Probability-based preservational variations within the early Cambrian Chengjiang biota (China)
The Chengjiang biota (Yunnan Province, China) is a treasure trove of soft-bodied animal fossils from the earliest stages of the Cambrian explosion. The mechanisms contributing to its unique preservation, known as the Burgess Shale-type preservation, are well understood. However, little is known about the preservation differences between various animal groups within this biota. This study compares tissue-occurrence data of 11 major animal groups in the Chengjiang biota using a probabilistic methodology. The fossil-based data from this study is compared to previous decay experiments. This shows that all groups are not equally preserved with some higher taxa more likely to preserve soft tissues than others. These differences in fossil preservation between taxa can be explained by the interaction of biological and environmental characteristics. A bias also results from differential taxonomic recognition, as some taxa are easily recognized from even poorly preserved fragments while other specimens are difficult to assign to higher taxa even with exquisite preservation.
Saleh et al. (2022) Probability-based preservational variations within the early Cambrian Chengjiang biota (China). PeerJ 10:e13869 https://doi.org/10.7717/peerj.13869
Long non-coding RNA BZRAP1-AS1 functions in malignancy and prognosis for non-small-cell lung cancer
Purpose The function of BZRAP1-AS1 is unknown in lung cancer. We evaluated the clinicopathologic significance of BZRAP1-AS1, and its role in non-small-cell lung cancer (NSCLC) progression. Patient and methods Sixty-three NSCLC patients from Beijing Chest Hospital were included. The expression of BZRAP1-AS1 was detected by real-time quantitative polymerase chain reaction (RT-qPCR) in tumor tissues and adjacent normal tissues. Then, the clinicopathological significance and prognostic value of BZRAP1-AS1 were analyzed by using our cohort and TCGA cohort. Finally, the effect of BZRAP1-AS1 on proliferation and motility of NSCLC cell lines were evaluated by cell growth assay, colony formation assay, xenograft tumorigenesis experiment in nude mice and transwell assays respectively. Results Compared with adjacent normal tissues, BZRAP1-AS1 showed lower expression in NSCLC tumor tissues. As for the relationship between BZRAP1-AS1 and clinical characteristics, our results were consistent with those of TCGA data. BZRAP1-AS1 was lower in T1 than T2–T4 patients, N1-N3 than N0 patients. Low level BZRAP1-AS1 was related to shorter overall survival time (OS) in lung adenocarcinoma (LUAD), and poor first progression time (FP) in LUAD and lung squamous cell carcinoma (LUSC) patients. BZRAP1-AS1 was significantly associated with the prognosis of NSCLC patients. Overexpression of BZRAP1-AS1 inhibited proliferation and migration of H1299 and HCC827 cells. Conclusion BZRAP1-AS1 expression decreases in tumor tissues with the increase of malignancy grades in NSCLC. BZRAP1-AS1 plays an anticancer role by inhibiting cell proliferation, invasion, and metastasis, and has a potential prognostic value in NSCLC. BZRAP1-AS1 may serve as a diagnostic marker and therapeutic target for NSCLC.
Hao et al. (2022) Long non-coding RNA BZRAP1-AS1 functions in malignancy and prognosis for non-small-cell lung cancer. PeerJ 10:e13871 https://doi.org/10.7717/peerj.13871
Predictability and transferability of local biodiversity environment relationships
Background Biodiversity varies in space and time, and often in response to environmental heterogeneity. Indicators in the form of local biodiversity measures–such as species richness or abundance–are common tools to capture this variation. The rise of readily available remote sensing data has enabled the characterization of environmental heterogeneity in a globally robust and replicable manner. Based on the assumption that differences in biodiversity measures are generally related to differences in environmental heterogeneity, these data have enabled projections and extrapolations of biodiversity in space and time. However so far little work has been done on quantitatively evaluating if and how accurately local biodiversity measures can be predicted. Methods Here I combine estimates of biodiversity measures from terrestrial local biodiversity surveys with remotely-sensed data on environmental heterogeneity globally. I then determine through a cross-validation framework how accurately local biodiversity measures can be predicted within (“predictability”) and across similar (“transferability”) biodiversity surveys. Results I found that prediction errors can be substantial, with error magnitudes varying between different biodiversity measures, taxonomic groups, sampling techniques and types of environmental heterogeneity characterizations. And although errors associated with model predictability were in many cases relatively low, these results question–particular for transferability–our capability to accurately predict and project local biodiversity measures based on environmental heterogeneity. I make the case that future predictions should be evaluated based on their accuracy and inherent uncertainty, and ecological theories be tested against whether we are able to make accurate predictions from local biodiversity data.
Spatial and Geographic Information Science
Jung (2022) Predictability and transferability of local biodiversity environment relationships. PeerJ 10:e13872 https://doi.org/10.7717/peerj.13872
Pediatrics HIV-positive status disclosure and its predictors in Ethiopia: a systematic review and meta-analysis
Introduction HIV-positive status disclosure for children is challenging for family members, guardians, and healthcare professionals. Disclosure is very challenging, particularly for children, yet no systematic synthesis of evidence accurately measures HIV-positive status disclosure in children. This systematic review and meta-analysis study aimed to quantify the national prevalence of pediatric HIV-positive status disclosure in Ethiopia and identify factors associated with HIV-positive status disclosure. Method We systematically searched PubMed, EMBASE, Web of Science databases, and google scholar for relevant published studies. Studies published in the English language and conducted with cohort, case-control, and cross-sectional designs were eligible for the review. The primary and secondary outcomes of the study were HIV-positive status disclosure and factors associated with HIV-positive status disclosure, respectively. The quality of the included studies was assessed using the Joanna Briggs Institute critical appraisal tools. A random effect- model was used to estimate the pooled prevalence of HIV-positive status disclosure. Heterogeneity and publication bias of included studies was determined using I2 and Egger’s test, respectively. Result From 601 records screened, nine relevant studies consisting of 2,442 HIV-positive children were included in the analysis. The overall pooled prevalence of HIV-positive status disclosure among children living with HIV/AIDS in Ethiopia was 31.2% (95% CI [23.9–38.5]). HIV-negative status of caregivers (AOR: 2.01; 95% CI [1.28–3.18]), long duration on ART (greater than 5 years) (AOR: 3.2; 95% CI [1.77–5.78]) and older age of the child (>10 years) (AOR: 7.2; 95% CI [4.37–11.88]) were significantly associated with HIV-positive status disclosure. Conclusion Low prevalence of pediatric HIV-positive status disclosure was observed in Ethiopia. The longer duration of ART, the HIV-negative status of the caregiver, and older age greater than 10 years were the predictors of pediatric HIV-positive status disclosure. Health system leaders and policymakers shall design training and counseling programs for healthcare professionals and caregivers to enhance their awareness about HIV-positive status disclosure. Trial registration This review was registered under PROSPERO and received a unique registration number, CRD42019119049.
Belay et al. (2022) Pediatrics HIV-positive status disclosure and its predictors in Ethiopia: a systematic review and meta-analysis. PeerJ 10:e13896 https://doi.org/10.7717/peerj.13896
Chemistry, taxonomy and ecology of the potentially chimpanzee-dispersed Vepris teva sp.nov. (Rutaceae) endangered in coastal thicket in the Congo Republic
Continuing a survey of the chemistry of species of the largely continental African genus Vepris, we investigate a species previously referred to as Vepris sp. 1 of Congo. From the leaves of Vepris sp. 1 we report six compounds. The compounds were three furoquinoline alkaloids, kokusaginine (1), maculine (2), and flindersiamine (3), two acridone alkaloids, arborinine (4) and 1-hydroxy-3-methoxy-10-methylacridone (5), and the triterpenoid, ß-amyrin (6). Compounds 1–4 are commonly isolated from other Vepris species, compound 5 has been reported before once, from Malagasy Vepris pilosa, while this is the first report of ß-amyrin from Vepris. This combination of compounds has never before been reported from any species of Vepris. We test the hypothesis that Vepris sp. 1 is new to science and formally describe it as Vepris teva, unique in the genus in that the trifoliolate leaves are subsessile, with the median petiolule far exceeding the petiole in length. Similar fleshy-leathery four-locular syncarpous fruits are otherwise only known in the genus in Vepris glaberrima (formerly the monotypic genus Oriciopsis Engl.), a potential sister species, but requiring further investigation to confirm this phylogenetic position. We briefly characterise the unusual and poorly documented Atlantic coast equatorial ecosystem, where Vepris teva is restricted to evergreen thicket on white sand, unusual in a genus usually confined to evergreen forest. This endemic-rich ecosystem with a unique amphibian as well as plants, extends along the coastline from the mouth of the Congo River to southern Rio Muni, a distance of about 1,000 km, traversing five countries. We map and illustrate Vepris teva and assess its extinction risk as Endangered (EN B1ab(iii)+B2ab(iii)) using the IUCN, 2012 standard. Only three locations are known, and threats include port and oil refinery construction and associated activities, with only one protected location, the Jane Goodall Institute’s Tchimpounga Reserve. Initial evidence indicates that the seeds of Vepris teva are dispersed by chimpanzees, previously unreported in the genus.
Langat et al. (2022) Chemistry, taxonomy and ecology of the potentially chimpanzee-dispersed Vepris teva sp.nov. (Rutaceae) endangered in coastal thicket in the Congo Republic. PeerJ 10:e13926 https://doi.org/10.7717/peerj.13926
An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi
Background Anthropogenic sources can lead to the accumulation of heavy metals in marine organisms through ingestion, absorption, or inhalation. For sea turtle embryos, heavy metals can be absorbed into the egg from the incubation environment or be maternally transferred to the offspring causing neurological, reproductive, and developmental problems. Here, we report heavy metal concentrations in green turtle hatchlings from the largest rookery on the Red Sea, Ras Baridi. Methods Deceased hatchlings were collected from two beaches near a cement factory at Ras Baridi, from which heavy metal concentrations (chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), and lead (Pb)) were measured from the liver, muscle, and residual yolk of the hatchlings. Results Although based on a small sample of hatchlings, the data presented here provides the first measurements of heavy metals from sea turtles in the Red Sea and highlights the link between human activity and its impact on the ecology of sea turtles. In general, the heavy metal concentrations of heavy metals were not significantly different between the beach next to the cement factory and the beach downwind from the factory. However, the concentrations of heavy metals were significantly different between sampled tissues (liver, muscle, and residual yolk). Discussion This study provides insight into current heavy metal levels in green turtle hatchlings, which can be used as bio-indicators for environmental contaminants as coastal development increases in the Red Sea. Moreover, we found a lack of standardized methodology to evaluate heavy metals in hatchling sea turtles. Future efforts should work toward creating comparable techniques for long-term heavy metal monitoring, as this is a useful determinant of anthropogenic pollution.
Environmental Contamination and Remediation
Tanabe et al. (2022) An assessment of heavy metals in green sea turtle (Chelonia mydas) hatchlings from Saudi Arabia’s largest rookery, Ras Baridi. PeerJ 10:e13928 https://doi.org/10.7717/peerj.13928
Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum
Precious corals belong to the family Coralliidae (Cnidaria, Octocorallia), and their axis, which consists of high magnesian calcium carbonate, has long been used in jewelry. With its low growth rate and long lifespan, precious coral is a representative taxon of the vulnerable marine ecosystem. Due to years of overfishing, coral fishery has become a controversial issue. To estimate the growth rate and clarify the uptake process of trace elements in relation to the growth of the carbonate axis, Japanese red coral (Corallium japonicum) was cultured at a depth of 135 m off Takeshima Island, Kagoshima, Japan for 98 months and analyzed by microscopic X-ray fluorescence/soft X-ray photoabsorption (µ-XRF/XAS) speciation mapping. The growth rate was estimated to be 0.37 mm/year in diameter, and 10–11 growth rings were observed in a cross section of the axis. This estimated growth-rate value is the first ever to be obtained from the in-situ culture of Japanese precious coral. The fluctuation in water temperature near the in-situ-culture site was recorded for part of the culture period and then compared with the changes in the growth ring and the distribution of trace elements in a cross section of the coral axis during the same period. When the water temperature was increasing, the growth ring was light in color, sulfur and phosphorus concentrations were low, and magnesium was high. Conversely, a dark band in the growth ring, high sulfur and phosphorus, and low magnesium concentrations were observed when the water temperature was decreasing. In a cross section of the coral axis, the distribution of sulfur and magnesium from the center to the surface corresponded, respectively, to dark and light bands in the annual growth ring. Sulfur concentration was high in the dark band and low in the light band, while magnesium was negatively correlated with sulfur.
Iwasaki et al. (2022) Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum. PeerJ 10:e13931 https://doi.org/10.7717/peerj.13931
Fish habitat restoration on the basis of water morphology simulation
The hydrodynamic conditions of rivers affect fish habitats by influencing parameters such as river bottom topography. Ecological restoration projects change the water morphological characteristics of rivers. Here, water flow characteristics of the upper Yangtze River before and after the construction of a restoration project were analyzed using the computational fluid dynamics simulation method. The longitudinal diversion dam could divide the river into two flow velocity zones, and the outer flow is similar to the original river with a flow velocity of 0.75 m/s. However, flow velocity on the inner side of the river was about 0.25 m/s, forming a larger buffer area. The eddy became more diversified and stable, with a high eddy viscosity coefficient and less fluctuations, at 9 Pa·s; this was conducive to fish aggregation and spawning. At different depths, large gradient differences were observed between the inner and outer sides of the longitudinal diversion dam, and the turbulent current and upward flow of the inner side were obvious; this was more favorable to the aggregation of different fish species. The longitudinal dam body was under a pressure of about 200.2 Pa at the same flow rate; this was significantly lower than the pressure on the transverse dam body. The field flow test and fish survey data showed that the error rate of the simulation using the RNG turbulent model was less than 10% compared with actual mapping. After the restoration of fish habitats by the longitudinal diversion dam, the number of fish species in the area increased from 40 to 49; The density of fish in the water increased from 71.40 fish per 1,000 m2 before the project to 315.70 fish per 1,000 m2 after the project. These results can provide a reference for the rapid assessment of water morphology and fish habitat restoration in the future.
Chen et al. (2022) Fish habitat restoration on the basis of water morphology simulation. PeerJ 10:e13943 https://doi.org/10.7717/peerj.13943
Estimating uncertainty in density surface models
Providing uncertainty estimates for predictions derived from species distribution models is essential for management but there is little guidance on potential sources of uncertainty in predictions and how best to combine these. Here we show where uncertainty can arise in density surface models (a multi-stage spatial modelling approach for distance sampling data), focussing on cetacean density modelling. We propose an extensible, modular, hybrid analytical-simulation approach to encapsulate these sources. We provide example analyses of fin whales Balaenoptera physalus in the California Current Ecosystem.
Miller et al. (2022) Estimating uncertainty in density surface models. PeerJ 10:e13950 https://doi.org/10.7717/peerj.13950
The high diversity of gametogenic pathways in amphispermic water frog hybrids from Eastern Ukraine
Interspecific hybridization can disrupt canonical gametogenic pathways, leading to the emergence of clonal and hemiclonal organisms. Such gametogenic alterations usually include genome endoreplication and/or premeiotic elimination of one of the parental genomes. The hybrid frog Pelophylax esculentus exploits genome endoreplication and genome elimination to produce haploid gametes with chromosomes of only one parental species. To reproduce, hybrids coexist with one of the parental species and form specific population systems. Here, we investigated the mechanism of spermatogenesis in diploid P. esculentus from sympatric populations of P. ridibundus using fluorescent in situ hybridization. We found that the genome composition and ploidy of germ cells, meiotic cells, and spermatids vary among P. esculentus individuals. The spermatogenic patterns observed in various hybrid males suggest the occurrence of at least six diverse germ cell populations, each with a specific premeiotic genome elimination and endoreplication pathway. Besides co-occurring aberrant cells detected during meiosis and gamete aneuploidy, alterations in genome duplication and endoreplication have led to either haploid or diploid sperm production. Diploid P. esculentus males from mixed populations of P. ridibundus rarely follow classical hybridogenesis. Instead, hybrid males simultaneously produce gametes with different genome compositions and ploidy levels. The persistence of the studied mixed populations highly relies on gametes containing a genome of the other parental species, P. lessonae.
Pustovalova et al. (2022) The high diversity of gametogenic pathways in amphispermic water frog hybrids from Eastern Ukraine. PeerJ 10:e13957 https://doi.org/10.7717/peerj.13957