title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1131 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions link: https://peerj.com/articles/9255 last-modified: 2020-05-21 description: Here we aim to describe early mutational events across samples from publicly available SARS-CoV-2 sequences from the sequence read archive and GenBank repositories. Up until 27 March 2020, we downloaded 50 illumina datasets, mostly from China, USA (WA State) and Australia (VIC). A total of 30 datasets (60%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA next-generation sequencing samples. Sequencing samples from North America in GenBank (22 April 2020) present this signature with up to 39% allele frequencies among samples (n = 1,359). Australian variant signatures were more diverse than USA samples, but still, clonal events were found in these samples. Mutations in the helicase, encoded by the ORF1ab gene in SARS-CoV-2 were predominant, among others, suggesting that these regions are actively evolving. Finally, we firmly urge that primer sets for diagnosis be carefully designed, since rapidly occurring variants would affect the performance of the reverse transcribed quantitative PCR (RT-qPCR) based viral testing. creator: Carlos Farkas creator: Francisco Fuentes-Villalobos creator: Jose Luis Garrido creator: Jody Haigh creator: María Inés Barría uri: https://doi.org/10.7717/peerj.9255 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Farkas et al. title: High expression of stromal signatures correlated with macrophage infiltration, angiogenesis and poor prognosis in glioma microenvironment link: https://peerj.com/articles/9038 last-modified: 2020-05-20 description: Glioma is one of the most fatal tumors in central nervous system. Previous studies gradually revealed the association between tumor microenvironment and the prognosis of gliomas patients. However, the correlation between tumor-infiltrating immune cell and stromal signatures are unknown. In our study, we obtained gliomas samples from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). The landscape of tumor infiltrating immune cell subtypes in gliomas was calculated by CIBERSORT. As a result, we found high infiltration of macrophages was correlated with poor outcome (P < 0.05). Then functional enrichment analysis of high/low macrophage-infiltrating groups was performed by GSEA. The results showed three gene sets includes 102 core genes about angiogenesis were detected in high macrophage-infiltrating group. Next, we constructed PPI network and analyzed prognostic value of 102 core genes. We found that five stromal signatures indicated poor prognosis which including HSPG2, FOXF1, KDR, COL3A1, SRPX2 (P < 0.05). Five stromal signatures were adopted to construct a classifier. The classifier showed powerful predictive ability (AUC = 0.748). Patients with a high risk score showed poor survival. Finally, we validated this classifier in TCGA and the result was consistent with CGGA. Our investigation of tumor microenvironment in gliomas may stimulate the new strategy in immunotherapy. Five stromal signature correlated with poor prognosis also provide a strong predator of gliomas patient outcome. creator: Yixin Tian creator: Yiquan Ke creator: Yanxia Ma uri: https://doi.org/10.7717/peerj.9038 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tian et al. title: Distribution of the acoustic occurrence of dolphins during the summers 2011 to 2015 in the Upper Gulf of California, Mexico link: https://peerj.com/articles/9121 last-modified: 2020-05-20 description: Baseline knowledge of spatial and temporal distribution patterns is essential for cetacean management and conservation. Such knowledge is particularly important in areas where gillnet fishing occurs, as the Upper Gulf of California, which increases the probability of bycatch of cetaceans. In this area, the vaquita porpoise (Phocoena sinus) has been widely studied, but the knowledge of other cetaceans is scarce and based on traditional visual survey methods. We used data collected by an array of acoustic click detectors (C-PODs) during the summers 2011 to 2015 to analyze the distribution of dolphins in the Vaquita Refuge in the Upper Gulf of California. We recorded 120,038 echolocation click trains of dolphins during 12,371 days of recording effort at 46 sampling sites. Based on simultaneous visual and acoustic data, we estimated a false positive acoustic detection rate of 19.4%. Dolphin acoustic activity varied among sites, with higher activity in the east of the Vaquita Refuge. Acoustic activity was higher at night than during the day. We used negative binomial generalized linear models to study the count of clicks of dolphins in relation to spatial, temporal, physical, biological and anthropogenic explanatory variables. The best model selected for the response variable included sampling site, day-night condition, and vertical component of tide speed. Patterns in the spatial distribution of predicted acoustic activity of dolphins were similar to the acoustic activity observed per sampling season. Higher acoustic activity was predicted at night, but the tide speed variable was not relevant under this condition. Acoustic activity patterns could be related to the availability of prey resources since echolocation click trains are associated with foraging activities of dolphins. This is the first study of the distribution of dolphins in Mexico using medium-term systematic passive acoustic monitoring, and the results can contribute to better management to the natural protected area located in the Upper Gulf of California. creator: Gustavo Cárdenas Hinojosa creator: Horacio de la Cueva creator: Tim Gerrodette creator: Armando M. Jaramillo-Legorreta uri: https://doi.org/10.7717/peerj.9121 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Impact of cost distance and habitat fragmentation on the daily path length of Rhinopithecus bieti link: https://peerj.com/articles/9165 last-modified: 2020-05-20 description: An understanding of primate movement patterns in response to natural and anthropogenically induced changes in habitat heterogeneity, food availability, and plant species distribution is essential for developing effective management and conservation programs. Therefore, from July 2013 to June 2014, we examined the effects of landscape configuration on the ranging behavior (daily path length, DPL) of the Endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) in the Baimaxueshan National Nature Reserve (27°34′N, 99°17′E) in Gehuaqing, China. Given the extreme difficulties in following the study group across high altitude mountainous terrain across an elevation of 2,500–4,000 m, we were only able to collect DPL using 3-4 GPS points per day on 21 individual days. We found that R. bieti traveled the shortest DPL in winter (1,141.31 m), followed by spring (2,034.06 m) and autumn (2,131.19 m). The cost distance, a statistical tool designed to estimate the difficulty of a species moving across its distributional range, was lowest in autumn (205.47), followed by spring (225.93) and winter (432.59) (one-way ANOVA: F = 3.852, P = 0.026, df = 2). The habitat fragmentation index (HFI), which measures the density of forest patches, indicated areas visited in the winter were more fragmented (HFI = 2.16) compared to spring (HFI = 1.83) or autumn (HFI = 1.3). Although our results should be considered preliminary, they suggest that both the availability of suitable travel routes and habitat fragmentation, driven by high-intensity human disturbance, constrain the movement of R. bieti. We found that undisturbed areas of the bands’ range contained a high density of lichens, which represent a nutritious and abundant and year-round food source for Yunnan snub-nosed monkeys. In order to protect this Endangered species, we recommend that researchers construct detailed maps of landscape heterogeneity, particularly habitat connectivity, forest fragmentation, and seasonal variation in the location of major food patches in order to better understand and mitigate the effects of seasonal habitat change on patterns of R. bieti habitat utilization and population viability. creator: Cong Li creator: Xumao Zhao creator: Dayong Li creator: Paul Alan Garber creator: Zuofu Xiang creator: Ming Li creator: Huijuan Pan uri: https://doi.org/10.7717/peerj.9165 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: The effect of landscape on functional connectivity and shell shape in the land snail Humboldtiana durangoensis link: https://peerj.com/articles/9177 last-modified: 2020-05-20 description: The populations of Humboldtiana durangoensis have experienced a drastic reduction in the effective population size; in addition, the species is threatened by anthropogenic activities. For the aforementioned, landscape genetics will serve as a tool to define the potential evolutionarily significant units (ESU) for this species. To complete our objective, we evaluated the effect of cover vegetation and climate on the functional connectivity of the species from the last glacial maximum (LGM) to the present as well as the effect of climate on shell shape. Partial Mantel tests, distance-based redundance analysis and a Bayesian framework were used to evaluate connectivity. On the other hand, geometric morphometrics, phylogenetic principal component analysis and redundancy analysis were used for the analysis of shell shape. Our results suggest that the suitable areas have been decreasing since the LGM; also, vegetation cover rather than climate has influenced the genetic connectivity among land snail populations, although temperature had a high influence on shell shape in this species. In conclusion, vegetation cover was the main factor that determined the functional connectivity for the land snail; however, local selective pressures led to different phenotypes in shell shape that allowed us to postulate that each one of the previously defined genetic groups must be considered as a different ESU. creator: Benjamín López creator: Omar Mejía creator: Gerardo Zúñiga uri: https://doi.org/10.7717/peerj.9177 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 López et al. title: A new species of freshwater crab of the genus Qianguimon Huang, 2018 (Decapoda: Brachyura: Potamidae) from Guangxi, Southern China link: https://peerj.com/articles/9194 last-modified: 2020-05-20 description: A new species of freshwater crab of the genus QianguimonHuang, 2018, is described from Guangxi Zhuang Autonomous Region, southern China. It can be distinguished from congeners by the following characters: male first gonopods bent inward at about 45° at base of terminal segment, carapace regions distinct and rugged and the female vulva opening inwards and downwards. In addition, molecular evidence derived from the 16S rRNA gene supported the species described in this study as a new species of Qianguimon. creator: Song-Bo Wang creator: Ya-Nan Zhang creator: Jie-Xin Zou uri: https://doi.org/10.7717/peerj.9194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Enhancement of specific T-lymphocyte responses by monocyte-derived dendritic cells pulsed with E2 protein of human papillomavirus 16 and human p16INK4A link: https://peerj.com/articles/9213 last-modified: 2020-05-20 description: IntroductionProphylactic vaccines are already available for prevention of human papillomavirus (HPV) infection. However, we still await development of therapeutic vaccines with high efficiency for stimulating specific T lymphocytes to clear HPV infection.ObjectiveThis study investigates the potential for subunits of human p16INK4a protein and E2 protein of HPV16 to stimulate dendritic cells and enhance the specific response of T lymphocytes against HPV-infected cells.MethodologyImmunogenic epitopes of HPV16 E2 and p16INK4a proteins were predicted through the common HLA class I and II alleles present in the Thai population. Then, monocyte-derived dendritic cells (MDCs) were pulsed with HPV16 E2 and/or p16INK4a protein s and their maturity assessed. MDCs pulsed with either or both of these proteins at optimal concentrations were used for activation of autologous T lymphocytes and IFN-γ production was measured for specific response function.ResultsHPV16 E2 and p16INK4a proteins contain various immunogenic epitopes which can be presented by antigen-presenting cells via both HLA class I and II molecules. The stimulation of MDCs with either HPV16 E2 or p16INK4a proteins increased percentages and mean fluorescence intensity (MFI) of CD83+ MDCs in a dose-dependent manner. An optimum concentration of 250 ng/mL and 150 ng/mL of HPV16 E2 and p16INK4a proteins, respectively, stimulated MDCs via the MAPK pathway (confirmed by use of MAPK inhibitors). T lymphocytes could be activated by MDCs pulsed with these proteins, leading to high percentages of both CD4+ IFN-γ+ T lymphocytes and CD8+ IFN-γ+ T lymphocytes. The production of IFN-γ was higher in co-cultures containing MDCs pulsed with HPV16 E2 protein than those pulsed with p16INK4a. Interestingly, MDCs pulsed with a combination of HPV16 E2 and p16INK4a significantly increased IFN-γ production of T lymphocytes. The IFN-γ production was inhibited by both HLA class I and II blockade, particularly in co-cultures with MDCs pulsed with a combination of HPV16 E2 and p16INK4a.ConclusionsThis suggests that MDCs pulsed with both proteins enhances specific response of both CD4+ and CD8+ T lymphocytes. This study might provide a strategy for further in vivo study of stimulation of T lymphocytes for therapy of HPV-associated cancer. creator: Nuchsupha Sunthamala creator: Neeranuch Sankla creator: Jureeporn Chuerduangphui creator: Piyawut Swangphon creator: Wanchareeporn Boontun creator: Supakpong Ngaochaiyaphum creator: Weerayut Wongjampa creator: Tipaya Ekalaksananan creator: Chamsai Pientong uri: https://doi.org/10.7717/peerj.9213 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sunthamala et al. title: Non-parallel changes in songbird migration timing are not explained by changes in stopover duration link: https://peerj.com/articles/8975 last-modified: 2020-05-19 description: Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration—the time that individuals spend resting and refueling at a site—are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration—the number of days that a study site is occupied by a particular species—by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies. creator: Nicholas N. Dorian creator: Trevor L. Lloyd-Evans creator: J. Michael Reed uri: https://doi.org/10.7717/peerj.8975 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dorian et al. title: Recent advances in biochar application for water and wastewater treatment: a review link: https://peerj.com/articles/9164 last-modified: 2020-05-19 description: In the past decade, researchers have carried out a massive amount of research on the application of biochar for contaminants removal from aqueous solutions. As an emerging sorbent with great potential, biochar has shown significant advantages such as the broad sources of feedstocks, easy preparation process, and favorable surface and structural properties. This review provides an overview of recent advances in biochar application in water and wastewater treatment, including a brief discussion of the involved sorption mechanisms of contaminants removal, as well as the biochar modification methods. Furthermore, environmental concerns of biochar that need to be paid attention to and future research directions are put forward to promote the further application of biochar in practical water and wastewater treatment. creator: Xiaoqing Wang creator: Zizhang Guo creator: Zhen Hu creator: Jian Zhang uri: https://doi.org/10.7717/peerj.9164 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The ability of oriental magpies (Pica serica) to solve baited multiple-string problems link: https://peerj.com/articles/9200 last-modified: 2020-05-19 description: BackgroundBaited multiple-string problems are commonly used in avian laboratory studies to evaluate complex cognition. Several bird species possess the ability to use a string pull for obtaining food.MethodsWe initially tested and trained 11 magpies to determine whether the oriental magpie (Pica sericia) possesses the ability to solve baited multiple-string problems. Eight of the birds obtained the bait by pulling, and were selected for formal multiple-string tasks in the second stage. Second stage tests were divided into seven tasks based on string configurations.ResultsOnly two magpies were able to solve two tasks: one solved the task of parallel strings, and the other solved the task of slanted strings with the bait farther from the middle point between the two strings and selected the short string in the task of long-short strings. When faced with more difficult tasks (i.e., the task of slanted strings with the bait closer to the middle point between the two strings, the task with two crossing strings, and the task of continuity and discontinuity), the birds initially observed the tasks and chose instead to adopt simpler strategies based on the proximity principle, side bias strategies and trial-and-error learning. Our results indicate that the oriental magpie had a partial understanding of the principle of multiple-string problems but adopted simpler strategies. creator: Lin Wang creator: Jinxin Guo creator: Heng jiu Tian creator: Jinling Sui uri: https://doi.org/10.7717/peerj.9200 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al.