Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja)
Background NDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress. Methods We identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR. Results In this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.
Zhang et al. (2022) Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja). PeerJ 10:e14451 https://doi.org/10.7717/peerj.14451
The effects of a set amount of regular maternal exercise during pregnancy on gut microbiota are diet-dependent in mice and do not cause significant diversity changes
Background Diet and exercise can affect the gut microbiota (GM); however, the effects of the same amount of exercise on gut microbiota changes in people on a low-fat diet (LFD) and high-fat diet (HFD) during pregnancy are unknown. Do different nutritional conditions respond equally to exercise intervention? This study aimed to investigate the effects of regular maternal exercise during pregnancy on the GM in mice fed different diets during pregnancy. Methods Six-week-old nulliparous female KunMing mice were fed either a HFD or LFD before and during pregnancy. Each group of mice were then randomly divided into two groups upon confirmation of pregnancy: sedentary (HFD or LFD; n = 4 and 5, respectively) and exercised (HFDex or LFDex, n = 5 and 6, respectively). Mice were sacrificed on day 19 of gestation and their colon contents were collected. We then performed 16S rDNA gene sequencing of the V3 and V4 regions of the GM. Results The pregnancy success rate was 60% for LFDex and 100% for HFDex. Both Chao1 and Simpson indices were not significantly different for either LFD vs. LFDex or HFD vs. HFDex. Desulfobacterota, Desulfovibrionia Desulfovibrionales, Desulfovibrionaceae, Desulfovibrio, Coriobacteriia, Coriobacteriales, and Eggerthellaceae were markedly decreased after exercise intervention in LFDex vs. LFD, whereas Actinobacteria, Bifidobacteriales, Bifidobacteriaceae, Bifidobacterium, and Bifidobacterium pseudolongum were significantly increased in LFDex vs. LFD. Furthermore, decreased Peptostreptococcales-Tissierellales and Peptostreptococcaceae and increased Bacteroides dorei were identified in the HFDex vs. HFD group. p_Desulfobacterota, c_Desulfovibrionia, o_Desulfovibrionales, f_Desulfovibrionaceae and g_Desulfovibrio were markedly decreased in the LFDex group vs. HFDex group. Conclusions Our data suggested that quantitative maternal exercise during pregnancy resulted in alterations in GM composition, but did not significantly change the diversity of the GM. These findings may have important implications when considering an individual’s overall diet when recommending exercise during pregnancy.
Duan et al. (2022) The effects of a set amount of regular maternal exercise during pregnancy on gut microbiota are diet-dependent in mice and do not cause significant diversity changes. PeerJ 10:e14459 https://doi.org/10.7717/peerj.14459
Cathepsin B plays a role in spermatogenesis and sperm maturation through regulating autophagy and apoptosis in mice
Spermatogenesis and sperm maturation are complex and highly ordered biological processes. Any failure or disorder in these processes can cause defects in sperm morphology, motility, and fertilization ability. Cathepsin B (CTSB) is involved in the regulation of a variety of pathological processes. In the present study, we found that CTSB was abundantly expressed in the male reproductive system, however, the specific role of CTSB in regulating spermatogenesis and sperm maturation remained elusive. Hence, we generated Ctsb-/- mice using CRISPR/Cas9 technology. In Ctsb-/- mice, sperm count was significantly decreased while the level of morphologically abnormal sperm was markedly increased. Additionally, these mice had significantly lower levels of progressive motility sperm and elevated levels of immobilized sperm. Histological analysis showed slight vacuolization in the testis epithelium, as well as the loss of epididymal epithelium cells. Further investigation showed that autophagic activity was inhibited and apoptotic activity was increased in both the testis and epididymis of Ctsb-/- mice. Together, our findings demonstrate that CTSB plays an important role in spermatogenesis and sperm maturation in mice.
Wen et al. (2022) Cathepsin B plays a role in spermatogenesis and sperm maturation through regulating autophagy and apoptosis in mice. PeerJ 10:e14472 https://doi.org/10.7717/peerj.14472
Litter inputs and standing stocks in riparian zones and streams under secondary forest and managed and abandoned cocoa agroforestry systems
Background Cocoa is an important tropical tree crop that is mainly cultivated in agroforestry systems (AFS). This system, known as cabruca in northeastern Brazil, holds promise to reconcile biodiversity conservation and economic development. However, since cocoa AFS alters forest structure composition, it can affect litter dynamics in riparian zones and streams. Thus, our objective was to determine litter inputs and standing stocks in riparian zones and streams under three types of forest: managed cocoa AFS, abandoned cocoa AFS, and secondary forest. Methods We determined terrestrial litter fall (TI), vertical (VI) and lateral (LI) litter inputs to streams, and litter standing stocks on streambeds (BS) in the Atlantic Forest of northeastern Brazil. Litter was collected every 30 days from August 2018 to July 2019 using custom-made traps. The litter was dried, separated into four fractions (leaves, branches, reproductive organs, and miscellaneous material) and weighed. Results Terrestrial litter fall was similar in all forests, ranging from 89 g m−2 month−1 in secondary forest (SF) to 96 g m−2 month−1 in abandoned cocoa AFS (AC). Vertical input were higher in AC (82 g m−2 month−1) and MC (69 g m−2 month−1) than in SF (40 g m−2 month−1), whereas lateral input were higher in MC (43 g m−2 month−1) than in AC (15 g m−2 month−1) and SF (24 g m−2 month−1). Standing stocks followed the order SF > AC > MC, corresponding to 425, 299 and 152 g m−2. Leaves contributed most to all litter fractions in all forests. Reproductive plant parts accounted for a larger proportion in managed AFS. Branches and miscellaneous litter were also similar in all forests, except for higher benthic standing stocks of miscellaneous litter in the SF. Despite differences in the amounts of litter inputs and standing stocks among the forests, seasonal patterns in the abandoned AFS (AC) were more similar to those of the secondary forest (SF) than the managed AFS, suggesting potential of abandoned AFS to restore litter dynamics resembling those of secondary forests.
Rialli Santos Brandão et al. (2022) Litter inputs and standing stocks in riparian zones and streams under secondary forest and managed and abandoned cocoa agroforestry systems. PeerJ 10:e13787 https://doi.org/10.7717/peerj.13787
Establishment of the non-native horned-face bee Osmia cornifrons and the taurus mason bee Osmia taurus (Hymenoptera: Megachilidae) in Canada
Established populations of the non-native horned-face bee, Osmia cornifrons (Radoszkowski, 1887), and the taurus mason bee, Osmia taurus Smith, 1873 (Hymenoptera: Megachilidae), have been identified from Canada for the first time. In the US, the importation of O. cornifrons, beginning in the 1970s, led to its release for agricultural crop pollination and spread across the country. In this article, we report on O. cornifrons captured while sampling wild bees in Toronto, Ontario using hand nets, bug vacuums, and vane traps, as well as established populations in trap nests, from 2017–2020. The morphologically similar O. taurus, which was accidentally introduced to the US with shipments of imported O. cornifrons, was also recorded in our samples. Recently, a few individual O. taurus specimens have been identified from Ontario and Quebec; however, the extent of our sampling included nests, indicating it is also established in Canada. Others have shown its population growth to have been associated with concordant declines in abundances of native mason bee species in the US, and similar impacts are possible in Canada if action is not taken. We propose three non-mutually exclusive possible pathways for the arrival of O. cornifrons, as well as O. taurus, in Canada: (1) natural migration northward from non-native populations in the US, (2) international importation in the 1980s–2000s to support agricultural research programs, and (3) unintentional release of mason bee cocoons purchased from non-local vendors. We argue that a focus on enhancing populations of locally occurring native bees and stronger policy on the importation and sale of non-native bees are needed.
MacIvor et al. (2022) Establishment of the non-native horned-face bee Osmia cornifrons and the taurus mason bee Osmia taurus (Hymenoptera: Megachilidae) in Canada. PeerJ 10:e14216 https://doi.org/10.7717/peerj.14216
Level of anxiety and depression among healthcare workers in Saudi Arabia during the COVID-19 pandemic
Background The coronavirus disease 2019 (COVID-19) pandemic places a high demand on frontline healthcare workers. Healthcare workers are at high-risk of contracting the virus and are subjected to its consequential emotional and psychological effects. This study aimed to measure the level of depression and anxiety among healthcare workers in Saudi Arabia during the early stages of the COVID-19 pandemic. Methods This was a cross-sectional study; data were collected from healthcare workers in Saudi Arabia using a survey that included the Zung Self-Rating Depression Scale and the Generalized Anxiety Disorder Scale-7. A total of 326 participants took part in the study by completing and submitting the survey. Results The vast majority of the participating healthcare workers were Saudi nationals (98.8%) working in a public healthcare facility (89.9%). The results indicated that most of the participants had mild levels of anxiety and depression. A total of 72.5% of the respondents had anxiety, ranging from mild (44.1%) to moderate (16.2%) and severe (12.2%). Moreover, 24.4% of the respondents had depression ranging from mild (21.7%) to moderate (2.1%) and severe (0.6%). The generalized linear models showed that the <30 age group (Beta = 0.556, p = 0.037) and the 30–39-year age group (Beta = 0.623, p = 0.019) were predicted to have anxiety. The analysis revealed that females were more anxious (Beta = 0.241, p = 0.005) than males. Healthcare providers working in primary healthcare centers (Beta = −0.315, p = 0.008) and labs (Beta = −0.845. p = 0.0001 were predicted to be less anxious than those working in other healthcare facilities. The data analysis showed that participants with good economic status had more depression than the participants in the other economic status groups (Beta = 0.067, p = 0.003). Conclusion This study found that the level of anxiety and depression in healthcare workers was mild. The factors that may contribute to anxiety in healthcare workers included being female, being younger than 30 or between the ages of 31 and 39, working in a specialized hospital facility, and the number of COVID-19 cases the workers dealt with. Economic status was associated with depression. A longitudinal study design is needed to understand the pattern of anxiety levels among healthcare workers over time during the COVID-19 pandemic.
Shamsan et al. (2022) Level of anxiety and depression among healthcare workers in Saudi Arabia during the COVID-19 pandemic. PeerJ 10:e14246 https://doi.org/10.7717/peerj.14246
Spatial and temporal trends in western polecat road mortality in Wales
Roads have considerable ecological effects that threaten the survival of some species, including many terrestrial carnivores. The western polecat is a small-medium sized mustelid native to Asia and Europe, including Britain where its historical stronghold is in Wales. Polecats are frequently killed on roads and road casualties represent the most common source of data on the species in the UK. However, little is known about the factors that increase the risk of collision. We used Generalized Additive Models to explore seasonal patterns in collisions as well as using Principal Component Analysis and regression modelling to identify landscape characteristics associated with polecat road casualties in Wales. Polecat road casualties had a bimodal distribution, occurring most frequently in March and October. Casualties were more frequently associated with road density, traffic volume, presence of rabbits, habitat patchiness and the abundance of proximal improved grassland habitat. Casualties were negatively associated with elevation and the abundance of semi-natural grassland habitat. The results of this study provide a framework for understanding and mitigating the impacts of roads on polecats in their historic stronghold, hence has considerable value to polecat conservation as well as broader applicability to ecologically similar species.
Barg et al. (2022) Spatial and temporal trends in western polecat road mortality in Wales. PeerJ 10:e14291 https://doi.org/10.7717/peerj.14291
Adherence to the Mediterranean diet, kinanthropometric characteristics and physical performance of young male handball players
Introduction Handball is a team sport whose performance depends on a large number of factors. The objectives of the present study were to analyze the differences in physical performance, kinanthropometric variables, and adherence to the Mediterranean diet (MD), in handball players according to sports category, as well as the possible relationships between these variables. Methods One hundred and thirty-three male handball players (35 infant; 46 cadets; 26 juniors and 26 seniors players) underwent a kinanthropometric analysis following the ISAK protocol, self-completed the KIDMED questionnaire, and their physical condition was evaluated with different physical tests. Results Significant differences (p < 0.001–0.007) were found between the sports categories in most of the physical condition variables and anthropometric characteristics, but not in the degree of adherence to the MD. The predominant level of adherence to the MD was medium (47.4%), followed by good (42.1%), and correlated with the body mass, the height, the BMI, the muscle mass and the ∑3-girths sum corrected, but not with physical test results. A multiple linear regression analysis showed that the fat mass and muscle mass variables had a more specific weight in the results of the physical fitness tests. Conclusions There are differences according to sports category in kinanthropometric characteristics and physical fitness tests in adolescent handball players. The predominant degrees of adherence to the MD were medium and good. A relationship was found between anthropometric characteristics and physical performance in handball players.
Romero-García et al. (2022) Adherence to the Mediterranean diet, kinanthropometric characteristics and physical performance of young male handball players. PeerJ 10:e14329 https://doi.org/10.7717/peerj.14329
METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner
Background As the most prevalent chemical modifications on eukaryotic mRNAs, N6-methyladenosine (m6A) methylation was reported to participate in the regulation of various metabolic diseases. This study aimed to investigate the roles of m6A methylation and methyltransferase-like16 (METTL16) in non-alcoholic fatty liver disease (NAFLD). Methods In this study, we used a model of diet-induced NAFLD, maintaining six male C57BL/6J mice on high-fat diet (HFD) to generate hepatic steatosis. The high-throughput sequencing and RNA sequencing were performed to identify the m6A methylation patterns and differentially expressed mRNAs in HFD mice livers. Furthermore, we detected the expression levels of m6A modify enzymes by qRT-PCR in liver tissues, and further investigated the potential role of METTL16 in NAFLD through constructing overexpression and a knockdown model of METTL16 in HepG2 cells. Results In total, we confirmed 15,999 m6A recurrent peaks in HFD mice and 12,322 in the control. Genes with differentially methylated m6A peaks were significantly associated with the dysregulated glucolipid metabolism and aggravated hepatic inflammatory response. In addition, we identified five genes (CIDEA, THRSP, OSBPL3, GDF15 and LGALS1) that played important roles in NAFLD progression after analyzing the differentially expressed genes containing differentially methylated m6A peaks. Intriguingly, we found that the expression levels of METTL16 were substantially increased in the NAFLD model in vivo and in vitro, and further confirmed that METTL16 upregulated the expression level of lipogenic genes CIDEA in HepG2 cells. Conclusions These results indicate the critical roles of m6A methylation and METTL16 in HFD-induced mice and cell NAFLD models, which broaden people’s perspectives on potential m6A-related treatments and biomarkers for NAFLD.
Tang et al. (2022) METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner. PeerJ 10:e14379 https://doi.org/10.7717/peerj.14379
Effects of land use types on soil erodibility in a small karst watershed in western Hubei
Background Soil erosion is a severe problem in the karst watershed, and analysis of soil erosion at the watershed scale is urgently needed. Methods This study tried to estimate the soil erodibility factor (K-factor) using the Erosion Productivity Impact Calculator (EPIC) nomograph and evaluate the spatial distribution of the predicted K-factor in a karst watershed. Soil properties and K-factors of five land use types (NF: natural mixed forest, CF: cypress forest, EF: economic forest, ST: stone dike terrace, VF: vegetable land) in the Xialaoxi small watershed were compared and key factors affecting erodibility were analyzed. Results Results showed that (1) The erodibility K-factor was unevenly distributed within different site types and strongly influenced by anthropogenic activities. The soil K-factors of sample sites subjected to frequent human disturbance (ST, VF) were high, ranging from 0.0480-0.0520 t hm2 h/(MJ mm hm2), while the soil K-factors of natural site types (NF, CF, and EF) were low, ranging from 0.0436-0.0448 t hm2 h/(MJ mm hm2). (2) The soil texture in the Xialaoxi watershed was mostly loamy, and that of the agricultural areas frequently disturbed by agricultural practices (ST, VF) was silty loam. (3) Soil carbon fractions were affected by land use types. Soil organic carbon storage of NF and CF had strong spatial heterogeneity. The soil organic carbon (SOC) and labile organic carbon (LOC) of the two were significantly higher than those of the disturbed EF and cultivated land soil. (4) There was a synergistic effect between the soil properties and the K-factor. K was significantly negatively related to sand fractions (2-0.05 mm) and non-capillary porosity, while positively related to silt content (0.05–0.002 mm). Overall, changes in bulk density (BD), total porosity (TP), non-capillary porosity (NCP), texture, and organic matter content caused by natural restoration or anthropogenic disturbance were the main reasons for soil erodibility. Natural care (sealing) and construction of stone dike planting practices were effective ways to reduce soil erosion in small karst watershed areas of western Hubei.
Luo et al. (2022) Effects of land use types on soil erodibility in a small karst watershed in western Hubei. PeerJ 10:e14423 https://doi.org/10.7717/peerj.14423