Biology-Basel最新文献

Two genetically engineered Bacillus subtilis strains, BMV9 and BsB6, were evaluated in terms of culture medium (effect of nutrients on surfactin yield) and potential biotechnological applications of surfactin in agriculture and the petrochemical industry. BMV9 (spo0A3; abrB*; ΔmanPA; sfp+) is, to date, the highest surfactin producer reported scientifically, and BsB6 is a sfp+ laboratory derivative strain that has also demonstrated considerable production potential. To assess their performance, fermentation experiments were conducted in shake flasks using two different culture media, a mineral salt medium and a complex medium, each supplemented with 2% (w/v) glucose. Lipopeptides (surfactin and fengycin) were extracted and quantified at multiple time points (up to 48 h) via high-performance thin-layer chromatography (HPTLC). Optical density, residual glucose, and pH were monitored throughout the cultivation. In parallel, microbial growth in both media were also validated in small-scale cultivation approaches. Antifungal activity of culture supernatants and lipopeptide extracts was tested against two Diaporthe species, key phytopathogens in soybean crops. Given the agricultural relevance of these pathogens, the biocontrol potential of lipopeptides represents a sustainable alternative to conventional chemical fungicides. Additionally, oil displacement tests were performed to evaluate the efficacy of surfactin in enhanced oil recovery (EOR), bioremediation, and related petrochemical processes. High-resolution LC-MS/MS analysis enabled structural characterization and relative quantification of the lipopeptides. Overall, these investigations provide a comprehensive comparison of strain production performance and the associated impact of cultivation media, aiming to define the optimal conditions for economically viable surfactin production and to explore its broader biotechnological applications in agriculture and the petrochemical industry.

Platelet-rich fibrin (PRF) is widely used in regenerative dentistry and oral surgery for its ability to promote tissue healing and modulate cellular responses. However, PRF contains not only platelets but also leukocytes and plasma components, complicating efforts to define the specific contribution of platelets to its biological activity. To address this, we used washed, leukocyte-depleted platelets activated with thrombin to generate platelet-released supernatant (PRS), which was applied to gingival fibroblasts. RNA sequencing identified 147 upregulated and 39 downregulated genes (|log₂ fold change| ≥ 2, FDR < 0.001), including cytokines IL11 and CXCL8 previously associated with PRF, as well as mitosis-related genes such as centromere-associated proteins, cell division cycle proteins, kinesin-like proteins, and shugoshins, consistent with gene ontology analyses. Validation by RT-PCR and immunoassays confirmed robust upregulation of IL11 and CXCL8. Functionally, PRS activated TGF-β signaling, indicated by Smad2/3 nuclear translocation, but did not induce NF-κB signaling. These findings demonstrate that platelets are major contributors to PRF's biological effects, independent of leukocytes and plasma, and elicit a pronounced mitogenic and TGF-β-dominant response in gingival fibroblasts. They also provide insight into the cellular mechanisms underlying PRF-mediated tissue regeneration.

Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.

Cardiac arrhythmias, especially premature beats and atrial fibrillation, pose substantial clinical risks and detection hurdles. While deep learning has shown promise for automated arrhythmia diagnosis, single-model architectures often lack sufficient performance in distinguishing these two arrhythmia types. This study seeks to address the limitations of individual deep learning models and boost classification accuracy for premature beats and atrial fibrillation. It proposes an arrhythmia classification model integrating multiscale feature enhancement and bidirectional temporal dependency. First, a four-layer convolutional residual module with skip connections extracts multiscale local electrocardiogram (ECG) features. Then, multi-head self-attention strengthens critical feature global correlations. Next, a bidirectional long-term temporal de-pendency network captures sequence contextual dependencies. Finally, a Dropout-regularized fully connected layer enables six-type arrhythmia classification. Experiments on a fused dataset (MIT-BIH arrhythmia, MIT-BIH atrial fibrillation, and CODE datasets) yield an overall accuracy of 98.55% and F1-score of 0.9531. Notably, the F1-scores for premature beats (0.9916) and atrial fibrillation (0.9888) outperform recent literature by 2.16% and 4.39%, respectively. The model demonstrates robust classification performance with effective identification of the target arrhythmias, highlighting its potential as a supportive tool for automated ECG diagnosis.

Phosphoenolpyruvate carboxykinase (PEPCK), a key gluconeogenic enzyme, is associated with adaptation to environmental stress. However, its potential role in diapause is not known. Here, two cytoplasmic genes encoding PEPCK (SmPEPCK1-1 and SmPEPCK1-2) in Sitodiplosis mosellana, a significant wheat pest undergoing obligatory larval diapause during the third instar, were cloned, and their expression patterns during diapause and thermal stress were assessed, together with the effects of SmPEPCK1-2 knockdown on larval development. Both SmPEPCK1-1 and SmPEPCK1-2 were evolutionarily conserved and contained canonical functional domains and motifs. Their expression was induced by diapause, and was found to be tissue-specific, with the highest levels observed in the fat bodies of diapausing larvae. Furthermore, exposure to heat stress in oversummering larvae or cold stress in overwintering larvae enhanced the expression of both genes within specific temperature ranges (35-40 °C and -10-0 °C, respectively). RNA interference-mediated knockdown of SmPEPCK1-2 did not affect cocoon-breaking rates and timing but significantly prolonged the duration of larval development from cocoon-breaking to pupation. These findings indicate that both SmPEPCK genes are closely involved in tolerance to diapause-related stress, with SmPEPCK1-2 also contributing to the regulation of larval development.

Plastic pollution is acknowledged as a serious problem for ecosystems. Among these plastics, polystyrene nanoplastics (PS-NPs) are emerging environmental pollutants, and their biological effects on hepatotoxicity are the least explored. Therefore, the present work examined the effect of PS-NPs on the hepatic transcription of the antioxidant genes Hmox1 and Sod3 in mice (n = 6, treatment (PS-NPs) vs. vehicle group (Veh)), mediated by RORγ and epigenetic modifications. The results show that PS-NP mice had significantly reduced body weight; increased activity of adenosine triphosphate (ATP), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH), and Complexes I, III, and V in the liver; and increased Alanine Transaminase (ALT), Aspartate Transaminase (ASP), Alkaline Phosphatase (ALP), malondialdehyde (MDA) and reactive oxygen species (ROS) compared to the Veh group. Furthermore, PS-NPs resulted in considerably lower relative mRNA expression of Hmox1, Sod3, and RORγ in the liver than the Veh group. Likewise, when compared to Veh, PS-NPs significantly reduced the enrichment of RORγ, as well as the occupancies of the key components of the transcriptional activation pathway (P300, SRC1, Pol II, Ser5-Pol II, and Ser2-Pol II) at the loci of Hmox1 and Sod3. In comparison to Veh, PS-NPs showed downregulated occupancies of the histone active marks H3K9ac and H3K18ac, while H3K4me3 and H3K27me3 were higher at the target loci of Hmox1 and Sod3. In conclusion, the present study highlights that PS-NPs induce oxidative stress by modifying Hmox1 and Sod3 in mice's livers through histone changes and nuclear receptor RORγ modulation.

Understanding the mechanisms underlying seasonal community dynamics is important for predicting biodiversity responses to environmental fluctuations, enhancing ecological forecasting, and informing conservation strategies. In this study, we use standard transect and mist netting methods investigated seasonal altitudinal migration patterns of montane bird species in the Gyirong Valley, Central Himalayas. Our results showed four distinct altitudinal migration patterns among montane bird species: no shift, downslope shift, upslope shift, and contraction to mid-elevation zones. Species with smaller body weight and higher ratios of wing length, tail length, and tarsus length to body weight tended to migrate to lower elevations. Insectivorous birds exhibited a collective downslope shift, while omnivorous birds showed a wider range of migratory responses to seasonal variation. Migratory behavior was found to dynamically modulate the association between phenotypic traits and habitat preferences. During the breeding season, species (70.44%) and functional turnover (80.02%) dominated, while in the non-breeding season, nestedness significantly contributed to species (49.37%) and functional diversity (38.09%). In addition, migration can disrupt the direct influence of environmental variables on biodiversity patterns, providing important insights for montane biodiversity conservation under climate change. Our results highlight the critical need to safeguard low-elevation winter habitats and create dynamic protected areas to aid bird conservation amidst climate change.

(1) Background: Modifications of histone methylation could alter chromatin structure and thereby have an impact on gene expressions. (2) Methods: To investigate whether ORY-1001 delay retinal photoreceptor degeneration, rd10 mice were intraperitoneally injected with ORY-1001 (0.075 mg/kg) every second day from the 14th to the 24th day after birth. Full-field electroretinogram detection (ff ERG), optical coherence tomography (OCT), visual behavioral testing, retinal tissue morphology observation, and protein expression detection experiments were performed on the 25th day. Simultaneously, ATAC-seq and RNA-seq were used to test the mice's retinal tissues, and metabolomics detection and quantitative real-time polymerase chain reaction (qRT-PCR) were carried out. (3) Results: Compared with the rd10 group, in the treatment group, the function in the electroretinogram response and the visual behavioral responses were improved, the nuclear layer morphology of retinal tissue was reserved more, and the protein expression of H3K4me2 and CoREST was increased. Conjoint analysis of our ATAC-seq and RNA-seq results showed that chromatin accessibility was changed, as was gene expression which was involved in metabolism changes. In addition, the effector gene in the retina was Gnat1. (4) Conclusions: ORY-1001 delays retinal photoreceptor degeneration by inhibiting H3K4me2 demethylation in rd10 mice, which suggests that ORY-1001, as a novel epigenetic modifier, has potential for treating RP.

The medicinally and ornamentally valuable genus Thunbergia faces taxonomic uncertainty, while certain Acanthaceae species are threatened by habitat loss, underscoring the need for chloroplast genome studies to support conservation efforts. The chloroplast genome of Thunbergia grandiflora was sequenced and assembled. Additionally, 28 Acanthaceae species with significant medicinal value were selected for comparative genomic analysis. Based on the chloroplast genome data of Acanthaceae species, this study conducted phylogenetic and comparative evolutionary analyses. The results preliminarily support a systematic framework that divides Acanthaceae into eight tribes within five subfamilies. Concurrently, the study revealed significant inverted repeat (IR) region structural variations. A clear correspondence was observed between the contraction of IR length and the topological structure of the phylogenetic tree. In particular, species within the genus Strobilanthes exhibited significant contraction in their IR regions, which corresponded consistently with their tendency to cluster into an independent clade in the phylogenetic tree. This suggests that structural variation in the IR regions may be closely associated with the evolutionary divergence of this group. SSR analysis revealed a prevalent mononucleotide A/T repeat dominant pattern across Acanthaceae species. Furthermore, selection pressure analysis detected positive selection acting on multiple key genes, including rbcL, rps3, rps12, cemA, and ycf4, suggesting that these genes may play important roles in the adaptive evolution of Acanthaceae. This study reveals that the chloroplast genomes of Acanthaceae exhibit distinctive characteristics in phylogenetic architecture, dynamic variations in IR regions, and adaptive evolution of key genes, providing important molecular insights for understanding the mechanisms underlying species diversity and for the conservation of medicinal resources within this family.

Retinitis pigmentosa (RP), an inherited retinal disorder, leads to progressive photoreceptor degeneration and irreversible blindness, with limited treatment options available. Emerging evidence implicates microRNAs (miRNAs) in the pathogenesis of retinal disease, yet understanding of their specific roles in RP remains incomplete. In this study, we employed high-throughput RNA sequencing to profile miRNA expression in a rd1 RP mouse model at postnatal day 14. Our analysis revealed 40 upregulated and 27 downregulated miRNAs in rd1 retinas compared to controls. Notably, miR-142a-5p, miR-223-3p, and miR-653-5p were significantly elevated, while miR-25-3p was downregulated. Given miR-142a-5p's established roles in apoptosis and inflammation, we investigated its contribution to retinal degeneration. Knockdown of miR-142a-5p in rd1 mice improved retinal function and preserved outer nuclear layer thickness, suggesting a protective effect against photoreceptor loss. These findings highlight miR-142a-5p as a key regulator of RP progression and a promising therapeutic target for mitigating vision loss in retinal degenerative diseases.