Genetic divergence at species boundaries of the dolphinfish (Coryphaena hippurus) in the Tropical Eastern Pacific
Background Marine species constitute commercially important resources, and knowledge about mechanisms that shape phylogeographic patterns and genetic structure provides valuable information for conservation. The dolphinfish, Coryphaena hippurus, is one of the most important species caught in the Tropical Eastern Pacific (TEP). However, the lack of consensus about the existence of genetically differentiated populations in the area has hindered the adoption of management strategies to ensure its viability. Methods We assessed genetic variation and phylogeographic structure using two mitochondrial genes and 14 nuclear DNA microsatellite loci. Population genetic tools were used to characterize the spatial distribution of genetic variation of C. hippurus in the TEP, evaluate the extent of connectivity between dolphinfish populations, infer potential barriers to gene flow, and test for signals of contemporary and historical demographic expansions. Results Mitochondrial DNA sequences showed genetic homogeneity across locations in the TEP, as well as a strong signal of population expansion dated to the late Pleistocene. In contrast, nuclear microsatellite markers resolved four genetically distinct groups with a remarked genetic differentiation between the most distant locations, at the northern and southern boundaries of the species’ range. High mean genetic diversity was found at all localities (Hs = 0.66–0.81). Notwithstanding, positive FIS and low effective population size (Ne = 77.9–496.4) were also recorded. Conclusions The distribution of genetic variation could be related to expansion-contraction cycles following seasonal temperature changes at transitional areas, promoting population subdivisions. However, we cannot rule out the effect of oceanographic dynamics to the observed patterns. Although this marine species remains highly abundant despite commercial exploitation, the low Ne values are of conservation concern and must be considered in fishery management plans.
Ochoa-Zavala et al. (2022) Genetic divergence at species boundaries of the dolphinfish (Coryphaena hippurus) in the Tropical Eastern Pacific. PeerJ 10:e14389 https://doi.org/10.7717/peerj.14389
Regulatory mechanism of Scutellaria baicalensis Georgi on bone cancer pain based on network pharmacology and experimental verification
Context Scutellaria baicalensis Georgi (SBG) may relieve bone cancer pain (BCP) by regulating cell proliferation, angiogenesis, and apoptosis. Objective The mechanism of SBG in the treatment of BCP remains to be further explored. Methods The active compounds and targets of SBG were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and SwissTargetPrediction databases. BCP-related targets were screened from NCBI and GeneCards databases. Additionally, Cytoscape software was applied to construct network diagrams, and OmicShare platform was used to enrich Gene Ontology (GO) and pathways. Finally, the verification of active compounds and core targets was performed based on quantitative real-time PCR (qRT-PCR). Results Interestingly, we identified baicalein and wogonin as the main active components of SBG. A total of 41 SBG targets, including VEGFA, IL6, MAPK3, JUN and TNF, were obtained in the treatment of BCP. In addition, pathways in cancer may be an essential way of SBG in the treatment of BCP. Experimental verification had shown that baicalein and wogonin were significantly related to BCP core targets. Conclusions The active components of SBG have been clarified, and the mechanism of the active components in treating BCP has been predicted and verified, which provides an experimental and theoretical basis for the in-depth elucidation of the pharmacodynamics material basis and mechanism of SBG.
Wang et al. (2022) Regulatory mechanism of Scutellaria baicalensis Georgi on bone cancer pain based on network pharmacology and experimental verification. PeerJ 10:e14394 https://doi.org/10.7717/peerj.14394
Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico
Background Genetic diversity is fundamental for the survival of species. In particular, in a climate change scenario, it is crucial that populations maintain genetic diversity so they can adapt to novel environmental conditions. Genetic diversity in wild agaves is usually high, with low genetic differentiation among populations, in part maintained by the agave pollinators such as the nectarivorous bats. In cultivated agaves, patterns of genetic diversity vary according to the intensity of use, management, and domestication stage. In Agave tequilana Weber var. azul (A. tequilana thereafter), the plant used for tequila production, clonal propagation has been strongly encouraged. These practices may lead to a reduction in genetic diversity. Methods We studied the diversity patterns with genome-wide SNPs, using restriction site associated DNA sequencing in cultivated samples of A. tequilana from three sites of Jalisco, Mexico. For one locality, seeds were collected and germinated in a greenhouse. We compared the genomic diversity, levels of inbreeding, genetic differentiation, and connectivity among studied sites and between adults and juvenile plants. Results Agave tequilana presented a genomic diversity of HT = 0.12. The observed heterozygosity was higher than the expected heterozygosity. Adults were more heterozygous than juveniles. This could be a consequence of heterosis or hybrid vigor. We found a shallow genetic structure (average paired FST = 0.0044). In the analysis of recent gene flow, we estimated an average migration rate among the different populations of m = 0.25. In particular, we found a population that was the primary source of gene flow and had greater genomic diversity (HE and HO), so we propose that this population should continue to be monitored as a potential genetic reservoir. Discussion Our results may be the consequence of more traditional management in the studied specific region of Jalisco. Also, the exchange of seeds or propagules by producers and the existence of gene flow due to occasional sexual reproduction may play an important role in maintaining diversity in A. tequilana. For populations to resist pests, to continue evolving and reduce their risk of extinction under a climate change scenario, it is necessary to maintain genetic diversity. Under this premise we encourage to continue acting in conservation programs for this species and its pollinators.
Ruiz Mondragon et al. (2022) Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico. PeerJ 10:e14398 https://doi.org/10.7717/peerj.14398
Evolution of sequence traits of prion-like proteins linked to amyotrophic lateral sclerosis (ALS)
Prions are proteinaceous particles that can propagate an alternative conformation to further copies of the same protein. They have been described in mammals, fungi, bacteria and archaea. Furthermore, across diverse organisms from bacteria to eukaryotes, prion-like proteins that have similar sequence characters are evident. Such prion-like proteins have been linked to pathomechanisms of amyotrophic lateral sclerosis (ALS) in humans, in particular TDP43, FUS, TAF15, EWSR1 and hnRNPA2. Because of the desire to study human disease-linked proteins in model organisms, and to gain insights into the functionally important parts of these proteins and how they have changed across hundreds of millions of years of evolution, we analyzed how the sequence traits of these five proteins have evolved across eukaryotes, including plants and metazoa. We discover that the RNA-binding domain architecture of these proteins is deeply conserved since their emergence. Prion-like regions are also deeply and widely conserved since the origination of the protein families for FUS, TAF15 and EWSR1, and since the last common ancestor of metazoa for TDP43 and hnRNPA2. Prion-like composition is uncommon or weak in any plant orthologs observed, however in TDP43 many plant proteins have equivalent regions rich in other amino acids (namely glycine and tyrosine and/or serine) that may be linked to stress granule recruitment. Deeply conserved low-complexity domains are identified that likely have functional significance.
Luo et al. (2022) Evolution of sequence traits of prion-like proteins linked to amyotrophic lateral sclerosis (ALS). PeerJ 10:e14417 https://doi.org/10.7717/peerj.14417
Chimpanzee play sequences are structured hierarchically as games
Social play is ubiquitous in the development of many animal species and involves players adapting actions flexibly to their own previous actions and partner responses. Play differs from other behavioural contexts for which fine-scale analyses of action sequences are available, such as tool use and communication, in that its form is not defined by its function, making it potentially more unpredictable. In humans, play is often organised in games, where players know context-appropriate actions but string them together unpredictably. Here, we use the sequential nature of play elements to explore whether play elements in chimpanzees are structured hierarchically and follow predictable game-like patterns. Based on 5,711 play elements from 143 bouts, we extracted individual-level play sequences of 11 Western chimpanzees (Pan troglodytes verus) of different ages from the Bossou community. We detected transition probabilities between play elements that exceeded expected levels and show that play elements form hierarchically clustered and interchangeable groups, indicative of at least six games that can be identified from transition networks, some with different roles for different players. We also show that increased information about preceding play elements improved predictability of subsequent elements, further indicating that play elements are not strung together randomly but that flexible action rules underlie their usage. Thus, chimpanzee play is hierarchically structured in short games which limit acceptable play elements and allow players to predict and adapt to partners’ actions. This “grammar of action” approach to social interactions can be valuable in understanding cognitive and communicative abilities within and across species.
Mielke et al. (2022) Chimpanzee play sequences are structured hierarchically as games. PeerJ 10:e14294 https://doi.org/10.7717/peerj.14294
The extended day length promotes earlier flowering of bermudagrass
Day length is a very critical environmental factor affecting plant growth and development. The extension of light application time has been shown to promote flowering in the long-day plant and to shorten breeding time in some crops. However, previous research on the regulation of bermudagrass flowering by light application time is scarce. Therefore, this study investigated the effect of day length on the growth and flowering of bermudagrass by prolonging the light application time in a controlled greenhouse. Three different light application times were set up in the experiment: 22/2 h (22 hours light/2 hours dark), 18/6 h (18 hours light/6 hours dark), 14/10 h (14 hours light/10 hours dark). Results showed that extending the light application time not only promoted the growth of bermudagrass (plant height, fresh weight, dry weight) but also its nutrient uptake (nitrogen (N) and phosphorous (P) content). In addition, daily light integrals were different when flowering under different light application times. Most importantly, under the 22/2 h condition, flowering time was successfully reduced to 44 days for common bermudagrass (Cynodon dactylon [L.] pers) genotype A12359 and 36 days for African bermudagrass (Cynodon transvaalensis Burtt-Davy) genotype ABD11. This study demonstrated a successful method of bermudagrass flowering earlier than usual time by manipulating light application time which may provide useful insights for bermudagrass breeding.
Ji et al. (2022) The extended day length promotes earlier flowering of bermudagrass. PeerJ 10:e14326 https://doi.org/10.7717/peerj.14326
Functional expression and purification of DoxA, a key cytochrome P450 from Streptomyces peucetius ATCC 27952
The antitumor drug doxorubicin is widely used in clinical practice. However, the low yield and high cost of this drug highlight the urgent need for cost-effective processes to rapidly manufacture antitumor drugs at scale. In the biosynthesis pathway, the multi-functional cytochrome P450 enzyme DoxA catalyzes the last three steps of hydroxylation. The final conversion of daunorubicin to doxorubicin is the rate-limiting step. In our work, the DoxA has been expressed with the ferredoxin reductase FDR2 and the ferredoxin FDX1 and purified to homogeneous. The reduced carbon monoxide difference spectroscopy, heme concentration, and enzymatic characteristic were characterized. These studies suggest an approach for engineering Streptomyces P450s with functional expression for mechanistic and structural studies.
Yang et al. (2022) Functional expression and purification of DoxA, a key cytochrome P450 from Streptomyces peucetius ATCC 27952. PeerJ 10:e14373 https://doi.org/10.7717/peerj.14373
The Mini Nutritional Assessment tool’s applicability for the elderly in Ethiopia: validation study
Background The Mini Nutrition Assessment (MNA) is a widely used and valid tool for screening and assessment of malnutrition among the elderly population worldwide. However, MNA has not been validated among the Ethiopian elderly population and this study assessed the validity of the tool for the target population. Methods Cross-sectional validation study design employed to validate MNA in Meki town, East Ethiopia. This study included 176 randomly selected elders living in the community, whereas amputated, bedridden, visible deformity, known liver and/or renal disorders were excluded. The original MNA questionnaires were translated to local language and administered to each participant after doing the pretest. The anthropometric, self-perception of nutritional status and serum albumin concentrations were measured. Reliability, validity, sensitivity, specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated. Receiver-operating characteristic (ROC) curve analysis was plotted to identify the area under the curve (AUC) and optimal cut-off value for the prediction of malnutrition. Result A total of one hundred and seventy-six elders participated in this study. Of the total participants, 78(44.3%) were males. The mean (SD) age of the participants was 67.6 (±5.8) years and ranged from 60 to 84 years. The prevalence of malnutrition based on the MNA criteria (MNA < 17 points) was 18.2%, and 13.1% based on serum albumin concentration (<3 g/dl).The MNA had an overall Internal consistency of Cronbach’s alpha 0.61. The tool also demonstrated significant criterion-related validity (0.75, p < 0.001) and concurrent validity (0.51, p < 0.001) with serum albumin concentration and self-perception of nutritional status respectively. Using the original cut-off point, the sensitivity, specificity, PPV and NPV of the tool were 93.5%, 44.6%, 65.4% and 86.0%, respectively. By modifying, the cut-off point to a value of <20.5, the sensitivity and specificity of the tool increases to 97.6% and 82.8% respectively. The AUC (95%CI) showed an overall accuracy of 92.7% (88.5, 96.9). Conclusion The MNA tool can be used as a valid malnutrition screening tool for the Ethiopian elderly population by modifying the original cut-off point.
Urgessa (2022) The Mini Nutritional Assessment tool’s applicability for the elderly in Ethiopia: validation study. PeerJ 10:e14396 https://doi.org/10.7717/peerj.14396
A manager’s guide to using eDNA metabarcoding in marine ecosystems
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
Gold et al. (2022) A manager’s guide to using eDNA metabarcoding in marine ecosystems. PeerJ 10:e14071 https://doi.org/10.7717/peerj.14071
A review of raptor carcass persistence trials and the practical implications for fatality estimation at wind farms
Bird and bat turbine collision fatalities are a principal biodiversity impact at wind energy facilities. Raptors are a group at particular risk and often the focus of post-construction fatality monitoring programs. To estimate fatalities from detected carcasses requires correction for biases, including for carcasses that are removed or decompose before the following search. This is addressed through persistence trials, where carcasses are monitored until no longer detectable or the trial ends. Sourcing sufficient raptor carcasses for trials is challenging and surrogates that are typically used often have shorter persistence times than raptors. We collated information from raptor carcass persistence trials to evaluate consistencies between trials and assess the implications of using persistence values from other studies in wind facility fatality estimates. We compiled individual raptor carcass persistence times from published sources along with information on methods and location, estimated carcass persistence using GenEst and ran full fatality estimates using the carcass persistence estimates and mock datasets for other information. We compiled results from 22 trials from 17 sites across four terrestrial biomes, with trials lasting between 7 and 365 days and involving between 11 and 115 carcasses. Median carcass persistence was estimated at 420 days (90% confidence interval (CI) of 290 to 607 days) for the full dataset. Persistence time varied significantly between trials (trial-specific persistence estimates of 14 (5–42) days to 1,586 (816–3,084) days) but not between terrestrial biomes. We also found no significant relationship between either the number of carcasses in the trial or trial duration and estimated carcass persistence. Using a mock dataset with 12 observed fatalities, we estimated annual fatalities of 25 (16–33) or 26 (17–36) individuals using a 14- or 28-day search interval respectively using global dataset. When using trial-specific carcass persistence estimates and the same mock dataset, estimated annual fatalities ranged from 22 (14–30) to 37 (21–63) individuals for a 14-day search interval, and from 22 (15–31) to 47 (26–84) individuals for a 28-day search interval. The different raptor carcass persistence rates between trials translated to small effects on fatality estimates when using recommended search frequencies, since persistence rates were generally much longer than the search interval. When threatened raptor species, or raptors of particular concern to stakeholders are present, and no site-specific carcass persistence estimates are available, projects should use the lowest median carcass persistence estimate from this study to provide precautionary estimates of fatalities. At sites without threatened species, or where the risk of collision to raptors is low, the global median carcass persistence estimate from this review could be used to provide a plausible estimate for annual raptor fatalities.
Wilson et al. (2022) A review of raptor carcass persistence trials and the practical implications for fatality estimation at wind farms. PeerJ 10:e14163 https://doi.org/10.7717/peerj.14163