Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries
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.
Petersen et al. (2020) Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries. PeerJ 8:e9288 https://doi.org/10.7717/peerj.9288
Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate
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.
Sarmento et al. (2020) Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate. PeerJ 8:e9296 https://doi.org/10.7717/peerj.9296
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
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.
Hou et al. (2020) 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. PeerJ 8:e9336 https://doi.org/10.7717/peerj.9336
Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests
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.
Lai et al. (2020) Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests. PeerJ 8:e9351 https://doi.org/10.7717/peerj.9351
A putative effector UvHrip1 inhibits BAX-triggered cell death in Nicotiana benthamiana, and infection of Ustilaginoidea virens suppresses defense-related genes expression
Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most detrimental rice fungal diseases and pose a severe threat to rice production and quality. Effectors in U. virens often act as a set of essential virulence factors that play crucial roles in the interaction between host and the pathogen. Thus, the functions of each effector in U. virens need to be further explored. Here, we performed multiple alignment analysis and demonstrated a small secreted hypersensitive response-inducing protein (hrip), named UvHrip1, was highly conserved in fungi. The predicted SP of UvHrip1 was functional, which guided SUC secreted from yeast and was recognized by plant cells. The localization of UvHrip1 was mainly in the nucleus and cytoplasm monitored through the GFP fusion protein in Nicotiana benthamiana cells. uvhrip1 was drastically up-regulated in the susceptible cultivar LYP9 of rice during the pathogen infection, while did not in the resistant cultivar IR28. We also proved that UvHrip1 suppressed the mammalian BAX-induced necrosis-like defense symptoms in N. benthamiana. Furthermore, patterns of expression of defense-related genes, OsPR1#012 and OsPR10b, were regulated over U. virens infection in rice. Collectively, our data demonstrated that infection of U. virens suppresses defense-related genes expression and UvHrip1 was most likely a core effector in regulating plant immunity.
Wang et al. (2020) A putative effector UvHrip1 inhibits BAX-triggered cell death in Nicotiana benthamiana, and infection of Ustilaginoidea virens suppresses defense-related genes expression. PeerJ 8:e9354 https://doi.org/10.7717/peerj.9354
The reproductive inhibitory effects of levonorgestrel, quinestrol, and EP-1 in Brandt’s vole (Lasiopodomys brandtii)
Background Rodent pests can inflict devastating impacts on agriculture and the environment, leading to significant economic damage associated with their high species diversity, reproductive rates and adaptability. Fertility control methods could indirectly control rodent pest populations as well as limit ecological consequences and environmental concerns caused by lethal chemical poisons. Brandt’s voles, which are common rodent pests found in the grasslands of middle-eastern Inner Mongolia, eastern regions of Mongolia, and some regions of southern Russia, were assessed in the present study. Methods We evaluated the effects of a 2-mg/kg dose of levonorgestrel and quinestrol and a 1:1 mixture of the two (EP-1) on reproductive behavior as well as changes in the reproductive system, reproductive hormone levels, and toxicity in Brandt’s voles. Results Our results revealed that all three fertility control agents can cause reproductive inhibition at a dosage of 2 mg/kg. However, quinestrol caused a greater degree of toxicity, as determined by visible liver damage and reduced expression of the detoxifying molecule CYP1A2. Of the remaining two fertility control agents, EP-1 was superior to levonorgestrel in inhibiting the secretion of follicle-stimulating hormone and causing reproductive inhibition. We believe that these findings could help promote the use of these fertility control agents and, in turn, reduce the use of chemical poisons and limit their detrimental ecological and environmental impacts.
Shi et al. (2020) The reproductive inhibitory effects of levonorgestrel, quinestrol, and EP-1 in Brandt’s vole (Lasiopodomys brandtii). PeerJ 8:e9140 https://doi.org/10.7717/peerj.9140
GISA: using Gauss Integrals to identify rare conformations in protein structures
The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a ”fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains. This allows fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds. Applying GISA to sets of several thousand high resolution structures, we first show how the most basic Gauss integral, the writhe, enables swift identification of pre-defined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, an application of the basic scan method in GISA’s tool-box revealed 10 known cases of knots as the top positive writhe cases, while placing at the top of the negative writhe 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed. Possible general applications of GISA are fold classification and structural alignment based on local Gauss integrals. Others include finding errors in protein models and identifying unusual conformations that might be important for protein folding and function. By its broad potential, we believe that GISA will be of general benefit to the structural bioinformatics community. GISA is coded in C and comes as a command line tool. Source and compiled code for GISA plus read-me and examples are publicly available at GitHub (https://github.com).
Grønbæk et al. (2020) GISA: using Gauss Integrals to identify rare conformations in protein structures. PeerJ 8:e9159 https://doi.org/10.7717/peerj.9159
Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment
Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.
Uchida et al. (2020) Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment. PeerJ 8:e9176 https://doi.org/10.7717/peerj.9176
A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes
Indirect transmission of pathogens can pose major risks to wildlife, yet the presence and persistence of wildlife pathogens in the environment has been little studied. Beak and feather disease virus (BFDV) is of global conservation concern: it can infect all members of the Psittaciformes, one of the most threatened bird orders, with infection often being lethal. Indirect transmission of BFDV through contaminated nest hollows has been proposed as a major infection source. However, data on whether and for how long nest sites in the wild remain contaminated have been absent. We determined the BFDV status of birds (parents and nestlings) for 82 nests of Crimson Rosellas, Platycercus elegans and Eastern Rosellas, Platycercus eximius. In 11 of these nests (13.4%, 95% confidence interval 6.9–22.7), we found an infected parent or nestling. Using nest swabs, we then compared BFDV presence at three points in time (before, during and after breeding) in three groups of nest boxes. These were nest boxes occupied by infected birds, and two control groups (nest boxes occupied by uninfected birds, and unoccupied nest boxes). Detection of BFDV on nest swabs was strongly associated with the infection status of parents in each nest box and with the timing of breeding. During breeding, boxes occupied by BFDV-positive birds were significantly more likely to have BFDV-positive nest swabs than boxes occupied by BFDV-negative birds; nest swabs tested BFDV-positive in 80% (28.4–99.5) of nests with parental antigen excretion, 66.7% (9.4–99.2) of nests occupied by parents with BFDV-positive cloacal swabs and 66.7% (22.3–95.7) of nests occupied by parents with BFDV–positive blood. 0% (0–52.2) of nests with BFDV–positive nestlings had BFDV–positive nest swabs. Across all boxes occupied by BFDV-positive birds (parents or nestlings), no nest swabs were BFDV–positive before breeding, 36.4% (95% CI 10.9–69.2) were positive during breeding and 9.1% (0.2–41.3) remained positive after breeding. BFDV was present on nest swabs for up to 3.7 months. Our study provides novel insights into the potential role of nest cavities and other fomites in indirect transmission of BFDV, and possibly other pathogens, and offers a non-invasive method for surveillance of pathogens in wild bird populations.
Martens et al. (2020) A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes. PeerJ 8:e9211 https://doi.org/10.7717/peerj.9211
Expression and clinical significance of HSP27 and its phosphorylation in lower extremity arteriosclerosis obliterans
Objectives This study set out to analyze the difference of heat shock protein 27 (HSP27) and its phosphorylation in patients with lower extremity arteriosclerosis obliterans (LEASO) at different stages. This research also examined their clinical significance in this disease. Methods Blood samples from 60 patients with LEASO were collected and divided into two groups according to ankle-brachial index (ABI): group A (ABI ≤ 0.43) and group B (ABI > 0.43). The expression of HSP27 in each stage of Fontaine was measured by ELISA, and the difference of HSP27 concentration and ABI between the two groups was analyzed. Meanwhile, three normal femoral artery specimens (normal group) and three atherosclerotic femoral artery specimens (lesion group) were collected, and HSP27 and its Phospho-HSP27 (Ser15), Phospho-HSP27 (Ser78) and Phospho-HSP27 (Ser82) were detected by western blotting. The data of the protein level between the normal group and the lesion group was made a statistical analysis. Results HSP27 concentration in group A was (40.73 ± 15.99) ng/ml, and ABI was 0.26 ± 0.20. HSP27 concentration in group B was (66.30 ± 24.70) ng/ml, and ABI was 0.64 ± 0.20. The protein expression of HSP27 and its phosphorylation in the normal group was 0.82 ± 0.13, 0.66 ± 0.12, 0.91 ± 0.24 and 0.90 ± 0.16, respectively; the protein expression of the lesion group was 0.45 ± 0.08, 0.42 ± 0.09, 0.39 ± 0.12 and 0.58 ± 0.11. Conclusion Patients with higher LEASO Fontaine stage and lower ABI had a lower HSP27 concentration. Serum HSP27 concentration was negatively correlated with the severity of LEASO, while HSP27 concentration was positively correlated with ABI value. The content of HSP27 and its phosphorylation of lesion group is significantly lower than that of normal group, which may be closely related to the occurrence and development of atherosclerosis.
Bai et al. (2020) Expression and clinical significance of HSP27 and its phosphorylation in lower extremity arteriosclerosis obliterans. PeerJ 8:e9305 https://doi.org/10.7717/peerj.9305