Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions
Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging to 11 genera. Median joining haplotype networks were constructed for each species for the mtDNA cytochrome C oxidase subunit I (COI), and an Analysis of Molecular Variance (AMOVA) was conducted to understand patterns of genetic diversity and structure across the three major ocean basins—the Indian, Atlantic and Pacific Oceans. Haplotype networks showed very shallow coalescence in most species, a finding previously reported for marine teleosts. Star topologies were predominant among sharks while complex mutational topologies predominated among rays, a finding we attribute to extremely limited dispersal in the early life history of rays. Population structuring varied amongst species groups, apparently due to differences in life history traits including reproductive philopatry, site fidelity, pelagic habitat, migratory habits, and dispersal ability. In comparison to reef-associated and demersal species, pelagic and semi pelagic species showed lower levels of structure between and within ocean basins. As expected, there is variation between taxa and groups, but there are also some broad patterns that can guide management and conservation strategies.
Kottillil et al. (2023) Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions. PeerJ 11:e15396 https://doi.org/10.7717/peerj.15396
Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories
Ocean warming and marine heatwaves induced by climate change are impacting coral reefs globally, leading to coral bleaching and mortality. Yet, coral resistance and resilience to warming are not uniform across reef sites and corals can show inter- and intraspecific variability. To understand changes in coral health and to elucidate mechanisms of coral thermal tolerance, baseline data on the dynamics of coral holobiont performance under non-stressed conditions are needed. We monitored the seasonal dynamics of algal symbionts (family Symbiodiniaceae) hosted by corals from a chronically warmed and thermally variable reef compared to a thermally stable reef in southern Taiwan over 15 months. We assessed the genera and photochemical efficiency of Symbiodiniaceae in three coral species: Acropora nana, Pocillopora acuta, and Porites lutea. Both Durusdinium and Cladocopium were present in all coral species at both reef sites across all seasons, but general trends in their detection (based on qPCR cycle) varied between sites and among species. Photochemical efficiency (i.e., maximum quantum yield; Fv/Fm) was relatively similar between reef sites but differed consistently among species; no clear evidence of seasonal trends in Fv/Fm was found. Quantifying natural Symbiodiniaceae dynamics can help facilitate a more comprehensive interpretation of thermal tolerance response as well as plasticity potential of the coral holobiont.
McRae et al. (2023) Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories. PeerJ 11:e15421 https://doi.org/10.7717/peerj.15421
The role of exercise in improving hyperlipidemia-renal injuries induced by a high-fat diet: a literature review
A diet that is high in sugar and fat is a precursor to various chronic diseases, especially hyperlipidemia. Patients with hyperlipidemia have increased levels of plasma free fatty acids and an ectopic accumulation of lipids. The kidney is one of the main organs affected by this disease and, recently, there have been more studies conducted on renal injury caused by hyperlipidemia. The main pathological mechanism is closely related to renal lipotoxicity. However, in different kidney cells, the reaction mechanism varies due to the different affinities of the lipid receptors. At present, it is believed that in addition to lipotoxicity, hyperlipidemia induced-renal injury is also closely related to oxidative stress, endoplasmic reticulum stress, and inflammatory reactions, which are the result of multiple factors. Exercise plays an important role in the prevention of various chronic diseases and recently emerging researches indicated its positive effects to renal injury caused by hyperlipidemia. However, there are few studies summarizing the effects of exercise on this disease and the specific mechanisms need to be further explored. This article summarizes the mechanisms of hyperlipidemia induced-renal injury at the cellular level and discusses the ways in which exercise may regulate it. The results provide theoretical support and novel approaches for identifying the intervention target to treat hyperlipidemia induced-renal injury.
Chen et al. (2023) The role of exercise in improving hyperlipidemia-renal injuries induced by a high-fat diet: a literature review. PeerJ 11:e15435 https://doi.org/10.7717/peerj.15435
Clinical diagnostic value of amino acids in laryngeal squamous cell carcinomas
Background Early diagnosis and treatment can improve the survival rates of patients with laryngeal squamous cell carcinoma (LSCC). Therefore, it is necessary to discover new biomarkers for laryngeal cancer screening and early diagnosis. Methods We collected fasting plasma from LSCC patients and healthy volunteers, as well as cancer and para-carcinoma tissues from LSCC patients, and performed quantitative detection of amino acid levels using liquid chromatography-mass spectrometry. We used overall analysis and multivariate statistical analysis to screen out the statistically significant differential amino acids in the plasma and tissue samples, conducted receiver operating characteristic (ROC) analysis of the differential amino acids to evaluate the sensitivity and specificity of the differential amino acids, and finally determined the diagnostic value of amino acids for laryngeal cancer. Additionally, we identified amino acids in the plasma and tissue samples that are valuable for the early diagnosis of laryngeal cancer classified according to the tumor-node-metastasis (TNM) classification. Results Asparagine (Asp) and homocysteine (Hcy) were two amino acids of common significance in plasma and tissue samples, and their specificity and sensitivity analysis showed that they may be new biomarkers for the diagnosis and treatment of LSCC. According to the TNM staging system, phenylalanine (Phe) and isoleucine (Ile) were screened out in the plasma of LSCC patients at early (I and II) and advanced (III and IV) stages; ornithine hydrochloride (Orn), glutamic acid (Glu), and Glycine (Gly) were selected in the tissue. These dysregulated amino acids found in LSCC patients may be useful as clinical biomarkers for the early diagnosis and screening of LSCC.
Hu et al. (2023) Clinical diagnostic value of amino acids in laryngeal squamous cell carcinomas. PeerJ 11:e15469 https://doi.org/10.7717/peerj.15469
Integrating robotics into wildlife conservation: testing improvements to predator deterrents through movement
Background Agricultural and pastoral landscapes can provide important habitat for wildlife conservation, but sharing these landscapes with wildlife can create conflict that is costly and requires managing. Livestock predation is a good example of the challenges involving coexistence with wildlife across shared landscapes. Integrating new technology into agricultural practices could help minimize human-wildlife conflict. In this study, we used concepts from the fields of robotics (i.e., automated movement and adaptiveness) and agricultural practices (i.e., managing livestock risk to predation) to explore how integration of these concepts could aid the development of more effective predator deterrents. Methods We used a colony of captive coyotes as a model system, and simulated predation events with meat baits inside and outside of protected zones. Inside the protected zones we used a remote-controlled vehicle with a state-of-the art, commercially available predator deterrent (i.e., Foxlight) mounted on the top and used this to test three treatments: (1) light only (i.e., without movement or adaptiveness), (2) predetermined movement (i.e., with movement and without adaptiveness), and (3) adaptive movement (i.e., with both movement and adaptiveness). We measured the time it took for coyotes to eat the baits and analyzed the data with a time-to-event survival strategy. Results Survival of baits was consistently higher inside the protected zone, and the three movement treatments incrementally increased survival time over baseline except for the light only treatment in the nonprotected zone. Incorporating predetermined movement essentially doubled the efficacy of the light only treatment both inside and outside the protected zone. Incorporating adaptive movement exponentially increased survival time both inside and outside the protected zone. Our findings provide compelling evidence that incorporating existing robotics capabilities (predetermined and adaptive movement) could greatly enhance protection of agricultural resources and aid in the development of nonlethal tools for managing wildlife. Our findings also demonstrate the importance of marrying agricultural practices (e.g., spatial management of livestock at night) with new technology to improve the efficacy of wildlife deterrents.
Breck et al. (2023) Integrating robotics into wildlife conservation: testing improvements to predator deterrents through movement. PeerJ 11:e15491 https://doi.org/10.7717/peerj.15491
Tolerogenic dendritic cell reporting: Has a minimum information model made a difference?
Minimum information models are reporting frameworks that describe the essential information that needs to be provided in a publication, so that the work can be repeated or compared to other work. In 2016, Minimum Information about Tolerogenic Antigen-Presenting cells (MITAP) was created to standardize the reporting on tolerogenic antigen-presenting cells, including tolerogenic dendritic cells (tolDCs). tolDCs is a generic term for dendritic cells that have the ability to (re-)establish immune tolerance; they have been developed as a cell therapy for autoimmune diseases or for the prevention of transplant rejection. Because protocols to generate these therapeutic cells vary widely, MITAP was deemed to be a pivotal reporting tool by and for the tolDC community. In this paper, we explored the impact that MITAP has had on the tolDC field. We did this by examining a subset of the available literature on tolDCs. Our analysis shows that MITAP is used in only the minority of relevant papers (14%), but where it is used the amount of metadata available is slightly increased over where it is not. From this, we conclude that MITAP has been a partial success, but that much more needs to be done if standardized reporting is to become common within the discipline.
Sahar et al. (2023) Tolerogenic dendritic cell reporting: Has a minimum information model made a difference?. PeerJ 11:e15352 https://doi.org/10.7717/peerj.15352
Quiz-style online training tool helps to learn birdsong identification and support citizen science
Citizen science is an important approach to monitoring for biodiversity conservation because it allows for data acquisition or analysis on a scale that is not possible for researchers alone. In citizen science projects, the use of online training is increasing to improve such skills. However, the effectiveness of quiz-style online training, assumed to be efficient to enhance participants’ skills, has not been evaluated adequately on species identification for citizen science biodiversity monitoring projects. Memory mechanisms in adaptive learning were hypothesized to guide the development of quiz-based online training tools for learning birdsong identification and for improving interest in birds and natural environments. To examine the hypothesis, we developed a quiz-style online training tool called TORI-TORE. We experimentally applied TORI-TORE in Fukushima, Japan, and examined its effectiveness for bird identification training using test scores and questionnaires to determine participants’ attitudes in a randomized control trial. We obtained the following key results: (1) TORI-TORE had positive effects on test scores and trainees’ attitudes toward birds. (2) Adaptive training, in which questions focused preferentially on unmastered bird species based on the answer history of individual trainees inspired by adaptive learning, unexpectedly led to lower scores and satisfaction in TORI-TORE. (3) Focusing on species that are relatively easy to remember, short lag times between training and testing, and long question intervals positively affected scores. While there is room for improvement, we expect TORI-TORE to contribute to online capacity building and to increase interest in natural environments.
Ogawa et al. (2023) Quiz-style online training tool helps to learn birdsong identification and support citizen science. PeerJ 11:e15387 https://doi.org/10.7717/peerj.15387
Ontogenetic progression of individual head size in the larvae of the beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): catch-up growth within stages and per-stage growth rate changes across stages
The ontogenetic progression of insect larval head size has received much attention due to its fundamental and practical importance. However, although previous studies have analyzed the population mean head size, such an approach may not be appropriate for developmental studies of larval head sizes when the trajectory of individual head size growth is correlated with pre-molt head size and developmental stage. Additionally, there is covariation between the head and body sizes; however, few studies have compared the ontogenetic progression of individual head sizes with that of individual body sizes. In this investigation, the per-stage growth rates (PSGRs) for head width (HW) and cubic-rooted body mass at the beginning of each instar (body size, BS) were assessed in Trypoxylus dichotomus. Linear models were used to test the size- and instar-dependence of the ontogenetic progression of individual HW and BS. The individual PSGRs of the HW (iPSGRH) and BS (iPSGRB) were then compared. In addition, the allometric relationship between HW and BS was examined. The iPSGRH was negatively correlated with the pre-molt HW at every instar (i.e., head catch-up growth). Furthermore, the mean iPSGRH at L2 was relatively higher than that at L1 when the pre-molt HW was used as covariate in the analysis (i.e., instar-effect), whereas the mean iPSGRH decreased ontogenetically. The iPSGRB showed catch-up growth and instar-effects similar to those of iPSGRH; however, iPSGRH was found to be lower than iPSGRB. Due to the differences between the PSGRs for the larval head and body, the larval head size showed negative ontogenetic allometry against body size.
Hoshizaki (2023) Ontogenetic progression of individual head size in the larvae of the beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): catch-up growth within stages and per-stage growth rate changes across stages. PeerJ 11:e15451 https://doi.org/10.7717/peerj.15451
Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous)
Isolated spinosaurid teeth are relatively well represented in the Lower Cretaceous Wealden Supergroup of southern England, UK. Until recently it was assumed that these teeth were referable to Baryonyx, the type species (B. walkeri) and specimen of which is from the Barremian Upper Weald Clay Formation of Surrey. British spinosaurid teeth are known from formations that span much of the c. 25 Ma depositional history of the Wealden Supergroup, and recent works suggest that British spinosaurids were more taxonomically diverse than previously thought. On the basis of both arguments, it is appropriate to doubt the hypothesis that isolated teeth from outside the Upper Weald Clay Formation are referable to Baryonyx. Here, we use phylogenetic, discriminant and cluster analyses to test whether an isolated spinosaurid tooth (HASMG G369a, consisting of a crown and part of the root) from a non-Weald Clay Formation unit can be referred to Baryonyx. HASMG G369a was recovered from an uncertain Lower Cretaceous locality in East Sussex but is probably from a Valanginian exposure of the Hastings Group and among the oldest spinosaurid material known from the UK. Spinosaurid affinities are both quantitatively and qualitatively supported, and HASMG G369a does not associate with Baryonyx in any analysis. This supports recent reinterpretations of the diversity of spinosaurid in the Early Cretaceous of Britain, which appears to have been populated by multiple spinosaurid lineages in a manner comparable to coeval Iberian deposits. This work also reviews the British and global records of early spinosaurids (known mainly from dental specimens), and revisits evidence for post-Cenomanian spinosaurid persistence.
Barker et al. (2023) Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous). PeerJ 11:e15453 https://doi.org/10.7717/peerj.15453
The significance of PD-1/PD-L1 imbalance in ulcerative colitis
Objectives To investigate the expression and significance of programmed cell death protein 1 (PD-1) and programmed cell death ligand-1 (PD-L1) in the mucosal tissues and peripheral blood of patients with ulcerative colitis (UC). Methods Eighty patients with UC were recruited from January 2021 to August 2022 from the Shanxi Province People’s Hospital. PD-1 and PD-L1 expression was assessed by immunohistochemistry in mucosal tissues. An enzyme-linked immunosorbent assay was used to measure soluble PD-1 and PD-L1 levels in peripheral blood serum, and the membrane-bound forms of PD-1 (mPD-1), (T-helper cell) Th1 and Th17, in peripheral blood were determined by flow cytometry. Result PD-1 expression was observed only in the monocytes of the mucosal lamina propria of UC patients, while PD-L1 was mainly located in both epithelial cells and monocytes on the cell membrane. The expression level of PD-1/PD-L1 in the monocytes and epithelial cells of mucosal lamina propria increased with disease activity (P < 0.05). The percentages of PD-1/T and PD-1/CD4+T in the peripheral blood of moderate UC patients (PD-1/T 12.83 ± 6.15% and PD-1/CD4+T 19.67 ± 9.95%) and severe UC patients (PD-1/T 14.29 ± 5.71% and PD-1/CD4+T 21.63 ± 11.44%) were higher than in mild UC patients (PD-1/T 8.17 ± 2.80% and PD-1/CD4+T 12.44 ± 4.73%; P < 0.05). There were no significant differences in PD-1/CD8+T cells between mild and severe UC patients (P > 0.05). There was a statistically significant difference in the expression level of sPD-L1 between the UC groups and healthy controls, and the expression level of sPD-L1 increased with disease severity (P < 0.05); however, there was no statistically significant difference in sPD-1 expression levels between the UC groups and healthy controls (P > 0.05). The correlation coefficients between Th1 and sPD-L1, PD-1/T, PD-1/CD4+T and PD-1/CD8+T were 0.427, 0.589, 0.486, and 0.329, respectively (P < 0.001). The correlation coefficients between Th17 and sPD-L1, PD-1/T, PD-1/CD4+T and PD-1/CD8+T were 0.323, 0.452, 0.320, and 0.250, respectively (P < 0.05). Conclusion The expression level of PD-1/PD-L1 was correlated with UC disease activity, and two forms of PD-1 and PD-L1 may be used as a potential marker for predicting UC and assessing disease progression in UC patients. PD-1/PD-L1 imbalance was a significant phenomenon of UC immune dysfunction. Future research should focus on two forms of PD-1/PD-L1 signaling molecules to better understand the pathogenesis of UC and to identify potential drug therapies.
Shi et al. (2023) The significance of PD-1/PD-L1 imbalance in ulcerative colitis. PeerJ 11:e15481 https://doi.org/10.7717/peerj.15481