title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1118 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb link: https://peerj.com/articles/9349 last-modified: 2020-06-15 description: Morphological shifts observed in the fossil record of a lineage potentially indicate concomitant shifts in ecology of that lineage. Mekosuchine crocodiles of Cenozoic Australia display departures from the typical eusuchian body-plan both in the cranium and postcranium. Previous qualitative studies have suggested that these crocodiles had a more terrestrial habitus than extant crocodylians, yet the capacity of mekosuchine locomotion remains to be tested. Limb bone shape, such as diaphyseal cross-section and curvature, has been related to habitual use and locomotory function across a wide variety of taxa. Available specimens of mekosuchine limbs, primarily humeri, are distinctly columnar compared with those of extant crocodylians. Here we apply a quantitative approach to biomechanics in mekosuchine taxa using both geomorphic morphometric and finite element methods to measure bone shape and estimate locomotory stresses in a comparative context. Our results show mekosuchines appear to diverge from extant semi-aquatic saltwater and freshwater crocodiles in cross-sectional geometry of the diaphysis and generate different structural stresses between models that simulate sprawling and high-walk gaits. The extant crocodylians display generally rounded cross-sectional diaphyseal outlines, which may provide preliminary indication of resistance to torsional loads that predominate during sprawling gait, whereas mekosuchine humeri appear to vary between a series of elliptical outlines. Mekosuchine structural stresses are comparatively lower than those of the extant crocodylians and reduce under high-walk gait in some instances. This appears to be a function of bending moments induced by differing configurations of diaphyseal curvature. Additionally, the neutral axis of structural stresses is differently oriented in mekosuchines. This suggests a shift in the focus of biomechanical optimisation, from torsional to axial loadings. Our results lend quantitative support to the terrestrial habitus hypothesis in so far as they suggest that mekosuchine humeri occupied a different morphospace than that associated with the semi-aquatic habit. The exact adaptational trajectory of mekosuchines, however, remains to be fully quantified. Novel forms appear to emerge among mekosuchines during the late Cenozoic. Their adaptational function is considered here; possible applications include navigation of uneven terrain and burrowing. creator: Michael D. Stein creator: Suzanne J. Hand creator: Michael Archer creator: Stephen Wroe creator: Laura A.B. Wilson uri: https://doi.org/10.7717/peerj.9349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Stein et al. title: A potential role for Galectin-3 inhibitors in the treatment of COVID-19 link: https://peerj.com/articles/9392 last-modified: 2020-06-15 description: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), has been declared a global pandemic by the World Health Organization. With no standard of care for the treatment of COVID-19, there is an urgent need to identify therapies that may be effective in treatment. Recent evidence has implicated the development of cytokine release syndrome as the major cause of fatality in COVID-19 patients, with elevated levels of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) observed in patients. Galectin-3 (Gal-3) is an animal lectin that has been implicated in the disease process of a variety of inflammatory conditions. Inhibitors of the small molecule Gal-3 have been shown to reduce the levels of both IL-6 and TNF-α in vitro and have shown anti-inflammatory effects in vivo. Additionally, a key domain in the spike protein of β-coronaviridae, a genus which includes SARS-CoV2, is nearly identical in morphology to human Gal-3. These spike proteins are critical for the virus’ entry into host cells. Here we provide a systematic review of the available literature and an impetus for further research on the use of Gal-3 inhibitors in the treatment of COVID-19. Further, we propose a dual mechanism by which Gal-3 inhibition may be beneficial in the treatment of COVID-19, both suppressing the host inflammatory response and impeding viral attachment to host cells. creator: John L. Caniglia creator: Maheedhara R. Guda creator: Swapna Asuthkar creator: Andrew J. Tsung creator: Kiran K. Velpula uri: https://doi.org/10.7717/peerj.9392 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Caniglia et al. title: Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods link: https://peerj.com/articles/9178 last-modified: 2020-06-12 description: Cataract formation is a slow accumulative process due to protein aggregates promoted by different factors over time. Zinc and copper ions have been reported to induce the formation of aggregates opaque to light in the human gamma D crystallin (HγD) in a concentration and temperature dependent manner. In order to gain insight into the mechanism of metal-induced aggregation of HγD under conditions that mimic more closely the slow, accumulative process of the disease, we have studied the non-equilibrium process with the minimal metal dose that triggers HγD aggregation. Using a wide variety of biophysics techniques such as turbidimetry, dynamic light scattering, fluorescence, nuclear magnetic resonance and computational methods, we obtained information on the molecular mechanisms for the formation of aggregates. Zn(II) ions bind to different regions at the protein, probably with similar affinities. This binding induces a small conformational rearrangement within and between domains and aggregates via the formation of metal bridges without any detectable unfolded intermediates. In contrast, Cu(II)-induced aggregation includes a lag time, in which the N-terminal domain partially unfolds while the C-terminal domain and parts of the N-terminal domain remain in a native-like conformation. This partially unfolded intermediate is prone to form the high-molecular weight aggregates. Our results clearly show that different external factors can promote protein aggregation following different pathways. creator: Arline Fernández-Silva creator: Leidys French-Pacheco creator: Lina Rivillas-Acevedo creator: Carlos Amero uri: https://doi.org/10.7717/peerj.9178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fernández-Silva et al. title: Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles link: https://peerj.com/articles/9248 last-modified: 2020-06-12 description: The western pond turtle (WPT), recently separated into two paripatrically distributed species (Emys pallida and Emys marmorata), is experiencing significant reductions in its range and population size. In addition to habitat loss, two potential causes of decline are female-biased road mortality and high juvenile mortality from non-native predatory bullfrogs (Rana catesbeiana). However, quantitative analyses of these threats have never been conducted for either species of WPT. We used a combination of historical museum samples and published and unpublished field studies shared with us through personal communications with WPT field researchers (B. Shaffer, P. Scott, R. Fisher, C. Brown, R. Dagit, L. Patterson, T. Engstrom, 2019, personal communications) to quantify the effect of roads and bullfrogs on WPT populations along the west coast of the United States. Both species of WPT shift toward increasingly male biased museum collections over the last century, a trend consistent with increasing, female-biased road mortality. Recent WPT population studies revealed that road density and proximity were significantly associated with increasingly male-biased sex ratios, further suggesting female-biased road mortality. The mean body size of museum collections of E. marmorata, but not E. pallida, has increased over the last 100 years, consistent with reduced recruitment and aging populations that could be driven by invasive predators. Contemporary WPT population sites that co-occur with bullfrogs had significantly greater average body sizes than population sites without bullfrogs, suggesting strong bullfrog predation on small WPT hatchlings and juveniles. Overall, our findings indicate that both species of WPT face demographic challenges which would have been difficult to document without the use of both historical data from natural history collections and contemporary demographic field data. Although correlational, our analyses suggest that female-biased road mortality and predation on small turtles by non-native bullfrogs are occurring, and that conservation strategies reducing both may be important for WPT recovery. creator: E. Griffin Nicholson creator: Stephanie Manzo creator: Zachary Devereux creator: Thomas Paul Morgan creator: Robert N. Fisher creator: Christopher Brown creator: Rosi Dagit creator: Peter A. Scott creator: H. Bradley Shaffer uri: https://doi.org/10.7717/peerj.9248 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nicholson et al. title: Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater link: https://peerj.com/articles/9267 last-modified: 2020-06-12 description: BackgroundUntreated wastewater carries substantial amount of heavy metals and causes potential ecological risks to the environment, food quality, soil health and sustainable agriculture.MethodologyIn order to reduce the incidence of nickel (Ni2+) contamination in soils, two separate experiments (incubation and greenhouse) were conducted to investigate the potentials of rice straw biochar and elemental sulfur in remediating Ni2+ polluted soil due to the irrigation with wastewater. Five incubation periods (1, 7, 14, 28 and 56 days), three biochar doses (0, 10 and 20 g kg−1 of soil) and two doses of sulfur (0 and 5 g kg−1 of soil) were used in the incubation experiment then the Ni2+ was extracted from the soil and analyzed, while ryegrass seeds Lolium perenne L. (Poales: Poaceae) and the same doses of biochar and sulfur were used in the greenhouse experiment then the plants Ni2+-uptake was determined.ResultsThe results of the incubation experiment revealed a dose-dependent reduction of DTPA-extractable Ni2+ in soils treated with biochar. Increasing the biochar dose from 0 g kg−1 (control) to 10 or 20 g kg−1 (treatments) decreased the DTPA-extractable Ni2+ from the soil by 24.6% and 39.4%, respectively. The application of sulfur increased the Ni2+-uptake by ryegrass plant which was used as hyper-accumulator of heavy metals in the green house experiment. However, the biochar decreased the Ni2+-uptake by the plant therefore it can be used as animal feed.ConclusionsThese results indicate that the biochar and sulfur could be applied separately to remediate the Ni2+-contaminated soils either through adsorbing the Ni2+ by biochar or increasing the Ni2+ availability by sulfur to be easily uptaken by the hyper-accumulator plant, and hence promote a sustainable agriculture. creator: Inas A. Hashem creator: Aonalah Y. Abbas creator: Abo El-Nasr H. Abd El-Hamed creator: Haythum M.S. Salem creator: Omr E.M. El-hosseiny creator: Mohamed A. Abdel-Salam creator: Muhammad Hamzah Saleem creator: Wenbing Zhou creator: Ronggui Hu uri: https://doi.org/10.7717/peerj.9267 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hashem et al. title: Identifying potential threats to soil biodiversity link: https://peerj.com/articles/9271 last-modified: 2020-06-12 description: A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils’ ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* “soil biodiversity”), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified emerging threats, particularly microplastics, in the 10 years following these knowledge based rankings. We found that many soil biodiversity studies do not focus on biodiversity sensu stricto, rather these studies examined either changes in abundance and/or diversity of individual groups of soil biota, instead of soil biodiversity as a whole, encompassing all levels of the soil food web. This highlights the complexity of soil biodiversity which is often impractical to assess in all but the largest studies. Published global scientific activity was only partially related to the threats identified by the expert panel assessment. The number of threats and the priority given to the threats (by number of publications) were quite different, indicating a disparity between research actions versus perceived threats. The lack of research effort in key areas of high priority in the threats to soil biodiversity are a concerning finding and requires some consideration and debate in the research community. creator: Mark Tibbett creator: Tandra D. Fraser creator: Sarah Duddigan uri: https://doi.org/10.7717/peerj.9271 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tibbett et al. title: Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries link: https://peerj.com/articles/9288 last-modified: 2020-06-12 description: A previous study found that use of the traditional halibut hook (čibu⋅d) of the Makah Tribe in present day recreational Pacific halibut (Hippoglossus stenolepis) fisheries significantly reduced bycatch compared to paired 8/0 circle hooks. The study also found that the čibu⋅d had a significantly reduced catch of halibut, but that the reduction may have been due to manufacturing flaws in the čibu⋅d used in the study. In this two-phased study, we first compared the fishing performance of redesigned čibu⋅d made from four different materials: brass, stainless steel, plastic, and wood. In the second phase, we compared the fishing performance of the brass čibu⋅d with two common recreational fishing set-ups: a single large 16/0 circle hook and paired 8/0 circle hooks. The fishing performance of the redesigned čibu⋅d was not statistically different for čibu⋅d made of brass, stainless steel, or plastic. However, the čibu⋅d made from wood had significantly lower catch of halibut than the other čibu⋅d. We selected the brass čibu⋅d for the second phase of the study for continuity with the previous study of čibu⋅d and found that it had significantly less bycatch and a lower bycatch ratio than both the paired 8/0 and single 16/0 circle hooks. No significant differences were found in catch rates of halibut for paired 8/0 circle hooks, 16/0 circle hook, and the brass čibu⋅d. This study demonstrates that the improved catching performance of čibu⋅d on halibut and reduced bycatch compared to other popular approaches can be achieved by using brass čibu⋅d. Managers of recreational halibut fisheries should consider the use of čibu⋅d in areas where bycatch is a concern. creator: Joseph R. Petersen creator: Jonathan J. Scordino creator: Cole I. Svec creator: Reginald H. Buttram creator: Maria R. Gonzalez creator: Joe Scordino uri: https://doi.org/10.7717/peerj.9288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Petersen et al. title: Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate link: https://peerj.com/articles/9296 last-modified: 2020-06-12 description: Understanding relationships between animals and their habitat is a central goal in ecology with important implications for conservation. Misidentified habitat requirements can have serious repercussions because land protection or reintroductions might occur in less than optimal habitat. Studies of resource selection have greatly facilitated an understanding of ecological relationships but can be improved when vital yet infrequently utilized habitat features are more fully described. A critical element for many prey species is escape terrain or some other form of refuge to avoid predation. Mountain goats (Oreamnos americanus) are well known for their use of cliffs to avoid predation, but a survey of the literature revealed at least twelve different approximations of goat escape terrain, ranging from > 25° to > 50° slopes. Here, we seek to (1) enhance estimates of mountain goat escape terrain and antipredator behavior, and (2) highlight the limitations of the assumption that the time an animal spends in an area is proportional to importance. To improve estimates of goat escape terrain, we conducted field work across two years (2014–15) in Glacier National Park, Montana USA and manipulated apparent predation risk by exposing mountain goats to a threatening simulated grizzly bear (Ursus arctos) treatment and a non-threatening ungulate (control) treatment. Mountain goats moved in response to the simulated bear but not in response to the simulated ungulate, with shorter latencies to move for subjects in larger groups and at shorter distances to the simulated threat. Through a used-unused resource selection function we tested 22 landscape variables to describe the use of escape terrain. Proximity to slopes greater than 60° best explained the locations to which mountain goats fled after exposure to the simulated bear, and the average slope of these escape locations was 56.5° (±14.1 S.D.). Our results suggest that mountain goat escape terrain be considered at slopes of 60° as a minimum because our simulated threat did not include pursuit of goats and, thus, slopes of 60° are likely underestimates of actual escape terrain. Additionally, because direct interactions between carnivores and goats seldom occur, serious escape terrain is infrequently used. Past estimates of escape may have miscalculated the slopes which goats select for in response to predation risk. Based on experimental approaches in the wild, we suggest that anti-predator behavior should be included in studies of resource selection when the goal is to consider habitat as a predictor for conservation success. Finally, we discuss evidence suggesting a past mountain goat introduction failed due to lack of adequate escape terrain and subsequent recolonization of a predator. creator: Wesley Sarmento creator: Joel Berger uri: https://doi.org/10.7717/peerj.9296 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sarmento and Berger title: Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress link: https://peerj.com/articles/9336 last-modified: 2020-06-12 description: Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus. creator: Zhihao Hou creator: Qiang Chen creator: Mengran Zhao creator: Chenyang Huang creator: Xiangli Wu uri: https://doi.org/10.7717/peerj.9336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hou et al. title: Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests link: https://peerj.com/articles/9351 last-modified: 2020-06-12 description: Epiphytic bryophytes (EB) are some of the most commonly found plant species in tropical montane cloud forests, and they play a disproportionate role in influencing the terrestrial hydrological and nutrient cycles. However, it is difficult to estimate the abundance of EB due to the nature of their “epiphytic” habitat. This study proposes an allometric scaling approach implemented in twenty-one 30 × 30 m plots across an elevation range in 16,773 ha tropical montane cloud forests of northeastern Taiwan to measure EB biomass, a primary metric for indicating plant abundance and productivity. A general allometry was developed to estimate EB biomass of 100 cm2 circular-shaped mats (n = 131) with their central depths. We developed a new point-intercept instrument to rapidly measure the depths of EB along tree trunks below 300 cm from the ground level (sampled stem surface area (SSA)) (n = 210). Biomass of EB of each point measure was derived using the general allometry and was aggregated across each SSA, and its performance was evaluated. Total EB biomass of a tree was estimated by referring to an in-situ conversion model and was interpolated for all trees in the plots (n = 1451). Finally, we assessed EB biomass density at the plot scale of the study region. The general EB biomass-depth allometry showed that the depth of an EB mat was a salient variable for biomass estimation (R2 = 0.72, p < 0.001). The performance of upscaling from mats to SSA was satisfactory, which allowed us to further estimate mean (±standard deviation) EB biomass of the 21 plots (272 ± 104 kg ha−1). Since a significant relationship between tree size and EB abundance is commonly found, regional EB biomass may be mapped by integrating our method and three-dimensional remotely sensed airborne data. creator: Guan-Yu Lai creator: Hung-Chi Liu creator: Ariel J. Kuo creator: Cho-ying Huang uri: https://doi.org/10.7717/peerj.9351 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lai et al.