Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea
Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300–2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf.
Mindel et al. (2016) Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea. PeerJ 4:e2387 https://doi.org/10.7717/peerj.2387
The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets
An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%–99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development.
Li et al. (2016) The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets. PeerJ 4:e2443 https://doi.org/10.7717/peerj.2443
Emotion recognition using Kinect motion capture data of human gaits
Automatic emotion recognition is of great value in many applications, however, to fully display the application value of emotion recognition, more portable, non-intrusive, inexpensive technologies need to be developed. Human gaits could reflect the walker’s emotional state, and could be an information source for emotion recognition. This paper proposed a novel method to recognize emotional state through human gaits by using Microsoft Kinect, a low-cost, portable, camera-based sensor. Fifty-nine participants’ gaits under neutral state, induced anger and induced happiness were recorded by two Kinect cameras, and the original data were processed through joint selection, coordinate system transformation, sliding window gauss filtering, differential operation, and data segmentation. Features of gait patterns were extracted from 3-dimentional coordinates of 14 main body joints by Fourier transformation and Principal Component Analysis (PCA). The classifiers NaiveBayes, RandomForests, LibSVM and SMO (Sequential Minimal Optimization) were trained and evaluated, and the accuracy of recognizing anger and happiness from neutral state achieved 80.5% and 75.4%. Although the results of distinguishing angry and happiness states were not ideal in current study, it showed the feasibility of automatically recognizing emotional states from gaits, with the characteristics meeting the application requirements.
Li et al. (2016) Emotion recognition using Kinect motion capture data of human gaits. PeerJ 4:e2364 https://doi.org/10.7717/peerj.2364
A juvenile subfossil crocodylian from Anjohibe Cave, Northwestern Madagascar
Madagascar’s subfossil record preserves a diverse community of animals including elephant birds, pygmy hippopotamus, giant lemurs, turtles, crocodiles, bats, rodents, and carnivorans. These fossil accumulations give us a window into the island’s past from 80,000 years ago to a mere few hundred years ago, recording the extinction of some groups and the persistence of others. The crocodylian subfossil record is limited to two taxa, Voay robustus and Crocodylus niloticus, found at sites distributed throughout the island. V. robustus is extinct while C. niloticus is still found on the island today, but whether these two species overlapped temporally, or if Voay was driven to extinction by competing with Crocodylus remains unknown. While their size and presumed behavior was similar to each other, nearly nothing is known about the growth and development of Voay, as the overwhelming majority of fossil specimens represent mature adult individuals. Here we describe a nearly complete juvenile crocodylian specimen from Anjohibe Cave, northwestern Madagascar. The specimen is referred to Crocodylus based on the presence of caviconchal recesses on the medial wall of the maxillae, and to C. niloticus based on the presence of an oval shaped internal choana, lack of rostral ornamentation and a long narrow snout. However, as there are currently no described juvenile specimens of Voay robustus, it is important to recognize that some of the defining characteristics of that genus may have changed through ontogeny. Elements include a nearly complete skull and many postcranial elements (cervical, thoracic, sacral, and caudal vertebrae, pectoral elements, pelvic elements, forelimb and hindlimb elements, osteoderms). Crocodylus niloticus currently inhabits Madagascar but is locally extinct from this particular region; radiometric dating indicates an age of ∼460–310 years before present (BP). This specimen clearly represents a juvenile based on the extremely small size and open sutures/detached neural arches; total body length is estimated to be ∼1.1 m (modern adults of this species range from ∼4–6 m). This fossil represents the only juvenile subfossil crocodylian specimen reported from Madagascar.
Mathews et al. (2016) A juvenile subfossil crocodylian from Anjohibe Cave, Northwestern Madagascar. PeerJ 4:e2296 https://doi.org/10.7717/peerj.2296
Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline
Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT (Pneumococcal Capsule Typing). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external validation set of 2964 isolates from Thailand (n = 2,531), USA (n = 181) and Iceland (n = 252). PneumoCaT was able to predict serotype in 99.1% of the typeable UK isolates and in 99.0% of the non-UK isolates. Concordance was evaluated in UK isolates where further investigation was possible; in 91.5% of the cases the predicted capsular type was concordant with the serologically derived serotype. Following retesting, concordance increased to 99.3% and in most resolved cases (97.8%; 135/138) discordance was shown to be caused by errors in original serotyping. Replicate testing demonstrated that PneumoCaT gave 100% reproducibility of the predicted serotype result. In summary, we have developed a WGS-based serotyping method that can predict capsular type to serotype level for 89/94 serotypes and to serogroup level for the remaining four. This approach could be integrated into routine typing workflows in reference laboratories, reducing the need for phenotypic immunological testing.
Kapatai et al. (2016) Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ 4:e2477 https://doi.org/10.7717/peerj.2477
Gua Sha, a press-stroke treatment of the skin, boosts the immune response to intradermal vaccination
Objective The skin is an important immunological barrier of the body as well as an optimal route for vaccine administration. Gua Sha, which involves press-stroke treatment of the skin, is an effective folk therapy, widely accepted in East Asia, for various symptoms; however, the mechanisms underlying its therapeutic effects have not been clarified. We investigated the influence of Gua Sha on the immunological features of the skin. Methods Gua Sha was performed on BALB/c mice and the effects were evaluated using anatomical, histological, and cytometric methods as well as cytokine determination locally and systemically. The effect on intradermal vaccination was assessed with antigen-specific subtype antibody responses. Results Blood vessel expansion, erythrocyte extravasation, and increased ratios of immune active cells were observed in the skin tissue following the treatment. Pro-inflammatory cytokines were up-regulated, and immunosuppressive cytokines, down-regulated, in the treated and untreated skin and systemic circulation; no obvious variations were detected in case of anti-inflammatory cytokines. Interestingly, intradermal delivery of a model vaccine following Gua Sha induced about three-fold higher IgG titers with a more Th1-biased antibody subtype profile. Conclusion Gua Sha treatment can up-regulate the innate and adaptive immune functions of the skin and boost the response against intradermal antigens. Thus, Gua Sha may serve as a safe, inexpensive, and independent physical adjuvant for intradermal vaccination.
Chen et al. (2016) Gua Sha, a press-stroke treatment of the skin, boosts the immune response to intradermal vaccination. PeerJ 4:e2451 https://doi.org/10.7717/peerj.2451
Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls
Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.
Belstrøm et al. (2016) Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PeerJ 4:e2433 https://doi.org/10.7717/peerj.2433
Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV
Pain burden is high in people living with HIV (PLWH), but the effect of this pain on functionality is equivocal. Resilience, the ability to cope with adversity, may promote adaptation to pain, so we hypothesised that higher resilience would correlate with less pain-related impairment of activity. We recruited 197 black South African PLWH, 99 with chronic pain (CP) and 98 patients without. We measured pain intensity and interference using the Brief Pain Inventory, and resilience using the Resilience Scale. Participants were generally highly resilient. Greater resilience correlated with better health-related quality of life, but not with pain intensity or interference. We also measured physical activity objectively, by actigraphy, in a subset of patients (37 with chronic pain and 31 without chronic pain), who wore accelerometers for two weeks. There was no difference in duration or intensity of activity between those with and without pain, and activity was not associated with resilience. In this sample, pain was not associated with altered physical activity. Resilience did not explain differences in pain intensity or pain interference but was associated with improved quality of life. Financial stresses and the fear of HIV stigma may have driven patients to conceal pain and to suppress its expected impairment of activity.
Wadley et al. (2016) Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV. PeerJ 4:e2464 https://doi.org/10.7717/peerj.2464
Lowland tapir distribution and habitat loss in South America
The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management.
Cordeiro et al. (2016) Lowland tapir distribution and habitat loss in South America. PeerJ 4:e2456 https://doi.org/10.7717/peerj.2456
An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus)
Background African grey parrots (Psittacus erithacus) are kept as pets and are frequently hand-reared. It has been observed that hand-reared African grey parrots may develop behavioral disorders such as feather damaging behavior (FDB). It is well known that chronic stress is involved in behavioral disorders in captive parrots. The main glucocorticoid in birds is corticosterone; its quantification provides information about adrenocortical activity and is considered to be a reliable indicator of stress levels in birds. We analyzed the differences in the excretion of corticosterone metabolites (CM) in the droppings of African grey parrots characterized by: 1. different rearing histories (parent rearing vs. hand rearing); and 2. the presence or absence of FDB in hand-reared parrots. Methods A total of 82 African grey parrots that were kept in captivity were considered. According to breeding methods, three groups of birds were defined: 1. The parent-reared (PR) parrots included birds kept in pairs (n = 30 pairs) with a conspecific partner of the opposite sex. All of these birds were healthy and never showed FDB signs; 2. The healthy hand-reared parrots (H-HR) included pet parrots individually kept, that were hand-reared and did not display any sign of FDB (n = 11, 7 males and 4 females); 3. The FDB hand-reared parrot (FDB-HR) included pet parrots individually kept, that were hand-reared and displayed FDB (n = 11, 7 males and 4 females). Droppings were collected in the morning over three alternating days in autumn 2014 and spring 2015. The CM were determined using a multi-species corticosterone enzyme immunoassay kit. Split-plot repeated-measure ANOVA was used to examine any differences using group, season and group × season as the main factors. Results Different quantities of CM in droppings were found for the three groups. The mean CM value was 587 ng/g in the PR parrots, 494 ng/g in the H-HR parrots and 1,744 ng/g in the FDB-HR parrots, irrespective of the season. The excretion of CM in FDB-HR was significantly higher than in PR or H-HR parrots. CM in droppings were not influenced by the season (autumn vs. spring); furthermore, the interaction between group and sampling season was not significant. Limited to the H-HR and FDB-HR groups, a trend in the significance of the difference in the mean CM excreted by male and female birds was observed, with the levels excreted by males being higher than those excreted by females. When the effect of age was considered (in the two separate groups), there was a statistically significant positive correlation only for H-HR. Conclusions The highest amount of CM excretion was found in FDB-HR parrots, and a positive correlation between age and CM excretion was found in H-HR. Given that the CM excretion of both PR and H-HR parrots was similar in our study, future research is recommended to investigate the specific aspects of hand-rearing to improve parrot welfare.
Costa et al. (2016) An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus). PeerJ 4:e2462 https://doi.org/10.7717/peerj.2462