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
Morphological variation of the relictual alveolar structures in the mandibles of baleen whales
Living baleen whales (mysticetes) are bulk filter feeders that use keratinous baleen plates to filter food from prey laden water. Extant mysticetes are born entirely edentulous, though they possess tooth buds early in ontogeny, a trait inherited from toothed ancestors. The mandibles of extant baleen whales have neither teeth nor baleen; teeth are resorbed in utero and baleen grows only on the palate. The mandibles of extant baleen whales also preserve a series of foramina and associated sulci that collectively form an elongated trough, called the alveolar groove. Despite this name, it remains unclear if the alveolar groove of edentulous mysticetes and the dental structures of toothed mammals are homologous. Here, we describe and quantify the anatomical diversity of these structures across extant mysticetes and compare their variable morphologies across living taxonomic groups (i.e., Balaenidae, Neobalaenidae, Eschrichtiidae, and Balaenopteridae). Although we found broad variability across taxonomic groups for the alveolar groove length, occupying approximately 60–80 percent of the mandible’s total curvilinear length (CLL) across all taxa, the relictual alveolar foramen showed distinct patterns, ranging between 15–25% CLL in balaenids, while ranging between 3–12% CLL in balaenopterids. This variability and the morphological patterning along the body of the mandible is consistent with the hypothesis that the foramina underlying the alveolar groove reflect relictual alveoli. These findings also lay the groundwork for future histological studies to examine the contents of these foramina and clarify their potential role in the feeding process.
Peredo et al. (2021) Morphological variation of the relictual alveolar structures in the mandibles of baleen whales. PeerJ 9:e11890 https://doi.org/10.7717/peerj.11890
Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data
Airborne remote sensing offers unprecedented opportunities to efficiently monitor vegetation, but methods to delineate and classify individual plant species using the collected data are still actively being developed and improved. The Integrating Data science with Trees and Remote Sensing (IDTReeS) plant identification competition openly invited scientists to create and compare individual tree mapping methods. Participants were tasked with training taxon identification algorithms based on two sites, to then transfer their methods to a third unseen site, using field-based plant observations in combination with airborne remote sensing image data products from the National Ecological Observatory Network (NEON). These data were captured by a high resolution digital camera sensitive to red, green, blue (RGB) light, hyperspectral imaging spectrometer spanning the visible to shortwave infrared wavelengths, and lidar systems to capture the spectral and structural properties of vegetation. As participants in the IDTReeS competition, we developed a two-stage deep learning approach to integrate NEON remote sensing data from all three sensors and classify individual plant species and genera. The first stage was a convolutional neural network that generates taxon probabilities from RGB images, and the second stage was a fusion neural network that “learns” how to combine these probabilities with hyperspectral and lidar data. Our two-stage approach leverages the ability of neural networks to flexibly and automatically extract descriptive features from complex image data with high dimensionality. Our method achieved an overall classification accuracy of 0.51 based on the training set, and 0.32 based on the test set which contained data from an unseen site with unknown taxa classes. Although transferability of classification algorithms to unseen sites with unknown species and genus classes proved to be a challenging task, developing methods with openly available NEON data that will be collected in a standardized format for 30 years allows for continual improvements and major gains for members of the computational ecology community. We outline promising directions related to data preparation and processing techniques for further investigation, and provide our code to contribute to open reproducible science efforts.
Spatial and Geographic Information Science
Scholl et al. (2021) Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data. PeerJ 9:e11790 https://doi.org/10.7717/peerj.11790
Transcriptional landscape in rat intestines under hypobaric hypoxia
Oxygen metabolism is closely related to the intestinal homeostasis environment, and the occurrence of many intestinal diseases is as a result of the destruction of oxygen gradients. The hypobaric hypoxic environment of the plateau can cause dysfunction of the intestine for humans, such as inflammation. The compensatory response of the small intestine cells to the harsh environment definitely changes their gene expression. How the small intestine cells response the hypobaric hypoxic environment is still unclear. We studied the rat small intestine under hypobaric hypoxic conditions to explore the transcriptional changes in rats under acute/chronic hypobaric hypoxic conditions. We randomly divided rats into three groups: normal control group (S), acute hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 2 weeks (W2S) and chronic hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 4 weeks (W4S). The RNA sequencing was performed on the small intestine tissues of the three groups of rats. The results of principal component analysis showed that the W4S and W2S groups were quite different from the control group. We identified a total of 636 differentially expressed genes, such as ATP binding cassette, Ace2 and Fabp. KEGG pathway analysis identified several metabolic and digestive pathways, such as PPAR signaling pathway, glycerolipid metabolism, fat metabolism, mineral absorption and vitamin metabolism. Cogena analysis found that up-regulation of digestive and metabolic functions began from the second week of high altitude exposure. Our study highlights the critical role of metabolic and digestive pathways of the intestine in response to the hypobaric hypoxic environment, provides new aspects for the molecular effects of hypobaric hypoxic environment on intestine, and raises further questions about between the lipid metabolism disorders and inflammation.
Tian et al. (2021) Transcriptional landscape in rat intestines under hypobaric hypoxia. PeerJ 9:e11823 https://doi.org/10.7717/peerj.11823