelli
creator: José R. Verdú
creator: Mario E. Zunino
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Environmental Sciences
subject: Veterinary Medicine
description: doi:10.7717/peerj.2780
publisher: PeerJ Inc.
rights: © 2017 Tonelli et al.
abstract: Grazing extensification and intensification are among the main problems affecting European grasslands. We analyze the impact of grazing intensity (low and moderate) and the use of veterinary medical products (VMPs) on the dung beetle community in the province of Pesaro-Urbino (Italy). Grazing intensity is a key factor in explaining the diversity of dung beetles. In the case of the alpha diversity component, sites with a low level of grazing activity—related in a previous step to the subsequent abandonment of traditional farming—is characterized by a loss of species richness (q = 0) and a reduction in alpha diversity at the levels q = 1 and q = 2. In the case of beta diversity, sites with a different grazing intensity show remarkable differences in terms of the composition of their species assemblages. The use of VMPs is another important factor in explaining changes in dung beetle diversity. In sites with a traditional use of VMPs, a significant loss of species richness and biomass is observed, as is a notable effect on beta diversity. In addition, the absence of indicator species in sites with a historical use of VMPs corroborates the hypothesis that these substances have a ubiquitous effect on dung beetles. However, the interaction between grazing activity and VMPs when it comes to explaining changes in dung beetle diversity is less significant (or is not significant) than the main effects (each factor separately) for alpha diversity, biomass and species composition. This may be explained if we consider that both factors affect the various species differently. In other words, the reduction in dung availability affects several larger species more than it does very small species, although this does not imply that the former are more susceptible to injury caused by the ingestion of dung contaminated with VMPs. Finally, in order to prevent negative consequences for dung beetle diversity, we propose the maintenance of a moderate grazing intensity and the rational use o…
bibliographic citation: Tonelli et al. (2017) Effects of grazing intensity and the use of veterinary medical products on dung beetle biodiversity in the sub-mountainous landscape of Central Italy. PeerJ 5:e2780 https://doi.org/10.7717/peerj.2780
date submitted: 2016-08-15
date accepted: 2016-11-10
issued: 2017-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tonelli
  given name: Mattia
author list: Agent
  family name: Verdú
  given name: José R.
author list: Agent
  family name: Zunino
  given name: Mario E.
doi: 10.7717/peerj.2780
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-12
copyright: ©2017 Tonelli et al.
attribution name: Tonelli et al.

Optimizing the use of a sensor resource for opponent polarization coding
type: item
type: AcademicArticle
description: Flies use specialized photoreceptors R7 and R8 in the dorsal rim area (DRA) to detect skylight polarization. R7 and R8 form a tiered waveguide (central rhabdomere pair, CRP) with R7 on top, filtering light delivered to R8. We examine how the division of a given resource, CRP length, between R7 and R8 affects their ability to code polarization angle. We model optical absorption to show how the length fractions allotted to R7 and R8 determine the rates at which they transduce photons, and correct these rates for transduction unit saturation. The rates give polarization signal and photon noise in R7, and in R8. Their signals are combined in an opponent unit, intrinsic noise added, and the unit’s output analysed to extract two measures of coding ability, number of discriminable polarization angles and mutual information. A very long R7 maximizes opponent signal amplitude, but codes inefficiently due to photon noise in the very short R8. Discriminability and mutual information are optimized by maximizing signal to noise ratio, SNR. At lower light levels approximately equal lengths of R7 and R8 are optimal because photon noise dominates. At higher light levels intrinsic noise comes to dominate and a shorter R8 is optimum. The optimum R8 length fractions falls to one third. This intensity dependent range of optimal length fractions corresponds to the range observed in different fly species and is not affected by transduction unit saturation. We conclude that a limited resource, rhabdom length, can be divided between two polarization sensors, R7 and R8, to optimize opponent coding. We also find that coding ability increases sub-linearly with total rhabdom length, according to the law of diminishing returns. Consequently, the specialized shorter central rhabdom in the DRA codes polarization twice as efficiently with respect to rhabdom length than the longer rhabdom used in the rest of the eye.
format: application/pdf
format: text/html
creator: Francisco J.H. Heras
creator: Simon B. Laughlin
subject: Animal Behavior
subject: Biophysics
subject: Mathematical Biology
subject: Neuroscience
subject: Zoology
description: doi:10.7717/peerj.2772
publisher: PeerJ Inc.
rights: © 2017 Heras and Laughlin
abstract: Flies use specialized photoreceptors R7 and R8 in the dorsal rim area (DRA) to detect skylight polarization. R7 and R8 form a tiered waveguide (central rhabdomere pair, CRP) with R7 on top, filtering light delivered to R8. We examine how the division of a given resource, CRP length, between R7 and R8 affects their ability to code polarization angle. We model optical absorption to show how the length fractions allotted to R7 and R8 determine the rates at which they transduce photons, and correct these rates for transduction unit saturation. The rates give polarization signal and photon noise in R7, and in R8. Their signals are combined in an opponent unit, intrinsic noise added, and the unit’s output analysed to extract two measures of coding ability, number of discriminable polarization angles and mutual information. A very long R7 maximizes opponent signal amplitude, but codes inefficiently due to photon noise in the very short R8. Discriminability and mutual information are optimized by maximizing signal to noise ratio, SNR. At lower light levels approximately equal lengths of R7 and R8 are optimal because photon noise dominates. At higher light levels intrinsic noise comes to dominate and a shorter R8 is optimum. The optimum R8 length fractions falls to one third. This intensity dependent range of optimal length fractions corresponds to the range observed in different fly species and is not affected by transduction unit saturation. We conclude that a limited resource, rhabdom length, can be divided between two polarization sensors, R7 and R8, to optimize opponent coding. We also find that coding ability increases sub-linearly with total rhabdom length, according to the law of diminishing returns. Consequently, the specialized shorter central rhabdom in the DRA codes polarization twice as efficiently with respect to rhabdom length than the longer rhabdom used in the rest of the eye.
bibliographic citation: Heras et al. (2017) Optimizing the use of a sensor resource for opponent polarization coding. PeerJ 5:e2772 https://doi.org/10.7717/peerj.2772
date submitted: 2016-06-27
date accepted: 2016-11-08
issued: 2017-01-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heras
  given name: Francisco J.H.
author list: Agent
  family name: Laughlin
  given name: Simon B.
doi: 10.7717/peerj.2772
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-12
copyright: ©2017 Heras and Laughlin
attribution name: Heras and Laughlin

Handling stress may confound murine gut microbiota studies
type: item
type: AcademicArticle
description: Background Accumulating evidence indicates interactions between human milk composition, particularly sugars (human milk oligosaccharides or HMO), the gut microbiota of human infants, and behavioral effects. Some HMO secreted in human milk are unable to be endogenously digested by the human infant but are able to be metabolized by certain species of gut microbiota, including Bifidobacterium longum subsp. infantis (B. infantis), a species sensitive to host stress (Bailey & Coe, 2004). Exposure to gut bacteria like B. infantisduring critical neurodevelopment windows in early life appears to have behavioral consequences; however, environmental, physical, and social stress during this period can also have behavioral and microbial consequences. While rodent models are a useful method for determining causal relationships between HMO, gut microbiota, and behavior, murine studies of gut microbiota usually employ oral gavage, a technique stressful to the mouse. Our aim was to develop a less-invasive technique for HMO administration to remove the potential confound of gavage stress. Under the hypothesis that stress affects gut microbiota, particularly B. infantis, we predicted the pups receiving a prebiotic solution in a less-invasive manner would have the highest amount of Bifidobacteria in their gut. Methods This study was designed to test two methods, active and passive, of solution administration to mice and the effects on their gut microbiome. Neonatal C57BL/6J mice housed in a specific-pathogen free facility received increasing doses of fructooligosaccharide (FOS) solution or deionized, distilled water. Gastrointestinal (GI) tracts were collected from five dams, six sires, and 41 pups over four time points. Seven fecal pellets from unhandled pups and two pellets from unhandled dams were also collected. Qualitative real-time polymerase chain reaction (qRT-PCR) was used to quantify and compare the amount of Bifidobacterium, Bacteroides, Bacteroidetes, and Firmicutes. Resul…
format: application/pdf
format: text/html
creator: Cary R. Allen-Blevins
creator: Xiaomeng You
creator: Katie Hinde
creator: David A. Sela
subject: Food Science and Technology
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Nutrition
subject: Pediatrics
description: doi:10.7717/peerj.2876
publisher: PeerJ Inc.
rights: © 2017 Allen-Blevins et al.
abstract: Background Accumulating evidence indicates interactions between human milk composition, particularly sugars (human milk oligosaccharides or HMO), the gut microbiota of human infants, and behavioral effects. Some HMO secreted in human milk are unable to be endogenously digested by the human infant but are able to be metabolized by certain species of gut microbiota, including Bifidobacterium longum subsp. infantis (B. infantis), a species sensitive to host stress (Bailey & Coe, 2004). Exposure to gut bacteria like B. infantisduring critical neurodevelopment windows in early life appears to have behavioral consequences; however, environmental, physical, and social stress during this period can also have behavioral and microbial consequences. While rodent models are a useful method for determining causal relationships between HMO, gut microbiota, and behavior, murine studies of gut microbiota usually employ oral gavage, a technique stressful to the mouse. Our aim was to develop a less-invasive technique for HMO administration to remove the potential confound of gavage stress. Under the hypothesis that stress affects gut microbiota, particularly B. infantis, we predicted the pups receiving a prebiotic solution in a less-invasive manner would have the highest amount of Bifidobacteria in their gut. Methods This study was designed to test two methods, active and passive, of solution administration to mice and the effects on their gut microbiome. Neonatal C57BL/6J mice housed in a specific-pathogen free facility received increasing doses of fructooligosaccharide (FOS) solution or deionized, distilled water. Gastrointestinal (GI) tracts were collected from five dams, six sires, and 41 pups over four time points. Seven fecal pellets from unhandled pups and two pellets from unhandled dams were also collected. Qualitative real-time polymerase chain reaction (qRT-PCR) was used to quantify and compare the amount of Bifidobacterium, Bacteroides, Bacteroidetes, and Firmicutes. Resul…
bibliographic citation: Allen-Blevins et al. (2017) Handling stress may confound murine gut microbiota studies. PeerJ 5:e2876 https://doi.org/10.7717/peerj.2876
date submitted: 2016-09-07
date accepted: 2016-12-07
issued: 2017-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Allen-Blevins
  given name: Cary R.
author list: Agent
  family name: You
  given name: Xiaomeng
author list: Agent
  family name: Hinde
  given name: Katie
author list: Agent
  family name: Sela
  given name: David A.
doi: 10.7717/peerj.2876
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-11
copyright: ©2017 Allen-Blevins et al.
attribution name: Allen-Blevins et al.

Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter
type: item
type: AcademicArticle
description: Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establi…
format: application/pdf
format: text/html
creator: Cara L. Fiore
creator: Christopher J. Freeman
creator: Elizabeth B. Kujawinski
subject: Biochemistry
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.2870
publisher: PeerJ Inc.
rights: © 2017 Fiore et al.
abstract: Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establi…
bibliographic citation: Fiore et al. (2017) Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter. PeerJ 5:e2870 https://doi.org/10.7717/peerj.2870
date submitted: 2016-06-21
date accepted: 2016-12-06
issued: 2017-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fiore
  given name: Cara L.
author list: Agent
  family name: Freeman
  given name: Christopher J.
author list: Agent
  family name: Kujawinski
  given name: Elizabeth B.
doi: 10.7717/peerj.2870
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-11
copyright: ©2017 Fiore et al.
attribution name: Fiore et al.

Hepatic fibrosis and factors associated with liver stiffness in HIV mono-infected individuals
type: item
type: AcademicArticle
description: Background Liver disease has become an important cause of morbidity and mortality even in those HIV-infected individuals who are devoid of hepatitis virus co-infection. The aim of this study was to evaluate the degree of hepatic fibrosis and the role of associated factors using liver stiffness measurement in HIV mono-infected patients without significant alcohol intake. Methods We performed a cross-sectional study of 101 HIV mono-infected patients recruited prospectively from March 1, 2014 to October 30, 2014 at the Center for HIV, St István and St László Hospital, Budapest, Hungary. To determine hepatic fibrosis, liver stiffness was measured with transient elastography. Demographic, immunologic and other clinical parameters were collected to establish a multivariate model. Bayesian Model Averaging (BMA) was performed to identify predictors of liver stiffness. Results Liver stiffness ranged from 3.0–34.3 kPa, with a median value of 5.1 kPa (IQR 1.7). BMA provided a very high support for age (Posterior Effect Probability-PEP: 84.5%), moderate for BMI (PEP: 49.3%), CD4/8 ratio (PEP: 44.2%) and lipodystrophy (PEP: 44.0%). For all remaining variables, the model rather provides evidence against their effect. These results overall suggest that age and BMI have a positive association with LS, while CD4/8 ratio and lipodystrophy are negatively associated. Discussion Our findings shed light on the possible importance of ageing, overweight and HIV-induced immune dysregulation in the development of liver fibrosis in the HIV-infected population. Nonetheless, further controlled studies are warranted to clarify causal relations.
format: application/pdf
format: text/html
creator: Mihály Sulyok
creator: Tamás Ferenci
creator: Mihály Makara
creator: Gábor Horváth
creator: János Szlávik
creator: Zsófia Rupnik
creator: Luca Kormos
creator: Zsuzsanna Gerlei
creator: Zita Sulyok
creator: István Vályi-Nagy
subject: Gastroenterology and Hepatology
subject: HIV
subject: Public Health
description: doi:10.7717/peerj.2867
publisher: PeerJ Inc.
rights: © 2017 Sulyok et al.
abstract: Background Liver disease has become an important cause of morbidity and mortality even in those HIV-infected individuals who are devoid of hepatitis virus co-infection. The aim of this study was to evaluate the degree of hepatic fibrosis and the role of associated factors using liver stiffness measurement in HIV mono-infected patients without significant alcohol intake. Methods We performed a cross-sectional study of 101 HIV mono-infected patients recruited prospectively from March 1, 2014 to October 30, 2014 at the Center for HIV, St István and St László Hospital, Budapest, Hungary. To determine hepatic fibrosis, liver stiffness was measured with transient elastography. Demographic, immunologic and other clinical parameters were collected to establish a multivariate model. Bayesian Model Averaging (BMA) was performed to identify predictors of liver stiffness. Results Liver stiffness ranged from 3.0–34.3 kPa, with a median value of 5.1 kPa (IQR 1.7). BMA provided a very high support for age (Posterior Effect Probability-PEP: 84.5%), moderate for BMI (PEP: 49.3%), CD4/8 ratio (PEP: 44.2%) and lipodystrophy (PEP: 44.0%). For all remaining variables, the model rather provides evidence against their effect. These results overall suggest that age and BMI have a positive association with LS, while CD4/8 ratio and lipodystrophy are negatively associated. Discussion Our findings shed light on the possible importance of ageing, overweight and HIV-induced immune dysregulation in the development of liver fibrosis in the HIV-infected population. Nonetheless, further controlled studies are warranted to clarify causal relations.
bibliographic citation: Sulyok et al. (2017) Hepatic fibrosis and factors associated with liver stiffness in HIV mono-infected individuals. PeerJ 5:e2867 https://doi.org/10.7717/peerj.2867
date submitted: 2015-07-31
date accepted: 2016-12-06
issued: 2017-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sulyok
  given name: Mihály
author list: Agent
  family name: Ferenci
  given name: Tamás
author list: Agent
  family name: Makara
  given name: Mihály
author list: Agent
  family name: Horváth
  given name: Gábor
author list: Agent
  family name: Szlávik
  given name: János
author list: Agent
  family name: Rupnik
  given name: Zsófia
author list: Agent
  family name: Kormos
  given name: Luca
author list: Agent
  family name: Gerlei
  given name: Zsuzsanna
author list: Agent
  family name: Sulyok
  given name: Zita
author list: Agent
  family name: Vályi-Nagy
  given name: István
doi: 10.7717/peerj.2867
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-11
copyright: ©2017 Sulyok et al.
attribution name: Sulyok et al.

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
type: item
type: AcademicArticle
description: The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.
format: application/pdf
format: text/html
creator: Ilias Lagkouvardos
creator: Sandra Fischer
creator: Neeraj Kumar
creator: Thomas Clavel
subject: Bioinformatics
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.2836
publisher: PeerJ Inc.
rights: © 2017 Lagkouvardos et al.
abstract: The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.
bibliographic citation: Lagkouvardos et al. (2017) Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 5:e2836 https://doi.org/10.7717/peerj.2836
date submitted: 2016-07-29
date accepted: 2016-11-28
issued: 2017-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lagkouvardos
  given name: Ilias
author list: Agent
  family name: Fischer
  given name: Sandra
author list: Agent
  family name: Kumar
  given name: Neeraj
author list: Agent
  family name: Clavel
  given name: Thomas
doi: 10.7717/peerj.2836
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-11
copyright: ©2017 Lagkouvardos et al.
attribution name: Lagkouvardos et al.

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