Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning
Background The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited. Methods Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron. Results The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5–10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.
Osathanunkul et al. (2021) Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning. PeerJ 9:e11753 https://doi.org/10.7717/peerj.11753
Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)
Background Cytochrome P450s play crucial roles in various biosynthetic reactions. Ginger (Zingiber officinale), which is often threatened by Ralstonia solanacearum, is the most economically important crop in the family Zingiberaceae. Whether the cytochrome P450 complement (CYPome) significantly responds to this pathogen has remained unclear. Methods Transcriptomic responses to R. solanacearum and soil moisture were analyzed in ginger, and expression profiles of the CYPome were determined based on transcriptome data. Results A total of 821 P450 unigenes with ORFs ≥ 300 bp were identified. Forty percent soil moisture suppressed several key P450 unigenes involved in the biosynthesis of flavonoids, gingerols, and jasmonates, including unigenes encoding flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase, steroid 22-alpha-hydroxylase, cytochrome P450 family 724 subfamily B polypeptide 1, and allene oxide synthase. Conversely, the expression of P450 unigenes involved in gibberellin biosynthesis and abscisic acid catabolism, encoding ent-kaurene oxidase and abscisic acid 8′-hydroxylase, respectively, were promoted by 40% soil moisture. Under R. solanacearum infection, the expression of P450 unigenes involved in the biosynthesis of the above secondary metabolites were changed, but divergent expression patterns were observed under different soil moisture treatments. High moisture repressed expression of genes involved in flavonoid, brassinosteroid, gingerol, and jasmonate biosynthesis, but promoted expression of genes involved in GA anabolism and ABA catabolism. These results suggest possible mechanisms for how high moisture causes elevated susceptibility to R. solanacearum infection.
Huang et al. (2021) Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale). PeerJ 9:e11755 https://doi.org/10.7717/peerj.11755
Neural correlates of tactile hardness intensity perception during active grasping
While tactile sensation plays an essential role in interactions with the surroundings, relatively little is known about the neural processes involved in the perception of tactile information. In particular, it remains unclear how different intensities of tactile hardness are represented in the human brain during object manipulation. This study aims to investigate neural responses to various levels of tactile hardness using functional magnetic resonance imaging while people grasp objects to perceive hardness intensity. We used four items with different hardness levels but otherwise identical in shape and texture. A total of Twenty-five healthy volunteers participated in this study. Before scanning, participants performed a behavioral task in which they received a pair of stimuli and they were to report the perceived difference of hardness between them. During scanning, without any visual information, they were randomly given one of the four objects and asked to grasp it. We found significant blood oxygen-level-dependent (BOLD) responses in the posterior insula in the right hemisphere (rpIns) and the right posterior lobe of the cerebellum (rpCerebellum), which parametrically tracked hardness intensity. These responses were supported by BOLD signal changes in the rpCerebellum and rpIns correlating with tactile hardness intensity. Multidimensional scaling analysis showed similar representations of hardness intensity among physical, perceptual, and neural information. Our findings demonstrate the engagement of the rpCerebellum and rpIns in perceiving tactile hardness intensity during active object manipulation.
Kim et al. (2021) Neural correlates of tactile hardness intensity perception during active grasping. PeerJ 9:e11760 https://doi.org/10.7717/peerj.11760
Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei
The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.
Garibay-Valdez et al. (2021) Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei. PeerJ 9:e11827 https://doi.org/10.7717/peerj.11827
Nectar secretion in a dry habitat: structure of the nectary in two endangered Mexican species of Barkeria (Orchidaceae)
Barkeria scandens and B. whartoniana are endangered, endemic taxa from Mexico. They are epiphytes adapted to dry habitats. Since these plants are xerophytic, their flowers were investigated for structural adaptations to nectar secretion. The flowers of both species are structurally similar, and contrary to most claims for the genus, have functional floral nectaries comprising a nectary chamber and a narrow tubular cuniculus. Nectar is present in both these structures, and contains sugars and lipid-like compounds. The nectary tissue is composed of a single-layered epidermis overlying 1–2 layers of subepidermal secretory parenchyma. The outer tangential wall of the epidermal cells is thick and multi-layered, whereas the cuticle, which often shows blistering, is lamellate and possesses micro-channels. Lipid-like material occurs both between the microfibrils of the cell wall and in the micro-channels. Robust secretory tissue, thick cell walls, and lipid-like nectar components limit nectar evaporation. Moreover, the rigidity of the nectary potentially makes it possible for red-flowered B. scandens to switch from entomophily to ornithophily.
Stpiczyńska et al. (2021) Nectar secretion in a dry habitat: structure of the nectary in two endangered Mexican species of Barkeria (Orchidaceae). PeerJ 9:e11874 https://doi.org/10.7717/peerj.11874
Developmental instability in wild Nigerian olive baboons (Papio anubis)
Background Developmental instability in archaeological samples can be detected through analysis of skeletal and dental remains. During life, disruptions to biological internal homeostasis that occur during growth and development redirect bodily resources to returning to homeostasis and away from normal processes such as symmetrical development. Because dental enamel does not remodel in life, any deviations from normal development are left behind. Even subtle disturbances to developmental trajectory may be detected in asymmetrical development of traits, specifically a random variation in sides termed fluctuating asymmetry. Human dental fluctuating asymmetry studies are common, but here we investigate the permanent dentition of a non-human primate Papio anubis, for potential fluctuating asymmetry relative to sex, weaning, and reproductive maturity. The sample stems from an outlier population that lives in the wettest and most humid habitat of any studied baboon group. Methods The skulls of adult baboons were collected after their natural death in Gashaka Gumti National Park, Nigeria. The permanent dentition of antimeric teeth (paired) were measured for maximum length and breadth using standard methods. The metrics were analyzed to assess the presence of fluctuating asymmetry in adult permanent mandibular and maxillary dentition. Measurement error and other forms of asymmetry (antisymmetry, directional asymmetry) were considered and dental measures expressing true fluctuating asymmetry were used to address three research questions. Results Males exhibit greater fluctuating asymmetry than females, suggesting that males experience greater overall instability during the developmental period. While weaning is not more stressful than other life history stages for males and females (using the first molar fluctuating asymmetry index as a proxy compared to other teeth), it is more stressful for females than males. The onset of reproduction is also not more stressful than other life history stages for males and females (using the third molar fluctuating asymmetry index as a proxy compared to other teeth), but it is more stressful for males than females. We explore possible explanations for these findings in the discussion.
Hoover et al. (2021) Developmental instability in wild Nigerian olive baboons (Papio anubis). PeerJ 9:e11832 https://doi.org/10.7717/peerj.11832
RNase H-dependent amplification improves the accuracy of rolling circle amplification combined with loop-mediated isothermal amplification (RCA-LAMP)
The hybrid method upon combining rolling circle amplification and loop-mediated isothermal amplification (RCA-LAMP) was developed to quantify very small amount of different type of RNAs, such as miRNAs. RCA-LAMP can help detect short sequences through padlock probe (PLP) circularization and exhibit powerful DNA amplification. However, one of the factors that determines the detection limit of RCA-LAMP is non-specific amplification. In this study, we improved the accuracy of RCA-LAMP through applying RNase H-dependent PCR (rhPCR) technology. In this method, the non-specific amplification was suppressed by using the rh primer, which is designed through blocking the modification at the 3′end to stop DNA polymerase reaction and replacing the 6th DNA molecule from the end with RNA using RNase H2 enzyme. Traditional RCA-LAMP amplified the non-specific amplicons from linear PLP without a targeting reaction, while RCA-LAMP with rh primer and RNase H2 suppressed the non-specific amplification. Conversely, we identified the risk posed upon conducting PLP cyclization reaction using Splint R ligase in the RNA-targeting step that occurred even in the RNA-negative condition, which is another factor determining the detection limit of RCA-LAMP. Therefore, this study contributes in improving the accuracy of RNA quantification using RCA-LAMP.
Hasegawa et al. (2021) RNase H-dependent amplification improves the accuracy of rolling circle amplification combined with loop-mediated isothermal amplification (RCA-LAMP). PeerJ 9:e11851 https://doi.org/10.7717/peerj.11851
Brain derived neurotrophic factor declines after complete curative resection in gastrointestinal cancer
Background Brain derived neurotrophic factor (BDNF) is a neurotrophin involved in neural and metabolic diseases, but it is also one of the crucial factors in cancer development and metastases. In the current study, we investigated serum BDNF concentrations in patients that underwent surgical treatment for colorectal cancer or pancreatic cancer. Methods Serum BDNF concentrations were measured with standard enzyme-linked immunosorbent assays, before and on the third day after the operation, in 50 consecutive patients with colorectal cancer and 25 patients with pancreatic cancer (tumours in the head of pancreas). We compared pre- and postoperative BDNF levels, according to the subsequent TNM stage, histologic stage, lymph node involvement, neuro- or angio-invasion, and resection range. Results In the pancreatic cancer group, BDNF concentrations fell significantly postoperatively (p = 0.011). In patients that underwent resections, BDNF concentrations fell (p = 0.0098), but not in patients that did not undergo resections (i.e., laparotomy alone). There were significant pre- and postoperative differences in BDNF levels among patients with (p = 0.021) and without (p = 0.034) distant metastases. Significant reductions in BDNF were observed postoperatively in patients with small tumours (i.e., below the median size; p = 0.023), in patients with negative angio- or lymphatic invasion (p = 0.028, p = 0.011, respectively), and in patients with lymph node ratios above 0.17 (p = 0.043). In the colon cancer group, the serum BDNF concentrations significantly fell postoperatively in the entire group (p = 0.0076) and in subgroups of patients with or without resections (p = 0.034, p = 0.0179, respectively). Significant before-after differences were found in subgroups with angioinvasions (p = 0.050) and in those without neuroinvasions (p = 0.049). Considering the TNM stages, the postoperative BDNF concentration fell in groups with (p = 0.0218) and without (p = 0.034) distant metastases and in patients with tumours below the median size (p = 0.018). Conclusion Our results suggested that BDNF might play an important role in gastrointestinal cancer development. BDNF levels were correlated with tumour volume, and with neuro-, angio- and lymphatic invasions. In pancreatic cancer, BDNF concentrations varied according to the surgical procedure and they fell significantly after tumour resections. Thus, BDNF may serve as a potential marker of complete resections in underdiagnosed patients. However, this hypothesis requires further investigation. In contrast, no differences according to the procedure was made in patients with colon cancer.
Guzel et al. (2021) Brain derived neurotrophic factor declines after complete curative resection in gastrointestinal cancer. PeerJ 9:e11718 https://doi.org/10.7717/peerj.11718
Validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire: a Bayesian multilevel approach
Background Reliable assessment and understanding of student-athletes’ motivation for dual careers are crucial to support their career development and transitions. The purpose of this research was to examine the validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire (SAMSAQ-PT) in the Brazilian higher education context. Four studies were performed. Methods In study one, conceptually and semantic translation of the questionnaire and Bayesian exploratory factor analysis were conducted. In study two, a Bayesian confirmatory factor analysis with an independent sample was performed. In study three, Bayesian multilevel modeling was applied to examine the construct validity of the questionnaire in a cross-sectional sample. In study four, the SAMSAQ-PT sensitiveness was examined in a longitudinal sample, and the results were interpreted based on multilevel regression and poststratification. Results Altogether the results provided evidence validity and usefulness of the SAMSAQ-PT in Brazilian student-athletes. The Brazilian student-athletes’ motivation scores were sensitive to the influence of sex, sport level, and type of university on career and sport motivation. SAMSAQ-PT estimate scores across an academic year showed a trend of stability in the scores, adjusting for sex, sport level, type of university, and student-athlete status. Conclusion The SAMSAQ-PT proved to be a robust and valuable questionnaire, which could be used in Portuguese-speaking countries. The findings of the cross-sectional and longitudinal surveys urge to consider individual and contextual characteristics when investigating motivation of dual-career of athletes, also concerning the sex-related opportunities in university sports. Furthermore, there is a need for a call for action to promote and nurture the student-athletes motivation to remain engaged in both sports and educational commitments.
Quinaud et al. (2021) Validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire: a Bayesian multilevel approach. PeerJ 9:e11863 https://doi.org/10.7717/peerj.11863
CASPredict: a web service for identifying Cas proteins
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins constitute the CRISPR-Cas systems, which play a key role in prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas systems have also been designed to facilitate target gene editing in eukaryotic genomes. As one of the important components of the CRISPR-Cas system, Cas protein plays an irreplaceable role. The effector module composed of Cas proteins is used to distinguish the type of CRISPR-Cas systems. Effective prediction and identification of Cas proteins can help biologists further infer the type of CRISPR-Cas systems. Moreover, the class 2 CRISPR-Cas systems are gradually applied in the field of genome editing. The discovery of Cas protein will help provide more candidates for genome editing. In this paper, we described a web service named CASPredict (http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl) for identifying Cas proteins. CASPredict first predicts Cas proteins based on support vector machine (SVM) by using the optimal dipeptide composition and then annotates the function of Cas proteins based on the hmmscan search algorithm. The ten-fold cross-validation results showed that the 84.84% of Cas proteins were correctly classified. CASPredict will be a useful tool for the identification of Cas proteins, or at least can play a complementary role to the existing methods in this area.
Yang et al. (2021) CASPredict: a web service for identifying Cas proteins. PeerJ 9:e11887 https://doi.org/10.7717/peerj.11887