Floral ontogeny of Tachigali (Caesalpinioideae, Fabaceae) species
Background The present ontogenetic study reveals variations throughout floral development in three morphologically representative species from the genus Tachigali, allowing a better understanding of floral organs diversity, flower symmetry and their homologies, especially in Fabaceae, a diverse family that exhibits a wide variation in floral architecture. Tachigali (Caesalpinioideae) corresponds to an important Neotropical legumes tree genus with 58 species in Brazil. Species of the genus Sclerolobium Vogel were incorporated in its circumscription, increasing the diversity of its floral morphology. Methods This work aims to perform an ontogenetic study of T. denudata, T. paratyensis and T. spathulipetala, morphologically representative species of Tachigali, in order to describe the floral development and to better comprehend the floral morphology varieties among the species, using scanning electron microscopy. Results We found the studied species to have floral buds with acropetal and helical development along the inflorescence axis; sepals and petals with helical development, varying the position of the primordia in the bud, according to the different species; stamens with unilateral development and carpel with adaxial curvature. These data correspond to original records of Tachigali ontogeny and contribute to an improved understanding of floral morphology and symmetry with data related to the zygomorphic and early development of the sepals and petals.
Marques Casanova et al. (2022) Floral ontogeny of Tachigali (Caesalpinioideae, Fabaceae) species. PeerJ 10:e13975 https://doi.org/10.7717/peerj.13975
The cold-stress responsive gene DREB1A involved in low-temperature tolerance in Xinjiang wild walnut
Background Low-temperatures have the potential to be a serious problem for plants and can negatively affect the normal growth and development of walnuts. DREB1/CBF (Dehydration Responsive Element Binding Protein 1/C-repeat Binding Factor), one of the most direct transcription factors in response to low-temperature stress, may improve the resistance of plants to low-temperatures by regulating their functional genes. However, few studies have been conducted in walnut. The Xinjiang wild walnut is a rare wild plant found in China, with a large number of excellent trait genes, and is hardier than cultivated walnuts in Xinjiang. Methods In this work, we identified all of the DREB1 members from the walnut genome and analyzed their expression levels in different tissues and during low-temperature stress on the Xinjiang wild walnut. The JfDREB1A gene of the Xinjiang wild walnut was cloned and transformed into Arabidopsis thaliana for functional verification. Results There were five DREB1 transcription factors in the walnut genome. Among them, the relative expression level of the DREB1A gene was significantly higher than other members in the different tissues (root, stem, leaf) and was immediately un-regulated under low-temperature stress. The overexpression of the JfDREB1A gene increased the survival rates of transgenic Arabidopsis lines, mainly through maintaining the stability of cell membrane, decreasing the electrical conductivity and increasing the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Additionally, the expression levels of cold-inducible genes like AtKIN1, AtERD10, AtRD29A, AtCOR15A and AtCOR47, were significantly increased. These results showed that the JfDREB1A gene may play an important role in the response to cold stress of the Xinjiang wild walnut. This study contributes to our understanding of the molecular mechanism of the Xinjiang wild walnut’s response to low-temperature stress and will be beneficial for developing walnut cultivars with improved cold resistance.
Han et al. (2022) The cold-stress responsive gene DREB1A involved in low-temperature tolerance in Xinjiang wild walnut. PeerJ 10:e14021 https://doi.org/10.7717/peerj.14021
First photographic evidence of oceanic manta rays (Mobula birostris) at two locations in the Fiji islands
Until the revision of the genus Manta in 2009, when a second manta species (Manta alfredi) was resurrected based on morphological and meristic data, all available records in Fijian literature were recorded as Manta birostris. Subsequently, documented sightings were recorded as M. alfredi. Another reclassification of the genus Manta was undertaken in 2018 when both manta ray species (Manta alfredi, Manta birostris) were moved to Mobula based on phylogenetic analysis. Here, we present the first unequivocal evidence of oceanic manta ray (Mobula birostris) occurrence in Fijian waters. In November 2018, two individuals were sighted foraging in Laucala Bay, a large lagoon adjacent to Suva, the capital city of Fiji. Subsequently, three more individuals were sighted in December 2018, two individuals in July 2020, at least six individuals were observed in November 2021, and eight individuals in May/June 2022, all foraging in the same geographical area. Unique ventral identification patterns could be obtained for nine individuals, and all nine individuals have been re-sighted since first identification, with one individual being documented in 2018, 2020, 2021 and 2022. Two additional individuals were recorded in the Yasawa Island Group in the west of Fiji while passing through and foraging in a channel between Drawaqa and Naviti Island in April and September 2020. We provide photographic identification of ten M. birostris individuals from two sites and discuss our findings in the context of local environmental parameters and other recorded sightings in the South Pacific region. In light of the global extinction risk of M. birostris and the recent reclassification from Vulnerable to Endangered on the Red List of Threatened Species, the expansion of their known distribution range to Fijian waters and the recurrence of individuals over consecutive years in the same location adds valuable information for the development of effective and data-driven conservation strategies.
Gordon et al. (2022) First photographic evidence of oceanic manta rays (Mobula birostris) at two locations in the Fiji islands. PeerJ 10:e13883 https://doi.org/10.7717/peerj.13883
Investigation and research on elderly people’s willingness to combine medical and health care and related factors in coastal cities in eastern China
Background The problem of global aging was becoming increasingly prominent. At present, the empty nest and miniaturization of family structure reduce the function of home-based elderly care. Methods A questionnaire survey was conducted on 347 elderly people in multiple communities and nursing homes in eastern coastal cities of China, and 13 institutional staff members of eight nursing institutions that carried out the medical-nursing integration model were interviewed as the research objects. The survey mainly focuses on the basic characteristics of the elderly, the family support system, and the acceptance of medical care and health care. The influencing factors were screened by t test, univariate analysis and multivariate logistic regression analysis. SPSS software was used to test the reliability and validity of the questionnaire, and the Crobach’s was 0.792, which can be considered that the questionnaire had good internal reliability. The classification of the questionnaire was reasonable, the reliability of the questionnaire was high, and the internal consistency of the scale was high. According to KMO and Bartlett test, KMO = 0.826, χ2 = 853.731, the degree of freedom was 36, and the P value was 0.000. Results The proportion of male and female respondents was 48.1% and 51.9% respectively. Multivariate logistic regression analysis results showed that gender had no statistical significances on the degree of support for combine medical and health care in the elderly (P > 0.05). The results showed that gender, age, marital status, medical insurance type and old-age insurance type had little effect on the support of the combination of medical care and health care for the elderly (P > 0.05). Compared with the control group with education below primary school, the elderly with bachelor’s degree or above are more willing to support the combination of medical care and health (P < 0.05). The registered residence type is more obvious than that of the urban residents (P < 0.05). Compared with the enterprise employees in the control group, the elderly who were employed as migrant workers before retirement were more willing to support the combination of medical care and health (P < 0.05). From the perspective of family monthly income, the elderly with family income ≥10,000 RMB have more obvious support for the combination of medical care and health than the elderly with family monthly income <3,000 RMB in the control group (P < 0.05). In terms of the degree of understanding, the degree of understanding and support in different degrees are significantly higher than that in the control group (P < 0.05). Conclusion Through multivariate logistic regression analysis, education level, registered residence, pre-retirement occupation and family income are more obvious for the elderly to support medical care and health. It is necessary to increase investment in elderly activity centers, actively carry out activities.
Wei et al. (2022) Investigation and research on elderly people’s willingness to combine medical and health care and related factors in coastal cities in eastern China. PeerJ 10:e14004 https://doi.org/10.7717/peerj.14004
An optimistic future of C4 crop broomcorn millet (Panicum miliaceum L.) for food security under increasing atmospheric CO2 concentrations
Broomcorn millet, a C4 cereal, has better tolerance to environmental stresses. Although elevated atmospheric CO2 concentration has led to grain nutrition reduction in most staple crops, studies evaluating its effects on broomcorn millet are still scarce. The yield, nutritional quality and metabolites of broomcorn millet were investigated under ambient CO2 (aCO2, 400 µmol mol–1) and elevated CO2 (eCO2, aCO2+ 200 µmol mol–1) for three years using open-top chambers (OTC). The results showed that the yield of broomcorn millet was markedly increased under eCO2 compared with aCO2. On average, eCO2 significantly increased the concentration of Mg (27.3%), Mn (14.6%), and B (21.2%) over three years, whereas it did not affect the concentration of P, K, Fe, Ca, Cu or Zn. Protein content was significantly decreased, whereas starch and oil concentrations were not changed by eCO2. With the greater increase in grain yield, eCO2 induced increase in the grain accumulations of P (23.87%), K (29.5%), Mn (40.08%), Ca (22.58%), Mg (51.31%), Zn (40.95%), B (48.54%), starch (16.96%) and oil (28.37%) on average for three years. Flavonoids such as kaempferol, apigenin, eriodictyol, luteolin, and chrysoeriol were accumulated under eCO2. The reduction in L-glutamine and L-lysine metabolites, which were the most representative amino acid in grain proteins, led to a reduction of protein concentration under eCO2. Broomcorn millet has more desirable nutritional traits for combating hidden hunger. This may potentially be useful for breeding more nutritious plants in the era of climate change.
Shi et al. (2022) An optimistic future of C4 crop broomcorn millet (Panicum miliaceum L.) for food security under increasing atmospheric CO2 concentrations. PeerJ 10:e14024 https://doi.org/10.7717/peerj.14024
Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation
Background Rotational cropping practices can change the fungal structure and diversity of cropping soil, and these changes can promote crop development. However, only a few studies have explored the effects of rotational cropping of pineapple on soil fungal diversity. Methods In this study, we investigated fungal diversity in continuous and rotational cropping soil of pineapple in Xuwen and Leizhou of China in summer and winter through high throughput sequencing of the fungal internal transcribed spacer region. Results The diversity and richness of the fungal community were observed to be significantly increased after rotational cropping in Xuwen and Leizhou in summer, whereas no changes were observed in winter. Furthermore, Ascomycota, Basidiomycota, Zygomcota, and Chytridiomycota were the dominant phyla, and Chaetomium, Penicillium, Fusarium, Trichoderma, and Cryptococcus were the dominant genera in the continuous and rotational cropping soil of pineapple, respectively, in both summer and winter. Chytridiomycota at phylum level and Gibberella at genus level were observed in rotational cropping soil; however, Ascomycota at the phylum level and Chaetomium at the genus level were the most abundant fungi, and their abundance dramatically decreased in continuous cropping soil. Redundancy analysis revealed that rotational cropping reduced the correlation between environmental parameters and the fungal community in winter. In addition, several fungal biomarkers were found in Xuwen in both continuous and rotational cropping soil samples, including Sporobolomyces, Aspergillus, Corynascus sp JHG 2007, and Corynascus at the genus level, Penicillium and fungal sp p1s11 at the species level in rotational cropping soil, and ales family Incertae sedis and Sordariomycetes at the class level in continuous cropping soil. These results revealed the changes in the structure and diversity of fungal community in continuous and rotational cropping practices for pineapple cultivation, which may be associated with crop yield and quality.
Chen et al. (2022) Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation. PeerJ 10:e13937 https://doi.org/10.7717/peerj.13937
Predictors of tuberculosis disease in smokers: a case-control study in northeastern Malaysia
Objective Tuberculosis (TB) is a leading infectious disease. However, many TB cases remain undetected and only present symptoms at a late stage of the infection. Therefore, targeted TB screening in high-risk populations, including smokers, is crucial. This study aimed to determine the predictors of TB disease among the smoker population in northeast Malaysia from 2019 to 2020. Methods A case-control study was conducted involving smokers aged 18 years and older from health clinics in Bachok Kelantan, Malaysia. Data were collected via face-to-face interviews or telephone calls from 159 participants, randomly selected from outpatient TB records. Simple and multiple logistic regression, using R software, were used to identify the determinants of TB. Results Most participants were male (59.1%) and had a secondary education (56.0%). Active smokers constituted 35.2% of the group, and the mean (SD) duration of exposure to smoking was 23.9 (16.47) and 18.4 (12.84) years for the case and control groups, respectively. Being an ex-smoker (adjusted odds ratio (AOR) 6.17; 95% CI [1.55–28.32]; p = 0.013), weight loss (AOR 13.45; 95% CI [4.58–44.46]; p < 0.005), night sweats (AOR 63.84; 95% CI [8.99–1392.75]; p < 0.005) and duration of symptoms (AOR 1.02; 95% CI [1.01–1.04]; p = 0.022) were shown to be significant predictors for TB disease. Conclusion Four predictors of TB disease in the population of smokers were recognised in this study and should be prioritised for early TB screening and diagnosis. This may help increase TB detection, initiate prompt treatment and reduce complications among the group at risk for TB.
Tengku Khalid et al. (2022) Predictors of tuberculosis disease in smokers: a case-control study in northeastern Malaysia. PeerJ 10:e13984 https://doi.org/10.7717/peerj.13984
Antibiotic resistance and genomic features of Clostridioides difficile in southwest China
Background Clostridioides difficile infection (CDI) caused by toxigenic strains leads to antibiotic-related diarrhea, colitis, or even fatal pseudomembranous enteritis. Previously, we conducted a cross-sectional study on prevalence of CDI in southwest China. However, the antibiotics resistance and characteristics of genomes of these isolates are still unknown. Methods Antibiotic susceptibility testing with E-test strips and whole genome sequence analysis were used to characterize the features of these C. difficile isolates. Results Forty-nine strains of C. difficile were used in this study. Five isolates were non-toxigenic and the rest carried toxigenic genes. We have previously reported that ST35/RT046, ST3/RT001 and ST3/RT009 were the mostly distributed genotypes of strains in the children group. In this study, all the C. difficile isolates were sensitive to metronidazole, meropenem, amoxicillin/clavulanic acid and vancomycin. Most of the strains were resistant to erythromycin, gentamicin and clindamycin. The annotated resistant genes, such as macB, vanRA, vanRG, vanRM, arlR, and efrB were mostly identified related to macrolide, glycopeptide, and fluoroquinolone resistance. Interestingly, 77.55% of the strains were considered as multi-drug resistant (MDR). Phylogenetic analysis based on core genome of bacteria revealed all the strains were divided into clade 1 and clade 4. The characteristics of genome diversity for clade 1 could be found. None of the isolates showed 18-bp deletion of tcdC as RT027 strain as described before, and polymorphism of tcdB showed a high degree of conservation than tcdA gene. Conclusions Most of the C. difficile isolates in this study were resistant to macrolide and aminoglycoside antibiotics. Moreover, the MDR strains were commonly found. All the isolates belonged to clade 1 and clade 4 according to phylogenetic analysis of bacterial genome, and highly genomic diversity of clade 1 was identified for these strains.
Gu et al. (2022) Antibiotic resistance and genomic features of Clostridioides difficile in southwest China. PeerJ 10:e14016 https://doi.org/10.7717/peerj.14016
Benchmark datasets for SARS-CoV-2 surveillance bioinformatics
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.
Xiaoli et al. (2022) Benchmark datasets for SARS-CoV-2 surveillance bioinformatics. PeerJ 10:e13821 https://doi.org/10.7717/peerj.13821
Practical guidance for firefighter applicants preparing for cardiorespiratory fitness testing: a secondary analysis of self-reported physical activity levels
Adequate cardiorespiratory fitness is critical for firefighters since an insufficient level of fitness threatens the integrity of their operations and could be dangerous for their lives. In fact, the leading cause of mortality for on-duty firefighters is not injury but sudden cardiac death. Therefore, to mitigate these risks, potential firefighter recruits are often required to perform a graded exercise test to determine their cardiorespiratory fitness as part of the recruitment process. However, there are currently limited data available to prospective firefighters on the amounts and types of exercises needed to be successful in the graded exercise test, commonly known as a V̇O2max test. Physiological parameters for the current secondary analysis were collected on firefighter applicants who performed the graded exercise test where 72% were successful and 28% were unsuccessful to meet the minimum standard set at 42.5 ml kg−1 min−1. Prior to their test, applicants were asked to describe their exercise training routine by indicating the number of minutes per week spent exercising. Activities were then divided into one of two categories: endurance exercise or strength and power exercise training. The total exercise training describes the sum of all activities performed each week. The sum of endurance exercise activities and the sum of strength and power exercise activities were compared between the successful and the unsuccessful groups and results showed that successful applicants had a higher training volume and performed more endurance exercise training as compared to unsuccessful applicants. Therefore, practical recommendations related to exercise training regime are presented for firefighter applicants to embrace as guidance to prepare for their graded exercise test as part of their recruitment process.
Fortier et al. (2022) Practical guidance for firefighter applicants preparing for cardiorespiratory fitness testing: a secondary analysis of self-reported physical activity levels. PeerJ 10:e13832 https://doi.org/10.7717/peerj.13832