Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands
Island bat species are disproportionately at risk of extinction, and Hawaiʻi’s only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as ʻōpeʻapeʻa, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988–2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawaiʻi, Maui, Oʻahu, and Kauaʻi. Genetic differentiation occurred between Hawaiʻi and Maui, both of which were differentiated from Oʻahu and Kauaʻi. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawaiʻi and Kauaʻi. Contemporary genetic effective population sizes were smaller on Oʻahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawaiʻi. Our study provides population-level estimates for the genetic diversity and geographic structure of ‘ōpeʻapeʻa, that could be used by agencies tasked with wildlife conservation in Hawaiʻi.
Pinzari et al. (2023) Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands. PeerJ 11:e14365 https://doi.org/10.7717/peerj.14365
Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development
Glutathione S-transferase (GSTs), a large and diverse group of multi-functional enzymes (EC 2.5.1.18), are associated with cellular detoxification, various biotic and abiotic stress responses, as well as secondary metabolites transportation. Here, 53 members of the FcGST gene family were screened from the genome database of fig (Ficus carica), which were further classified into five subfamilies, and the tau and phi were the major subfamilies. These genes were unevenly distributed over all the 13 chromosomes, and 12 tandem and one segmental duplication may contribute to this family expansion. Syntenic analysis revealed that FcGST shared closer genetic evolutionary origin relationship with species from the Ficus genus of the Moraceae family, such as F. microcarpa and F. hispida. The FcGST members of the same subfamily shared similar gene structure and motif distribution. The α helices were the chief structure element in predicted secondary and tertiary structure of FcGSTs proteins. GO and KEGG indicated that FcGSTs play multiple roles in glutathione metabolism and stress reactions as well as flavonoid metabolism. Predictive promoter analysis indicated that FcGSTs gene may be responsive to light, hormone, stress stimulation, development signaling, and regulated by MYB or WRKY. RNA-seq analysis showed that several FcGSTs that mainly expressed in the female flower tissue and peel during ‘Purple-Peel’ fig fruit development. Compared with ‘Green Peel’, FcGSTF1, and FcGSTU5/6/7 exhibited high expression abundance in the mature fruit purple peel. Additionally, results of phylogenetic sequences analysis, multiple sequences alignment, and anthocyanin content together showed that the expression changes of FcGSTF1, and FcGSTU5/6/7 may play crucial roles in fruit peel color alteration during fruit ripening. Our study provides a comprehensive overview of the GST gene family in fig, thus facilitating the further clarification of the molecular function and breeding utilization.
Liu et al. (2023) Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development. PeerJ 11:e14406 https://doi.org/10.7717/peerj.14406
Evidence of validity and reliability of Jumpo 2 and MyJump 2 for estimating vertical jump variables
Background We investigated the concurrent validity and test-retest reliability of the Jumpo 2 and MyJump 2 apps for estimating jump height, and the mean values of force, velocity, and power produced during countermovement (CMJ) and squat jumps (SJ). Methods Physically active university aged men (n = 10, 20 ± 3 years, 176 ± 6 cm, 68 ± 9 kg) jumped on a force plate (i.e., criterion) while being recorded by a smartphone slow-motion camera. The videos were analyzed using Jumpo 2 and MyJump 2 using a Samsung Galaxy S7 powered by the Android system. Validity and reliability were determined by regression analysis, typical error of estimates and measurements, and intraclass correlation coefficients. Results Both apps provided a reliable estimate of jump height and the mean values of force, velocity, and power. Furthermore, estimates of jump height for CMJ and SJ and the mean force of the CMJ were valid. However, the apps presented impractical or poor validity correlations for velocity and power. Compared with criterion, the apps underestimated the velocity of the CMJ. Conclusions Therefore, Jumpo 2 and MyJump 2 both provide a valid measure of jump height, but the remaining variables provided by these apps must be viewed with caution since the validity of force depends on jump type, while velocity (and as consequence power) could not be well estimated from the apps.
Vieira et al. (2023) Evidence of validity and reliability of Jumpo 2 and MyJump 2 for estimating vertical jump variables. PeerJ 11:e14558 https://doi.org/10.7717/peerj.14558
Facilitation of a free-roaming apex predator in working lands: evaluating factors that influence leopard spatial dynamics and prey availability in a South African biodiversity hotspot
Apex predators ideally require vast intact spaces that support sufficient prey abundances to sustain them. In a developing world, however, it is becoming extremely difficult to maintain large enough areas to facilitate apex predators outside of protected regions. Free-roaming leopards (Panthera pardus) are the last remaining apex predator in the Greater Cape Floristic Region, South Africa, and face a multitude of threats attributable to competition for space and resources with humans. Using camera-trap data, we investigated the influence of anthropogenic land modification on leopards and the availability of their natural prey species in two contrasting communities—primarily protected (Cederberg) and agriculturally transformed (Piketberg). Potential prey species composition and diversity were determined, to indicate prey availability in each region. Factors influencing spatial utilisation by leopards and their main prey species were also assessed. Estimated potential prey species richness (Cederberg = 27, Piketberg = 26) and diversity indices (Cederberg—H′ = 2.64, Ds = 0.90; Piketberg—H′ = 2.46, Ds = 0.89), supported by both the Jaccard’s Index (J = 0.73) and Sørensen’s Coefficient (CC = 0.85), suggested high levels of similarity across the two regions. Main leopard prey species were present in both regions, but their relative abundances differed. Grey rhebok, klipspringer, and rock hyrax were more abundant in the Cederberg, while Cape grysbok, Cape porcupine, chacma baboon, and common duiker were more abundant in Piketberg. Leopards persisted across the agriculturally transformed landscape despite these differences. Occupancy modelling revealed that the spatial dynamics of leopards differed between the two regions, except for both populations preferring areas further away from human habitation. Overall, anthropogenic factors played a greater role in affecting spatial utilisation by leopards and their main prey species in the transformed region, whereas environmental factors had a stronger influence in the protected region. We argue that greater utilisation of alternative main prey species to those preferred in the protected region, including livestock, likely facilitates the persistence of leopards in the transformed region, and believe that this has further implications for human-wildlife conflict. Our study provides a baseline understanding of the potential direct and indirect impacts of agricultural landscape transformation on the behaviour of leopards and shows that heavily modified lands have the potential to facilitate mammalian diversity, including apex predators. We iterate that conservation measures for apex predators should be prioritised where they are present on working lands, and encourage the collaborative development of customised, cost-effective, multi-species conflict management approaches that facilitate coexistence.
Greyling et al. (2023) Facilitation of a free-roaming apex predator in working lands: evaluating factors that influence leopard spatial dynamics and prey availability in a South African biodiversity hotspot. PeerJ 11:e14575 https://doi.org/10.7717/peerj.14575
Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study
Background and Objective Epidemiological studies report associations between coronavirus disease 2019 (COVID-19) and periodontitis; however, causality has not been proven. The aim of this study is to assess the associations between COVID-19 susceptibility and periodontitis with two-sample Mendelian randomization (MR) analyses. Methods A two-sample summary MR analysis was performed using data for outcome and exposure from the OpenGWAS database on people of European descent. Periodontal complex traits (PCTs) were chosen as a proxy for the periodontitis phenotype. The causal association between PCT3 (Aggregatibacter actinomycetemcomitans), PCT5 (Porphyromonas gingivalis), and gingival crevicular fluid (GCF) interleukin-1β (IL-1β) and COVID-19 were considered. Genome-wide association study (GWAS) data with the two largest sample sizes were selected as COVID-19 outcomes (datasets ebi-a-GCST010776 and ebi-a-GCST010777). Single-nucleotide polymorphisms (SNPs) associated with PCT3, PCT5, and GCF IL-1β at statistical significance at genome-wide level (P < 5 × 10−8) were identified as genetic instruments. We used two-sample summary MR methods and tested the existence of a pleiotropic effect with MR-Egger. Results Inverse-variance weighted (IVW) estimates showed that there was a positive association between COVID-19 risk and periodontitis (ebi-a-GCST010776: odds ratio [OR] = 1.02 (95% confidence interval (CI), 1.00–1.05), P = 0.0171; ebi-a-GCST010777: OR = 1.03 (95% CI, 1.00–1.05), P = 0.0397). The weighted median also showed directionally similar estimates. Exploration of the causal associations between other PCTs and COVID-19 identified a slight effect of local inflammatory response (GCF IL-1β) on COVID-19 risk across the two datasets (ebi-a-GCST010776: IVW OR = 1.02 (95% CI, [1.01–1.03]), P < 0.001; ebi-a-GCST010777: IVW OR = 1.03 (95% CI, [1.02–1.04]), P < 0.001). The intercepts of MR-Egger yielded no proof for significant directional pleiotropy for either dataset (ebi-a-GCST010776: P = 0.7660; ebi-a-GCST010777: P = 0.6017). Conclusions The findings suggests that periodontitis and the higher GCF IL-1β levels is causally related to increase susceptibility of COVID-19. However, given the limitations of our study, the well-designed randomized controlled trials are needed to confirm its findings, which may represent a new non-pharmaceutical intervention for preventing COVID-19.
Meng et al. (2023) Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study. PeerJ 11:e14595 https://doi.org/10.7717/peerj.14595
Combination of Vitamin C and Lenvatinib potentiates antitumor effects in hepatocellular carcinoma cells in vitro
Lenvatinib has become a first-line drug in the treatment of advanced hepatocellular carcinoma (HCC). Investigating its use in combination with other agents is of great significance to improve the sensitivity and durable response of Lenvatinib in advanced HCC patients. Vitamin C (L-ascorbic acid, ascorbate, VC) is an important natural antioxidant, which has been reported to show suppressive effects in cancer treatment. Here, we investigated the effect of the combination of VC and Lenvatinib in HCC cells in vitro. We found that treatment of VC alone significantly inhibited the proliferation, migration and invasion in HCC cells. Additionally, VC was strongly synergistic with Lenvatinib in inhibition of the proliferative, migratory and invasive capacities of HCC cells in vitro. In conclusion, our results demonstrate that the combination of VC and Lenvatinib has synergistic antitumor activities against HCC cells, providing a promising therapeutic strategy to improve the prognosis of HCC patients.
Wang et al. (2023) Combination of Vitamin C and Lenvatinib potentiates antitumor effects in hepatocellular carcinoma cells in vitro. PeerJ 11:e14610 https://doi.org/10.7717/peerj.14610
Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep
Background Stevia straw is a byproduct of sugar crop stevia. It is a good feed material because of richness in nutrients and active substances (steviosides and flavonoids). However, due to improper utilization such as piling, burning and so on, it became a large amount of wasted straw resources and lead to environmental pollution. Methods We added 0%, 0.2%, 0.4%, 0.6%, 0.8%, 1.0% and 1.5% of stevia stalk to study the effects of different stevia stalk concentrations on nutrient utilization and rumen fermentation in sheep (based on sheep diet). In vitro fermentation method was used, with 17 repetitions for each treatment. All fermentation substrate based on sheep diet with different stevia stalk concentrations were fermented for 2 h, 6 h, 12 h, 24 h and 48 h, then the gas production, dry matter degradability (DMD), crude protein degradability (CPD), neutral detergent fiber degradability (NDFD), acid detergent fiber degradability (ADFD), pH, ammonia nitrogen (NH3-N) and volatile fatty acids (VFAs) were determined. Results The results showed that at different fermentation time, the change trend of gas production in each teatment was basically same, but the maximum occurred in 1.0% treatment at 48 h. The DMD, CPD, NDFD and ADFD of sheep diets increased with fermentation time increasing, especially the CPD48h, NDFD48h and ADFD48h of diets in 0.8%, 1.0% and 1.5% treatments were significantly higher than those in control (P < 0.05). The pH of fermentation substrate in each treatment remained within the normal range of 6.21∼7.25. NH3-N24h–48hin 0.8%, 1.0% and 1.5% treatments were higher than that in control. At 6 h–12 h, the total acid content of 0.8% and 1.0% treatments were significantly higher than those of other treatments (P < 0.05), it reached the highest in 1.0% treatment. According to overall evaluation, effect ranking of stevia stalk on sheep nutrient utilization was as follows: 1.0% >0.8% >1.5% >0.4% >0.6% >0.2%. Overall, 1.0% stevia stalk could promote nutrient degradation and sheep rumen fermentation.
Zhang et al. (2023) Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep. PeerJ 11:e14689 https://doi.org/10.7717/peerj.14689
Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance
Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23,and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains.
Ababneh et al. (2023) Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance. PeerJ 11:e14709 https://doi.org/10.7717/peerj.14709
Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells
Background S100 calcium-binding protein A9 (S100A9) is a commonly known pro-inflammatory factor involved in various inflammatory responses. Clostridium perfringens (C. perfringens ) type C is known to cause diarrhea in piglets. However, the role of S100A9 in C. perfringens type C-induced infectious diarrhea is unclear. Methods Here, the S100A9 gene was overexpressed and knocked down in the IPEC-J2 cells, which were treated with C. perfringens beta2 (CPB2) toxin. The role of S100A9 in CPB2 toxin-induced injury in IPEC-J2 cells was assessed by measuring the levels of inflammatory cytokines, reactive oxygen species (ROS), lactate dehydrogenase (LDH), cell proliferation, and tight junction-related proteins. Results The results showed elevated expression of S100A9 in diarrhea-affected piglet tissues, and the elevation of S100A9 expression after CPB2 toxin treatment of IPEC-J2 was time-dependent. In CPB2 toxin-induced IPEC-J2 cells, overexpression of S100A9 had the following effects: the relative expression of inflammatory factors IL-6, IL8, TNF-α, and IL-1β was increased; the ROS levels and LDH viability were significantly increased; cell viability and proliferation were inhibited; the G0/G1 phase cell ratio was significantly increased. Furthermore, overexpression of S100A9 reduced the expression of tight junction proteins in CPB2-induced IPEC-J2 cells. The knockdown of S100A9 had an inverse effect. In conclusion, our results confirmed that S100A9 exacerbated inflammatory injury in CPB2 toxin-induced IPEC-J2 cells, inhibited cell viability and cell proliferation, and disrupted the tight junctions between cells. Thus, decreased S100A9 expression alleviates CPB2 toxin-induced inflammatory injury in IPEC-J2 cells.
Li et al. (2023) Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells. PeerJ 11:e14722 https://doi.org/10.7717/peerj.14722
Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing
Background The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated. Methods In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function. Results After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.
Wu et al. (2023) Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing. PeerJ 11:e14733 https://doi.org/10.7717/peerj.14733