Contribution of hippocampal BDNF/CREB signaling pathway and gut microbiota to emotional behavior impairment induced by chronic unpredictable mild stress during pregnancy in rats offspring
Background Numerous studies have shown that exposure to prenatal maternal stress (PMS) is associated with various psychopathological outcomes of offspring. The accumulating evidence linking bacteria in the gut and neurons in the brain (the microbiota-gut-brain axis) has been aconsensus; however, there is a lack of research on the involvement mechanism of gut microbiota in the regulation of the BDNF/CREB signaling pathway in the hippocampus of prenatally stressed offspring. Methods Pregnant rats were subjected to chronic unpredictable mild stress (CUMS) to establish the prenatal maternal stress model. The body weight was measured and the behavioral changes were recorded. Offspring were tested to determine emotional state using sucrose preference test (SPT), open-field test (OFT) and suspended tail test (STT). Gut microbiota was evaluated by sequencing the microbial 16S rRNA V3–V4 region, and the interactive analysis of bacterial community structure and diversity was carried out. The expression of hippocampal BDNF, TrkB and CREB mRNA and proteins were respectively measured using RT-PCR and Western blotting. Results Prenatal maternal stress increased maternal plasma corticosterone levels, slowed maternal weight gain and caused depression-like behaviors (all P < 0.05). In offspring, prenatal maternal stress increased plasma corticosterone levels (P < 0.05) and emotional behavior changes (depression-like state) were observed (P < 0.05). The species abundance, diversity and composition of the offspring’s gut microbiota changed after the maternal stress during pregnancy (P < 0.05). Compared with the control group’s offspring, the species abundance of Lactobacillaceae was dropped, while the abundance of the Muribaculaceae species abundance was risen. Concurrent, changes in the hippocampal structure of the offspring and decreases in expression of BDNF/CREB signaling were noted (P < 0.05). Conclusions Prenatal maternal stress leads to high corticosterone status and abnormal emotion behavior of offspring, which may be associated with the abnormal BDNF/CREB signaling in hippocampus of offspring caused by the change of gut microbiota composition.
Zhao et al. (2022) Contribution of hippocampal BDNF/CREB signaling pathway and gut microbiota to emotional behavior impairment induced by chronic unpredictable mild stress during pregnancy in rats offspring. PeerJ 10:e13605 https://doi.org/10.7717/peerj.13605
The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences.
Routhier et al. (2022) Genomics enters the deep learning era. PeerJ 10:e13613 https://doi.org/10.7717/peerj.13613
Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalves but across many other clades.
Edie et al. (2022) Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia). PeerJ 10:e13617 https://doi.org/10.7717/peerj.13617
Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress
Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea.
Qin et al. (2022) Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress. PeerJ 10:e13620 https://doi.org/10.7717/peerj.13620
Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells
The widespread two-component system (TCS), QseBC, involves vital virulence regulators in Enterobacteriaceae and Pasteurellaceae. Here we studied the function of QseBC in Glaesserella parasuis. A ΔqseBC mutant was constructed using a Glaesserella parasuis serovar 11 clinical strain SC1401 by natural transformation. Immunofluorescence was used to evaluate cellular adhesion, the levels of inflammation and apoptosis. The ability of ΔqseBC and ΔqseC mutant strains to adhere to PAM and MLE-12 cells was significantly reduced. Additionally, by focusing on the clinical signs, H&E, and IFA for inflammation and apoptosis, we found that the ΔqseBC mutant weakened virulence in the murine models. Together, these findings suggest that QseBC plays an important role in the virulence of Glaesserella parasuis.
Yan et al. (2022) Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells. PeerJ 10:e13648 https://doi.org/10.7717/peerj.13648
Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area
Coral reefs in Culebra Bay (North Pacific of Costa Rica) are threatened by multiple anthropogenic disturbances including global warming, overfishing, eutrophication, and invasive species outbreaks. It is possible to assist their recovery by implementing ecological restoration techniques. This study used artificial hexagonal steel structures, called “spiders” to compare growth of Pocillopora spp. coral fragments of different sizes. Three initial fragment class sizes were used: 2, 5 and 8 cm, with each class size having 42 initial fragments. Changes in fragment length, width and area were measured monthly from January to December 2020. Results showed an overall survivorship of 70.21%, and no significant differences in survivorship and linear growth rate were detected between class sizes. The linear growth rates are 4.49 ± 1.19 cm year−1, 5.35 ± 1.48 cm year−1 and 3.25 ± 2.22 cm year−1 for the 2, 5 and 8 cm initial class sizes, respectively. Our results do not show significant differences in growth rates between the different initial fragment sizes. However, since small fragments (2 cm) present higher mortality during the first month, we recommend using larger fragments. In addition, coral fragments grew 48% more during the non-upwelling season, which may suggest that it might be more effective and safer to start the restoration efforts during this period.
Combillet et al. (2022) Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area. PeerJ 10:e13248 https://doi.org/10.7717/peerj.13248
Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)
The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC.
Tyagi et al. (2022) Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC). PeerJ 10:e13562 https://doi.org/10.7717/peerj.13562
Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche
Caddisfly larvae commonly inhabit freshwater ecosystems, where they often create multi-species aggregations. However, while several strategies have been developed to avoid or reduce inter- and intraspecific interactions, most species choose the same time to seek a suitable place for pupation, which can increase competition. The current study assesses the competitive interactions among larvae (5th instar) of three co-existing Hydropsyche species, viz. H. contubernalis, H. pellucidula, and H. modesta, analysing their direct one-on-one interaction and various morphological features, such as size, weight, and mandibles. More than half of the interspecific conflicts ended with a draw, and 80% of intraspecific interactions with a decisive outcome. In fights between species, H. pellucidula was the most successful, and H. modesta the weakest. Our results confirm that among the larvae, competitive interactions were usually decided by body size, especially that of the head capsule. Although wider head capsule and higher weight were advantageous for ~60% of winning larvae, there were no distinct winning species. The chewing mouthpart turned out to be supportive in the fight: regardless of the species, longer and wider mandibles were significant for winning specimens, but not the distance between mandibles. Hence, acquiring a suitable place for pupation is determined by the possession of certain features enhancing the fighting potential of individual larvae, which does not exclude any species from the possibility of closing the life cycle. Future studies on interactions among caddisfly larvae could include experience in fights, volitional features and stridulation (not tested).
Tszydel et al. (2022) Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche. PeerJ 10:e13576 https://doi.org/10.7717/peerj.13576
Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease
Objective Patients with Parkinson’s disease (PD) have an obvious motor inhibition disorder, which is closely related to their motor symptoms. Although previous studies have shown that exercise can improve their inhibition deficits, the effect of exercise on different types of inhibition (proactive and reactive inhibition) has not been addressed. Methods We used a behavioral paradigm combined with a series of questionnaires to explore the effect of long-term exercise on different types of motor inhibition in 59 patients with PD aged 55–75 years. According to the intensity and frequency of exercise, the participants were divided into regular-exercise and no-exercise groups. To obtain the average reference value for inhibition ability at the same age, we also recruited 30 healthy elderly people as controls. Results The main defect in the motor inhibition of PD is reactive inhibition, while proactive inhibition has no obvious differences compared with healthy controls. Additionally, compared with the non-exercise group, PD in the exercise group showed significantly better reaction speeds and reactive control ability, fewer motor symptoms and negative emotions. Conclusions Taken together, the motor inhibition defects of patients with PD affect only reactive inhibition. In addition, PD with exercise reported fewer negative emotions than that of the non-exercise group, indicating that exercise can relieve negative emotions and improve behavioral symptoms and quality of life in PD to a certain extent. We demonstrate for the first time that exercise has and can improve reactive inhibition in PD patients and has no effect on proactive inhibition.
Wang et al. (2022) Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease. PeerJ 10:e13628 https://doi.org/10.7717/peerj.13628
Inflammation and fibrosis in the coal dust-exposed lung described by confocal Raman spectroscopy
Background Coal workers’ pneumoconiosis (CWP) is an occupational disease that severely damages the life and health of miners. However, little is known about the molecular and cellular mechanisms changes associated with lung inflammation and fibrosis induced by coal dust. As a non-destructive technique for measuring biological tissue, confocal Raman spectroscopy provides accurate molecular fingerprints of label-free tissues and cells. Here, the progression of lung inflammation and fibrosis in a murine model of CWP was evaluated using confocal Raman spectroscopy. Methods A mouse model of CWP was constructed and biochemical analysis in lungs exposed to coal dust after 1 month (CWP-1M) and 3 months (CWP-3M) vs control tissues (NS) were used by confocal Raman spectroscopy. H&E, immunohistochemical and collagen staining were used to evaluate the histopathology alterations in the lung tissues. Results The CWP murine model was successfully constructed, and the mouse lung tissues showed progression of inflammation and fibrosis, accompanied by changes in NF-κB, p53, Bax, and Ki67. Meanwhile, significant differences in Raman bands were observed among the different groups, particularly changes at 1,248, 1,448, 1,572, and 746 cm−1. These changes were consistent with collagen, Ki67, and Bax levels in the CWP and NS groups. Conclusion Confocal Raman spectroscopy represented a novel approach to the identification of the biochemical changes in CWP lungs and provides potential biomarkers of inflammation and fibrosis.
Wang et al. (2022) Inflammation and fibrosis in the coal dust-exposed lung described by confocal Raman spectroscopy. PeerJ 10:e13632 https://doi.org/10.7717/peerj.13632