title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1728 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The evolution of logic circuits for the purpose of protein contact map prediction link: https://peerj.com/articles/3139 last-modified: 2017-04-18 description: Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset. creator: Samuel D. Chapman creator: Christoph Adami creator: Claus O. Wilke creator: Dukka B KC uri: https://doi.org/10.7717/peerj.3139 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chapman et al. title: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab link: https://peerj.com/articles/3040 last-modified: 2017-04-18 description: Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement. The system processes digital photographs from a photo apparatus into landmarks, and uses ratios of measurements among those landmarks, as well as (in a preliminary exploration) two measurements that approximate aspects of coloration, as the basis for classification. This project has thus produced a working prototype that achieves reasonably robust correct identification rates, although many more developments can and will be added, and—more broadly—the project illustrates the value of multidisciplinary collaborations in resolving difficult and complex challenges. creator: Rodrigo Gurgel-Gonçalves creator: Ed Komp creator: Lindsay P. Campbell creator: Ali Khalighifar creator: Jarrett Mellenbruch creator: Vagner José Mendonça creator: Hannah L. Owens creator: Keynes de la Cruz Felix creator: A Townsend Peterson creator: Janine M. Ramsey uri: https://doi.org/10.7717/peerj.3040 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gurgel-Gonçalves et al. title: Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California link: https://peerj.com/articles/3202 last-modified: 2017-04-13 description: The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D. Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species. We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren’t infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results also raise interesting possibilities about the effects of putative vertebrate hosts on the tick microbiome. creator: Nikos Gurfield creator: Saran Grewal creator: Lynnie S. Cua creator: Pedro J. Torres creator: Scott T. Kelley uri: https://doi.org/10.7717/peerj.3202 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gurfield et al. title: Rates of morphological evolution in Captorhinidae: an adaptive radiation of Permian herbivores link: https://peerj.com/articles/3200 last-modified: 2017-04-13 description: The evolution of herbivory in early tetrapods was crucial in the establishment of terrestrial ecosystems, although it is so far unclear what effect this innovation had on the macro-evolutionary patterns observed within this clade. The clades that entered this under-filled region of ecospace might be expected to have experienced an “adaptive radiation”: an increase in rates of morphological evolution and speciation driven by the evolution of a key innovation. However such inferences are often circumstantial, being based on the coincidence of a rate shift with the origin of an evolutionary novelty. The conclusion of an adaptive radiation may be made more robust by examining the pattern of the evolutionary shift; if the evolutionary innovation coincides not only with a shift in rates of morphological evolution, but specifically in the morphological characteristics relevant to the ecological shift of interest, then one may more plausibly infer a causal relationship between the two.Here I examine the impact of diet evolution on rates of morphological change in one of the earliest tetrapod clades to evolve high-fibre herbivory: Captorhinidae. Using a method of calculating heterogeneity in rates of discrete character change across a phylogeny, it is shown that a significant increase in rates of evolution coincides with the transition to herbivory in captorhinids. The herbivorous captorhinids also exhibit greater morphological disparity than their faunivorous relatives, indicating more rapid exploration of new regions of morphospace. As well as an increase in rates of evolution, there is a shift in the regions of the skeleton undergoing the most change; the character changes in the herbivorous lineages are concentrated in the mandible and dentition. The fact that the increase in rates of evolution coincides with increased change in characters relating to food acquisition provides stronger evidence for a causal relationship between the herbivorous diet and the radiation event. creator: Neil Brocklehurst uri: https://doi.org/10.7717/peerj.3200 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Brocklehurst title: Burden and predictors of Staphylococcus aureus and S. pseudintermedius infections among dogs presented at an academic veterinary hospital in South Africa (2007–2012) link: https://peerj.com/articles/3198 last-modified: 2017-04-13 description: BackgroundStaphylococci are commensals of the mucosal surface and skin of humans and animals, but have been implicated in infections such as otitis externa, pyoderma, urinary tract infections and post-surgical complications. Laboratory records provide useful information to help investigate these infections. Therefore, the objective of this study was to investigate the burdens of these infections and use multinomial regression to examine the associations between various Staphylococcus infections and demographic and temporal factors among dogs admitted to an academic veterinary hospital in South Africa.MethodsRecords of 1,497 clinical canine samples submitted to the bacteriology laboratory at a veterinary academic hospital between 2007 and 2012 were included in this study. Proportions of staphylococcal positive samples were calculated, and a multinomial logistic regression model was used to identify predictors of staphylococcal infections.ResultsTwenty-seven percent of the samples tested positive for Staphylococcus spp. The species of Staphylococcus identified were S. pseudintermedius (19.0%), S. aureus (3.8%), S. epidermidis (0.7%) and S. felis (0.1%). The remaining 2.87% consisted of unspeciated Staphylococcus. Distribution of the species by age of dog showed that S. pseudintermedius was the most common (25.6%) in dogs aged 2–4 years while S. aureus was most frequent (6.3%) in dogs aged 5–6 years. S. pseudintermedius (34.1%) and S. aureus (35.1%) were the most frequently isolated species from skin samples. The results of the multivariable multinomial logistic regression model identified specimen, year and age of the dog as significant predictors of the risk of infection with Staphylococcus. There was a significant temporal increase (RRR = 1.17; 95% CI [1.06–1.29]) in the likelihood of a dog testing positive for S. pseudintermedius compared to testing negative. Dogs ≤ 8 years of age were significantly more likely to test positive for S. aureus than those >8 years of age. Similarly, dogs between 2–8 years of age were significantly more likely to test positive for S. pseudintermedius than those >8 years of age. In addition, dogs 2–4 years of age (RRR = 1.83; 1.09–3.06) were significantly more likely to test positive for S. pseudintermedius compared to those <2 years of age. The risk of infection with S. pseudintermedius or S. aureus was significantly higher in ear canal and skin specimens compared to other specimens.ConclusionsThe findings suggest that S. pseudintermedius and S. aureus were the most commonly isolated species from dogs presented at the study hospital. Age of the dog and the location of infection were significant predictors of infection with both Staphylococcus species investigated. Significant increasing temporal trend was observed for S. pseudintermedius but not S. aureus. This information is useful for guiding clinical decisions as well as future research. creator: Daniel N. Qekwana creator: James Wabwire Oguttu creator: Fortune Sithole creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.3198 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Qekwana et al. title: Susceptibility of Human Oral Squamous Cell Carcinoma (OSCC) H103 and H376 cell lines to Retroviral OSKM mediated reprogramming link: https://peerj.com/articles/3174 last-modified: 2017-04-13 description: Although numbers of cancer cell lines have been shown to be successfully reprogrammed into induced pluripotent stem cells (iPSCs), reprogramming Oral Squamous Cell Carcinoma (OSCC) to pluripotency in relation to its cancer cell type and the expression pattern of pluripotent genes under later passage remain unexplored. In our study, we reprogrammed and characterised H103 and H376 oral squamous carcinoma cells using retroviral OSKM mediated method. Reprogrammed cells were characterized for their embryonic stem cells (ESCs) like morphology, pluripotent gene expression via quantitative real-time polymerase chain reaction (RT-qPCR), immunofluorescence staining, embryoid bodies (EB) formation and directed differentiation capacity. Reprogrammed H103 (Rep-H103) exhibited similar ESCs morphologies with flatten cells and clear borders on feeder layer. Reprogrammed H376 (Rep-H376) did not show ESCs morphologies but grow with a disorganized morphology. Critical pluripotency genes Oct4, Sox2 and Nanog were expressed higher in Rep-H103 against the parental counterpart from passage 5 to passage 10. As for Rep-H376, Nanog expression against its parental counterpart showed a significant decrease at passage 5 and although increased in passage 10, the level of expression was similar to the parental cells. Rep-H103 exhibited pluripotent signals (Oct4, Sox2, Nanog and Tra-1-60) and could form EB with the presence of three germ layers markers. Rep-H103 displayed differentiation capacity into adipocytes and osteocytes. The OSCC cell line H103 which was able to be reprogrammed into an iPSC like state showed high expression of Oct4, Sox2 and Nanog at late passage and may provide a potential iPSC model to study multi-stage oncogenesis in OSCC. creator: Nalini Devi Verusingam creator: Swee Keong Yeap creator: Huynh Ky creator: Ian C. Paterson creator: Suan Phaik Khoo creator: Soon Keng Cheong creator: Alan H.K. Ong creator: Tunku Kamarul uri: https://doi.org/10.7717/peerj.3174 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Verusingam et al. title: Metformin ameliorates insulitis in STZ-induced diabetic mice link: https://peerj.com/articles/3155 last-modified: 2017-04-13 description: Background & AimsMetformin is currently the most widely used first-line hypoglycemic agent for diabetes mellitus. Besides glucose-lowering action, there is increasingly interest in the potential anti-inflammatory action of this drug. In the present study, we investigated the actions of metformin on experimental insulitis using STZ-induced diabetic mice.MethodsMice with acute diabetes induced by STZ were administered metformin by gavage. Changes of blood glucose and body weight, and the daily amount of food and water intake were measured. Pancreatic tissues were collected for histologic analyses. Pathological assessment and immunohistochemistry analysis were used to determine the effect of metformin on insulitis. Inflammatory cytokines in the pancreas and insulin levels were measured through ELISA analysis.ResultsMetformin significantly reduced blood glucose levels and improved aberrant water intake behavior in experimental diabetic mice. No significant differences were observed in terms of body weight and food intake behavior in metformin-treated animals. In the STZ-induced model of diabetes, we found the appearance of pronounced insulitis. However, metformin administration reduced the severity of insulitis assessed by blind pathological scoring. In addition, metformin treatment improved insulin levels in experimental diabetic mice. ELISA assay revealed decreased levels of inflammatory response marker IL-1β and TNF-α in the pancreatic tissues following metformin treatment.ConclusionMetformin attenuated insulitis in the STZ-induced mice model of diabetes. This islet-protective effect might be partly correlated with the anti-inflammatory action of metformin. creator: Xue Han creator: Yu-Long Tao creator: Ya-Ping Deng creator: Jia-Wen Yu creator: Jian Cai creator: Guo-Fei Ren creator: Yuan-Nan Sun creator: Guo-Jun Jiang uri: https://doi.org/10.7717/peerj.3155 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Han et al. title: Meloxicam ameliorates the cartilage and subchondral bone deterioration in monoiodoacetate-induced rat osteoarthritis link: https://peerj.com/articles/3185 last-modified: 2017-04-12 description: ObjectiveThis study aimed to quantify the cartilage- and subchondral bone-related effects of low-dose and high-dose meloxicam treatment in the late phase of mono-iodoacetate-induced osteoarthritis of the stifle.MethodsThirty-four male Wistar rats received intra-articular injection of mono-iodoacetate to trigger osteoarthritis; 10 control animals (Grp Co) received saline. The mono-iodoacetate-injected rats were assigned to three groups and treated from week 4 to the end of week 7 with placebo (Grp P, n = 11), low-dose (GrpM Lo, 0.2 mg/kg, n = 12) or high-dose (GrpM Hi, 1 mg/kg, n = 11) meloxicam. After a period of 4 additional weeks (end of week 11) the animals were sacrificed, and the stifle joints were examined histologically and immunohistochemically for cyclooxygenase 2, in conformity with recommendations of the Osteoarthritis Research Society International. Serum cytokines IL-6, TNFα and IL-10 were measured at the end of weeks 3, 7, and 11.ResultsCompared with saline-treated controls, animals treated with mono-iodoacetate developed various degrees of osteoarthritis. The cartilage degeneration score and the total cartilage degeneration width were significantly lower in both the low-dose (p = 0.012 and p = 0.014) and high-dose (p = 0.003 and p = 0.006) meloxicam-treated groups than in the placebo group. In the subchondral bone, only high-dose meloxicam exerted a significant protective effect (p = 0.011). Low-grade Cox-2 expression observed in placebo-treated animals was abolished in both meloxicam groups. Increase with borderline significance of TNFα in GrpP from week 3 to week 7 (p = 0.049) and reduction of IL-6 in GrpM Lo from week 3 to week 11 (p = 0.044) were observed.ConclusionIn this rat model of osteoarthritis, both low-dose and high-dose meloxicam had a chondroprotective effect, and the high dose also protected against subchondral bone lesions. The results suggest a superior protection of the high-dose meloxicam arresting the low-grade inflammatory pathway accompanied by chronic cartilage deterioration. creator: Előd Nagy creator: Enikő Vajda creator: Camil Vari creator: Sándor Sipka creator: Ana-Maria Fárr creator: Emőke Horváth uri: https://doi.org/10.7717/peerj.3185 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nagy et al. title: Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing link: https://peerj.com/articles/3176 last-modified: 2017-04-12 description: There is an urgent need to identify and understand the ecosystem services of pollination and seed dispersal provided by threatened mammals such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of bats presents a particularly challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through DNA metabarcoding of plants in flying fox droppings, using primers targeting the rbcL gene, we identified at least 29 Operationally Taxonomic Units (OTUs) comprising the diet of this giant pteropodid. OTU sequences matched at least four genera and 14 plant families from online reference databases based on a conservative Least Common Ancestor approach, and eight species from our site-specific plant reference collection. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. At this point in time, more accurate genus- and species-level identification of OTUs not only requires support from databases with more representative sequences of relevant plant DNA, but probably necessitates in situ collection of plant specimens to create a reference collection. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa and spatio-temporal patterns in flying fox diets. creator: Sheema Abdul Aziz creator: Gopalasamy Reuben Clements creator: Lee Yin Peng creator: Ahimsa Campos-Arceiz creator: Kim R. McConkey creator: Pierre-Michel Forget creator: Han Ming Gan uri: https://doi.org/10.7717/peerj.3176 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Aziz et al. title: gb4gv: a genome browser for geminivirus link: https://peerj.com/articles/3165 last-modified: 2017-04-12 description: BackgroundGeminiviruses (family Geminiviridae) are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, the NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc.MethodsWe have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases.ResultsThese data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser.DiscussionWith the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in the Geminiviridae.Availability and ImplementationThe database can be found at: http://gb4gv.lafayette.edu. creator: Eric S. Ho creator: Catherine M. Newsom-Stewart creator: Lysa Diarra creator: Caroline S. McCauley uri: https://doi.org/10.7717/peerj.3165 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ho et al.