Treating coral bleaching as weather: a framework to validate and optimize prediction skill
Few coral reefs remain unscathed by mass bleaching over the past several decades, and much of the coral reef science conducted today relates in some way to the causes, consequences, or recovery pathways of bleaching events. Most studies portray a simple cause and effect relationship between anomalously high summer temperatures and bleaching, which is understandable given that bleaching rarely occurs outside these unusually warm times. However, the statistical skill with which temperature captures bleaching is hampered by many “false alarms”, times when temperatures reached nominal bleaching levels, but bleaching did not occur. While these false alarms are often not included in global bleaching assessments, they offer valuable opportunities to improve predictive skill, and therefore understanding, of coral bleaching events. Here, I show how a statistical framework adopted from weather forecasting can optimize bleaching predictions and validate which environmental factors play a role in bleaching susceptibility. Removing the 1 °C above the maximum monthly mean cutoff in the typical degree heating weeks (DHW) definition, adjusting the DHW window from 12 to 9 weeks, using regional-specific DHW thresholds, and including an El Niño threshold already improves the model skill by 45%. Most importantly, this framework enables hypothesis testing of other factors or metrics that may improve our ability to forecast coral bleaching events.
DeCarlo (2020) Treating coral bleaching as weather: a framework to validate and optimize prediction skill. PeerJ 8:e9449 https://doi.org/10.7717/peerj.9449
Preservation of latest Cretaceous (Maastrichtian)—Paleocene frogs (Eorubeta nevadensis) of the Sheep Pass Formation of east-central Nevada and implications for paleogeography of the Nevadaplano
Here we report on exceptional preservation of remains of the frog Eorubeta nevadensis in deposits of the Sheep Pass Formation, ranging from Late Cretaceous to Eocene, in the south Egan Range, Nevada. This formation represents a lacustrine basin within the Sevier retroarc hinterland. The formation is subdivided into six members (A–F); of interest here are members B and C. The base of member B is ?uppermost Cretaceous-Paleocene, while member C is Paleocene. Member B frogs are preserved in three taphonomic modes. Mode 1 frogs are nearly complete and accumulated under attritional processes, with frogs settling on microbial mats, as evidenced by crenulated fabric of entombing limestone. Mode 2 involves accumulation of frogs as a result of attritional processes. These frogs are mostly complete with some showing evidence of invertebrate scavenging. Possible scavengers are gastropods, ostracods, and decapods. Mode 3 is represented by isolated, reworked remains of frogs as a result of storm activity, supported by the association of elements with disarticulated bivalves and mud rip-up clasts. Member C preserves frogs in two taphonomic modes. Mode 4 are nearly complete frogs that accumulated during discrete mass mortality events. Numerous individuals are preserved along bedding planes in identical preservational states. Mode 5 is beds of frog bone hash, which represent increased energy to the depositional system (likely tempestites) and reworking of previously buried frog remains. Taphonomy of the frogs, along with the associated fauna and flora, are consistent with preservation in a cool, temperate lake basin, supporting previous interpretations that the Nevadaplano was an elevated plateau during the late Cretaceous through the Eocene. This is a period of time coincident with a climatic thermal optimum, thus the most parsimonious explanation for a temperate lake at the latitude of east-central Nevada is to invoke high elevation, which is consistent with independent structural and clumped stable isotope studies.
Bonde et al. (2020) Preservation of latest Cretaceous (Maastrichtian)—Paleocene frogs (Eorubeta nevadensis) of the Sheep Pass Formation of east-central Nevada and implications for paleogeography of the Nevadaplano. PeerJ 8:e9455 https://doi.org/10.7717/peerj.9455
Selection of Beauveria bassiana (Hypocreales: Cordycipitaceae) strains to control Xyleborus affinis (Curculionidae: Scolytinae) females
Background Xyleborus affinis Eichhoff (Coleoptera: Curculionidae) is an ambrosia beetle reported to affect avocado trees (Persea americana Mill.). The use of the entomopathogenic fungus (EPF) Beauveria bassiana (Bals.-Criv.) Vuill. for ambrosia beetle control represents an alternative to insecticides. Methods This study was designed in two stages to select B. bassiana strains with potential to control X. affinis females. In the first stage, 19 B. bassiana Mexican strains from EPF collection, isolated from Coleoptera (CHE-CNRCB, http://www.gob.mx/senasica/documentos/coleccion-de-hongos-entomopatogenos), were tested. Analyses included radial growth rate, conidial yield, spore germination, and germ tube length. Results were analysed by Principal Component Analysis (PCA) to identify clusters within favourable growth phenotypes. For the second stage, 10 selected strains were re-analysed for virulence-related metabolic characteristic, including cell wall-bound cuticle-degrading enzymes–Pr1-like proteases and β-N-acetyl glucosaminidases (NAGase) chitinases, conidial hydrophobicity and monopolar germination parameters. A second PCA analysis was run for those virulence parameters analysed, and upon results strains CHE-CNRCB 44, 171, 431 and 485 were selected and tested against X. affinis females. Females were treated with a 1 × 108 conidia mL−1 suspension (recommended rate), using a Potter Tower. Results All strains showed insecticidal activity, inducing up to 58% mortality; about 30% dead beetles developed aerial mycelia (CHE-CNRCB 485) and the fastest mortality rate was t0 = 1.95 (CHE-CNRCB 44). Conclusion Since all selected strains showed virulence against X. affinis females, results indicated the possibility of selecting B. bassiana strains based on multiple metabolic attributes, as a preliminary test to perform bioassays against order-related target insects.
Castrejón-Antonio et al. (2020) Selection of Beauveria bassiana (Hypocreales: Cordycipitaceae) strains to control Xyleborus affinis (Curculionidae: Scolytinae) females. PeerJ 8:e9472 https://doi.org/10.7717/peerj.9472
Diminishing returns as a function of disturbance
According to Spearman’s law of diminishing returns (SLODR), IQ test scores are more g saturated among those with low, compared to those with high, ability. The present simulation shows that such difference in saturation can be observed if test scores are affected by a disturbing factor, for example, low motivation, illness, or linguistic confusion, that varies in magnitude between individuals. More contemporary criteria of SLODR can also be satisfied if test scores are affected by disturbance, especially if the disturbance variable is negatively skewed. This indicates a possible threat against the validity of findings supporting SLODR and points at the importance for researchers to try to eliminate the influence of such disturbing factors from their studies.
Sorjonen et al. (2020) Diminishing returns as a function of disturbance. PeerJ 8:e9490 https://doi.org/10.7717/peerj.9490
Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure
The rapid development of the SARS-CoV-2 mediated COVID-19 pandemic has been the cause of significant health concern, highlighting the immediate need for effective antivirals. SARS-CoV-2 is an RNA virus that has an inherently high mutation rate. These mutations drive viral evolution and genome variability, thereby facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance. Viral RNA-dependent RNA polymerases (RdRp) perform viral genome duplication and RNA synthesis. Therefore, we compared the available RdRp sequences of SARS-CoV-2 from Indian isolates and the ‘Wuhan wet sea food market virus’ sequence to identify, if any, variation between them. Our data revealed the occurrence of seven mutations in Indian isolates of SARS-CoV-2. The secondary structure prediction analysis of these seven mutations shows that three of them cause alteration in the structure of RdRp. Furthermore, we did protein modelling studies to show that these mutations can potentially alter the stability of the RdRp protein. Therefore, we propose that RdRp mutations in Indian SARS-CoV-2 isolates might have functional consequences that can interfere with RdRp targeting pharmacological agents.
Chand et al. (2020) Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure. PeerJ 8:e9492 https://doi.org/10.7717/peerj.9492
Contextual violence and its link to social aggression: a study of community violence in Juárez
The city of Juárez, Mexico has been immersed in an atmosphere of violence and danger for more than a decade. Due to this violence, residents of Juárez may be at risk of severe contextual victimization, which occurs when individuals are indirectly affected by the physical and socio-cultural conditions of their violent communities through second-hand information (e.g., witnessing or hearing about violent acts in their everyday life). The objective of this study was to explore the effects of contextual victimization on variables related to community violence such as aggression, post-traumatic stress disorder (PTSD), and acceptance of violence. Data were collected from a sample of university students in Juárez (n = 298) using the Aggression Questionnaire (AQ), the Acceptance of Violence Scale (AVS), Checklist for PTSD Traits scale, and the Contextual Victimization by Community Violence scale (CVCV). Participants’ responses were analyzed in structural equation models (SEM) to uncover the latent variables behind each scale and test the hypothesized effects of CVCV on PTSD, AQ and AVS. Good validity indexes and internal consistency of all instruments were confirmed. SEM show significant positive effects of contextual violence on PTSD and PTSD on the disposition to aggression, but not on the acceptance of violence. Also, the variance explained of PTSD and AQ found in the sample of women (20% of PTSD and 23% of AQ) is almost twice than in men’s sample (9% for PTSD and 14% for AQ).
© 2020 Martín del Campo-Ríos and Cruz-Torres
Martín del Campo-Ríos et al. (2020) Contextual violence and its link to social aggression: a study of community violence in Juárez. PeerJ 8:e9162 https://doi.org/10.7717/peerj.9162
Foliar application of abscisic acid mitigates cadmium stress and increases food safety of cadmium-sensitive lettuce (Lactuca sativa L.) genotype
Cadmium (Cd2 +) is among the toxic non-essential heavy metals that adversely affect plants metabolic processes and the safety of produce. However, plant hormones can improve plant’s tolerance to various stresses. This study investigated the effect of exogenous abscisic acid (ABA) on the biochemical and physiological processes and food safety of cadmium (Cd2 +)-sensitive lettuce genotype (Lüsu). Seedlings were subjected to five treatments: [(i) Control (untreated plants), (ii) 100 µM CdCl2, (iii) 100 µM CdCl2+10 µg L−1 ABA (iv) 10 µg L−1 ABA, and (v) 0.01 g L−1 ABA-inhibitor (fluridone)] for fourteen days in hydroponic system. The 100 µM CdCl2 increased the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA), decreased photosynthesis and plant biomass. Moreover, it decreased the contents of essential nutrients (except copper) in the leaves but increased the contents of toxic Cd2 + in the leaves and roots of the plants. Foliar application of fluridone (0.01 g L−1) also caused oxidative stress by increasing the contents of H2O2 and MDA. It also decreased the contents of nutrient elements in the leaves of the plants. However, exogenous ABA (10 µg L−1) mitigated the Cd2 +-induced stress, increased antioxidant enzymes activities, photosynthesis and plant biomass under CdCl2 treatment. Remarkably, exogenous ABA increased the contents of essential nutrient elements but decreased the Cd2 + content in leaves under the CdCl2 treatment. Our results have demonstrated that foliar application of ABA mitigates Cd2 + stress and increases the nutritional quality and food safety of Cd2 +-sensitive lettuce genotype under CdCl2 treatment.
Dawuda et al. (2020) Foliar application of abscisic acid mitigates cadmium stress and increases food safety of cadmium-sensitive lettuce (Lactuca sativa L.) genotype. PeerJ 8:e9270 https://doi.org/10.7717/peerj.9270
Association of retinal nerve fiber abnormalities with serum CNTF and cognitive functions in schizophrenia patients
Background Recent studies have reported reductions in retinal nerve fiber layers (RNFL) in schizophrenia. Ciliary neurotrophic factor (CNTF) has shown protective effects on both the neurogenesis and retina. This study aimed at investigating retinal abnormalities and establishing their correlation with serum CNTF and cognitive impairments in schizophrenic Chinese patients. Methods In total, 221 patients diagnosed with schizophrenia and 149 healthy controls were enrolled. Serum CNTF and clinical features of patients were investigated. Cognitive functions were evaluated with Repeatable Battery for the Assessment of Neuropsychology Status (RBANS). RNFL thickness and macular thickness (MT) of both eyes were measured with optical coherence tomography (OCT). T-tests and analysis of covariance were used to compare the variables between the patient and control groups, while multiple linear regression analysis was performed to determine the associations of RNFL thickness, CNTF and cognitive impairments. Results RNFL was found thinner in patients than in healthy controls (right: 88.18 ± 25.84 µm vs.102.13 ± 14.32 µm, p = 0.001; left: 92.84 ± 13.54 µm vs.103.71 ± 11.94 µm, p < 0.001). CNTF was lower in the schizophrenia group (1755.45 ± 375.73 pg/ml vs. 1909.99 ± 368.08 pg/ml, p = 0.001). Decline in RNFL thickness was found correlated with course of illness and serum CNTF in patients (all p < 0.05). Similarly, cognitive functions such as immediate memory and visuospatial functions were also found correlated with decline in RNFL thickness. Conclusion Decline in RNFL thickness was associated with cognitive impairments of schizophrenia and CNFT serum concentration. The possibility of reduction in RNFL thickness as a biomarker for schizophrenia needs to be further examined.
Liu et al. (2020) Association of retinal nerve fiber abnormalities with serum CNTF and cognitive functions in schizophrenia patients. PeerJ 8:e9279 https://doi.org/10.7717/peerj.9279
SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis
Microsatellite (SSR) markers are the most popular markers for genetic analyses and molecular selective breeding in plants and animals. However, the currently available methods to develop SSRs are relatively time-consuming and expensive. One of the most factors is low frequency of polymorphic SSRs. In this study, we developed a software, SSREnricher, which composes of six core analysis procedures, including SSR mining, sequence clustering, sequence modification, enrichment containing polymorphic SSR sequences, false-positive removal and results output and multiple sequence alignment. After running of transcriptome sequences on this software, a mass of polymorphic SSRs can be identified. The validation experiments showed almost all markers (>90%) that were identified by the SSREnricher as putative polymorphic markers were indeed polymorphic. The frequency of polymorphic SSRs identified by SSREnricher was significantly higher (P < 0.05) than that of traditional and HTS approaches. The software package is publicly accessible on GitHub (https://github.com/byemaxx/SSREnricher).
Luo et al. (2020) SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis. PeerJ 8:e9372 https://doi.org/10.7717/peerj.9372
Elephants in the neighborhood: patterns of crop-raiding by Asian elephants within a fragmented landscape of Eastern India
Loss of forest cover, rise in human populations and fragmentation of habitats leads to decline in biodiversity and extinction of large mammals globally. Elephants, being the largest of terrestrial mammals, symbolize global conservation programs and co-occur with humans within multiple-use landscapes of Asia and Africa. Within such shared landscapes, poaching, habitat loss and extent of human–elephant conflicts (HEC) affect survival and conservation of elephants. HEC are severe in South Asia with increasing attacks on humans, crop depredation and property damage. Such incidents reduce societal tolerance towards elephants and increase the risk of retaliation by local communities. We analyzed a 2-year dataset on crop depredation by Asian elephants (N = 380) events in North Bengal (eastern India). We also explored the effect of landscape, anthropogenic factors (area of forest, agriculture, distance to protected area, area of human settlements, riverine patches and human density) on the spatial occurrence of such incidents.Crop depredation showed a distinct nocturnal pattern (22.00–06:00) and majority of the incidents were recorded in the monsoon and post-monsoon seasons. Results of our spatial analysis suggest that crop depredation increased with an increase in the area of forest patches, agriculture, presence of riverine patches and human density. Probability of crop depredation further increased with decreasing distance from protected areas. Villages within 1.5 km of a forest patch were most affected. Crop raiding incidents suggest a deviation from the “high-risk high-gain male biased” foraging behavior and involved proportionately more mixed groups (57%) than lone bulls (43%). Demographic data suggest that mixed groups comprised an average of 23 individuals with adult and sub adult females, bulls and calves. Crop depredation and fatal elephant attacks on humans were spatially clustered with eastern, central and western parts of North Bengal identified as hotspots of HEC. Our results will help to prioritize mitigation measures such as prohibition of alcohol production within villages, improving condition of riverine patches, changing crop composition, fencing agriculture fields, implement early warning systems around protected areas and training local people on how to prevent conflicts.
Naha et al. (2020) Elephants in the neighborhood: patterns of crop-raiding by Asian elephants within a fragmented landscape of Eastern India. PeerJ 8:e9399 https://doi.org/10.7717/peerj.9399