PeerJ最新文献

Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.

A new species of Croton, microendemic of the dry forests of northeastern Brazil in the state of Pernambuco, is here described. Morphological and ITS molecular data provide evidence for placing C. buiquensis sp. nov. as part of Croton section Pedicellati. Specimens of C. buiquensis had been previously identified in herbaria as C. pedicellatus, but the former can be distinguished from the latter by the hispid indumentum of the leaf blade, the ovate shape of the petals of staminate flowers, pistillate flowers with 4-fid to multifid styles, and a crossbow-shape caruncle. Evidence from ecological niche modeling points to other areas in the state of Pernambuco, specifically the "Agreste" region, as likely locations for the occurrence of the new species, which could be the target of future botanical surveys. Croton buiquensis is here provisionally considered as Critically Endangered based on IUCN criteria. This is the first record of multifid styles (more than six stigmatic tips) in C. sect. Pedicellati and also the first species of the section endemic to the state of Pernambuco.

Myosin IXb (Myo9b) is a single-headed motor protein in the myosin superfamily. It contains a unique Rho guanosine triphosphatase-activating protein domain, which enables it to regulate cytoskeletal dynamics and cell migration. Most studies on Myo9b are focused on epithelial repair, intestinal barrier function, and immune cell motility; however, its roles in immune regulation, inflammatory responses, tumorigenesis, and various autoimmune diseases have garnered notable attention in recent years. This study comprehensively reviews the structural characteristics, regulatory mechanisms, and biological functions of Myo9b, along with emphasizing its crucial roles in various pathological conditions and its potential as a therapeutic target.

Background: The study aimed to provide evidence to support optimal interventions for alleviating anxiety and depression symptoms in patients with polycystic ovarian syndrome (PCOS) through a systematic review and network meta-analysis.

Methods: A comprehensive literature search of PubMed, Embase, Cochrane Library, and Web of Science from their inceptions to January 2, 2025 was performed. The criteria for inclusion defined were as follows: (1) The study population consisted of female PCOS patients; (2) interventions included psychological therapy, exercise, drug treatment, or digital intervention; (3) studies that reported changes in anxiety and depression scores; and (4) randomized controlled trials (RCTs). Two reviewers independently screened the literature and extracted the data. Disagreements were resolved by consulting a third party. Standardized mean difference (SMD) was used for data recording in this study. The analysis of data was carried out based on a random-effects model, while network meta-analysis was implemented through R 4.4.0 and Just Another Gibbs Sampler (JAGS) 4.3.1. We conducted a Bayesian random-effects network meta-analysis (NMA) and ranked interventions using the surface under the cumulative ranking curve (SUCRA).

Results: This study included a total of 25 RCTs, involving 1,453 female PCOS patients, to evaluate the effects of various interventions in alleviating anxiety and depression symptoms. Effective interventions included emotion-focused therapy (EFT), peer support (PS), omega-3 plus vitamin E (O3+VE), and mindfulness stress management (MSM). Other interventions, such as metformin and vitamin D plus probiotics (VD+Pro), showed no significant benefit compared with control. Data on PS for anxiety were not analyzed in the present network meta-analysis because relevant trials could not be connected within the network structure.

Conclusion: Our study demonstrates that EFT and PS emerge as promising interventions in alleviating anxiety and depression symptoms in PCOS patients. Interventions such as O3+VE and MSM also showed potential in improving emotional states.Review registration: PROSPERO CRD420250655513.

Rapid socioeconomic development has intensified nitrogen and phosphorus pollution in the Yangtze River Economic Belt (YREB), posing severe threats to the water environment. Notably, agricultural sources have surpassed industrial sources to become the primary contributor to this pollution. To explore the spatiotemporal characteristics and impacts of agricultural nitrogen and phosphorus pollution in this region, this study constructed an improved output coefficient model. Using panel data from 11 provinces and municipalities in the YREB spanning 2005-2020, combined with Geographic Information System (GIS) spatial analysis tools, we calculated the pollution loads of agricultural nitrogen and phosphorus from three key sources: land use, rural domestic activities, and livestock and poultry breeding (LPB). The results show a consistent downward trend in total nitrogen (TN) and total phosphorus (TP) pollution loads from the three sources. Specifically, TN load decreased from 2,686.68 × 10³ tons/yr in 2005 to 2,035.67 × 10³ tons/yr in 2020, while TP load declined from 139.42 × 10³ tons/yr to 102.52 × 10³ tons/yr, with an average TN-to-TP pollution load ratio of approximately 19.40. GIS-generated spatial distribution maps confirm a widespread reduction in agricultural TN and TP pollution across the region. To effectively mitigate agricultural nitrogen and phosphorus pollution risks, we recommend strengthening research on fertilization techniques for major crops and exploring the establishment of centralized treatment stations for agricultural solid waste in regions within the YREB.

Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa-highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress-such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.

Background: Coix lacryma-jobi L. is a vital medicinal and dual-purpose crop in Guizhou, requiring optimal cultivation conditions to preserve its therapeutic properties. Waterlogging stress significantly reduces its productivity, yet the underlying molecular mechanisms remain poorly understood.

Methods: We investigated the species' adaptive responses using controlled waterlogging experiments on potted plants. Morphological alterations and key growth parameters (culm diameter, plant height, dry biomass) were quantified. We performed transcriptomic profiling by RNA-Seq to identify differentially expressed genes (DEGs). To elucidate the functional implications of these DEGs, we conducted systematic enrichment analyses using the clusters of orthologous groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Expression patterns of candidate genes were validated using Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR).

Results: Flooded plants exhibited significant morphological changes, with key growth parameters decreasing by 14.4-21.8%. A pronounced adaptive response was a 76.6% increase in adventitious root formation. RNA-Seq revealed 207 DEGs (133 upregulated, 74 downregulated). Enrichment analyses indicated these DEGs were predominantly involved in photosynthetic processes, carbohydrate dynamics, and signaling pathways. qRT-PCR confirmed consistent expression patterns for six candidate genes associated with photosynthesis and carbohydrate metabolism. These findings demonstrate that Coix lacryma-jobi L. activates coordinated molecular responses, including photosynthetic efficiency adjustment and metabolic pathway remodeling, to enhance waterlogging tolerance. This work identifies critical genetic components governing waterlogging adaptation, providing molecular markers for developing stress-tolerant cultivars through targeted breeding.

Neuropathic pain (NP) is a common complication following spinal cord injury (SCI), significantly impairing patients' physical/mental health and quality of life. While activity-based exercise has demonstrated efficacy in alleviating SCI-NP in rodent models, the mechanisms underlying this effect remain unclear. Specifically, it requires investigation whether exercise mediates its benefits through the following mechanisms: improving aberrant primary afferents and circuit inhibition in the lumbar dorsal horn after thoracic contusion SCI. In this study, we implemented an exercise training protocol in rats with incomplete thoracic SCI. We evaluated its effects on several factors, including mechanical withdrawal thresholds (MWTs), thermal withdrawal latencies (TWLs), and rate-dependent depression (RDD) of H-reflex. Additionally, we examined the changes in vesicular glutamate transporter 1 (VGluT1, specifically labeled in myelinated primary afferent terminals), calcitonin gene-related peptide (CGRP)-labeled nociceptive unmyelinated primary afferents, glutamic acid decarboxylase 65+67 (GAD 65+67), and potassium-chloride cotransporter 2 (KCC2). Our results showed that exercise training significantly improved MWTs and TWLs, enhanced the RDD of H-reflex, increased the synthesis of VGluT1, GAD 65+67, and KCC2 within the spinal dorsal horn, while reducing the CGRP-labeled nociceptive unmyelinated primary afferents. These findings indicate that exercise alleviates mechanical allodynia and thermal hyperalgesia, which is paralleled by improvements in aberrant primary afferents, enhanced RDD of the H-reflex, and increased synthesis of GAD 65+67 and KCC2 in the lumbar dorsal horn following thoracic contusion SCI.

Litter is considered a major constraint that affects the sexual reproduction and regeneration of populations of Rhododendron seedlings. In this study, we analyzed the effects of litter accumulation and its allelopathy on the regeneration potential of four Rhododendron species, and investigated the impacts of different litter amounts and coverage methods on Rhododendron seed germination through indoor pot experiments. The results showed that low amounts of litter promoted the rate of emergence of seedlings, while high amounts of litter inhibited this process. The rate of emergence of Rhododendron reached its maximum value when the amount of litter was between 200 and 400 g/m² . The seeds of four species of Rhododendron began to germinate between days 7 and 8 of the experiment. The duration of germination for the four Rhododendron species ranged from 8 to 11 days. Extracts from different decomposition layers of litter had a "suppressive" effect or a "low promotion and high inhibition" effect on the germination rates of four species of Rhododendron. The litter extract inhibited the germination of Rhododendron decorum and Rhododendron delavayi at 2 mg/mL of extract, while it promoted the germination of Rhododendron irroratum and Rhododendron agastum seeds. Therefore, the presence of litter under Rhododendron shrubs in Northwest Guizhou Province, China, likely reduces the germination of the populations of Rhododendron and may limit their renewal through sexual reproduction. Thus, this study suggests that the presence of litter under Rhododendron shrubs in Northwest Guizhou Province may significantly limit their reproduction by seeds.