High-throughput Sequencing Analysis Research Articles

Bacterial community and dissolved organic matter networks in urban river: The role of human influence

Human activities have significantly altered the biogeochemical cycles of carbon, nitrogen, and sulfur in aquatic ecosystems, leading to ecological problems.This study utilized 16S rRNA gene high-throughput sequencing and excitation-emission matrix parallel factor analysis (EEM-PARAFAC) to evaluate the bacterial community composition and dissolved organic matter structure in the upstream (less impacted) and downstream (severely impacted) sections of the river, with a focus on the interactions between bacterial diversity and dissolved organic matter (DOM) characteristics.Results indicated significant spatial diversity in bacterial communities, with a higher α-diversity upstream compared to the more polluted downstream sections. Environmental parameters, particularly total phosphorus (TP) and dissolved oxygen (DO), were found to significantly influence the distribution and composition of bacterial phyla through redundancy analysis. The pattern of bacterial community assembly has shifted from predominantly deterministic to predominantly stochastic as a result of human activities. The analysis of DOM through EEM-PARAFAC identified three main fluorescent components, reflecting varied sources and interactions with bacterial communities. Upstream, microbial activities predominantly contributed to autochthonous DOM, while downstream, increased inputs of allochthonous DOM from human activities were evident. Furthermore, the study revealed that through the introduction of various organic pollutants and nutrient loads that shift microbial metabolic functions towards increased degradation and transformation of complex organic compounds downstream. Structural equation modeling (SEM) revealed that upstream human activities primarily affected bacterial communities indirectly by altering DOM properties. In contrast, downstream activities had both direct and indirect effects due to higher pollutant loads and more complex environmental conditions. These interactions underline the profound effect of anthropogenic factors on riverine ecosystems and emphasize the importance of managing human impacts to preserve microbial biodiversity and water quality.

Using grass inflorescence as source material for biomonitoring through environmental DNA metabarcoding

BackgroundOver the last decade, increasing attention has been directed to using different substrates as sources of environmental DNA (eDNA) in ecological research. Reports on the use of environmental DNA located on the surface of plant leaves and flowers have highlighted the utility of this DNA source in studies including, but not limited to, biodiversity, invasive species, and pollination ecology. The current study assesses grass inflorescence as a source of eDNA for detecting invertebrate taxa.Methods and resultsInflorescences from four common grass species in a central South African grassland were collected for high-throughput sequencing analysis. Universal COI primers were utilised to detect Metazoan diversity. The sequencing results allowed for the detection of three Arthropoda orders, with most OTUs assigned to fungal taxa (Ascomycota and Basidiomycota). Some biases were detected while observing the relative read abundance (RRA) results.DiscussionThe observed biases could be explained by the accidental inclusion of invertebrate specimens during sample collection and DNA extraction. Primer biases towards the amplified taxa could be another reason for the observed RRA results. This study provided insight into the invertebrate community associated with the four sampled grass species. It should be noted that with the lack of negative field controls, it is impossible to rule out the influence of airborne eDNA on the observed diversity associated with each grass species. The lack of the inclusion of PCR and extraction blanks in the sequencing step, as well as the inclusion of negative field controls, including other areas for refinement were highlighted, and suggestions were provided to improve the outcomes of future studies.

Hesperetin Attenuates T-2 Toxin-Induced Chondrocyte Injury by Inhibiting the p38 MAPK Signaling Pathway.

Hesperetin, a flavonoid derived from citrus fruits, exhibits potent antioxidant and anti-inflammatory activities and has been implicated in cartilage protection. However, its effectiveness against T-2 toxin-induced knee cartilage damage remains unclear. In this study, high-throughput sequencing analysis was employed to identify the key signaling pathways involved in T-2 toxin-induced articular cartilage damage in rats. Animal models were divided into the following groups: control, low-dose T-2 toxin, high-dose T-2 toxin, T-2 toxin + hesperetin, hesperetin, and vehicle. Pathological staining and immunohistochemistry were used to assess pathological changes, as well as the expression levels of the cartilage matrix-related proteins MMP13 and collagen II, along with the activation of the p38 MAPK signaling pathway. Additionally, primary rat chondrocytes were cultured to establish an in vitro model for investigating the underlying mechanism. High-throughput sequencing analysis revealed the involvement of the MAPK signaling pathway in T-2 toxin-induced articular cartilage damage in rats. Hesperetin intervention in T-2 toxin-exposed rats attenuated pathological cartilage damage. Immunohistochemistry results demonstrated a significant reduction in collagen II protein expression in the high-dose T-2 toxin group (p < 0.01), accompanied by a significant increase in MMP13 protein expression (p < 0.01). In both the articular cartilage and the epiphyseal plate, the T-2 toxin + hesperetin group exhibited significantly higher collagen II protein expression than the high-dose T-2 toxin group (p < 0.05), along with significantly lower MMP13 protein expression (p < 0.05). Hesperetin inhibited the over-activation of the p38/MEF2C signaling axis induced by T-2 toxin in primary rat chondrocytes. Compared to the T-2 toxin group, the T-2 toxin + hesperetin group showed significantly reduced phosphorylation levels of p38 and protein expression levels of MEF2C (p < 0.001 or p < 0.05). Moreover, the T-2 toxin + hesperetin group exhibited a significant decrease in MMP13 protein expression (p < 0.05) and a significant increase in collagen II protein expression (p < 0.01) compared to the T-2 toxin group. T-2 toxin activates the p38 MAPK signaling pathway, causing knee cartilage damage in rats. Treatment with hesperetin inhibits the p38/MEF2C signaling axis, regulates collagen II and MMP13 protein expression, and reduces cartilage injury significantly.

Weak effects of prebiotically plausible peptides on self-triphosphorylation ribozyme function.

Catalytic RNAs (ribozymes) were central to early stages of life on earth. The first ribozymes probably emerged in the presence of prebiotically generated peptides because amino acids can be generated under abiotic conditions, and amino acids can oligomerize into peptides under prebiotically plausible conditions. Here we tested whether the presence of prebiotically plausible peptides could have aided the emergence of ribozymes, by an in vitro selection of self-triphosphorylation ribozymes from random sequence in the presence of ten different octapeptides. These peptides were composed of ten different, prebiotically plausible amino acids, each as mixture of d- and l-stereoisomers. After five rounds of selection and high throughput sequencing analysis, ten ribozymes that appeared most promising for peptide benefits were tested biochemically for possible benefits from each of the ten peptides. The strongest peptide benefit enhanced ribozyme activity by 2.6-fold, similar to the effect from an increase in the pH by one-half unit. Four arbitrarily chosen ribozymes from a previous selection without peptides showed no significant change in their activity in the presence of the ten peptides. Therefore, the used prebiotically plausible peptides - peptides without evolutionarily optimized sequence, without cationic or aromatic side chains - did not provide a strong benefit for the emergence of ribozyme activity. This finding stands in contrast to previously identified polycationic peptides, conjugates between peptides and polyaromatic hydrocarbons, and modern mRNA encoded proteins, all of which can strongly increase ribozyme function. The results are discussed in the context of origins of life.

Engineering exosomes derived from TNF-α preconditioned IPFP-MSCs enhance both yield and therapeutic efficacy for osteoarthritis

BackgroundThe pathogenesis of osteoarthritis (OA) involves the progressive degradation of articular cartilage. Exosomes derived from mesenchymal stem cells (MSC-EXOs) have been shown to mitigate joint pathological injury by attenuating cartilage destruction. Optimization the yield and therapeutic efficacy of exosomes derived from MSCs is crucial for promoting their clinical translation. The preconditioning of MSCs enhances the therapeutic potential of engineered exosomes, offering promising prospects for application by enabling controlled and quantifiable external stimulation. This study aims to address these issues by employing pro-inflammatory preconditioning of MSCs to enhance exosome production and augment their therapeutic efficacy for OA.MethodsThe exosomes were isolated from the supernatant of infrapatellar fat pad (IPFP)-MSCs preconditioned with a pro-inflammatory factor, TNF-α, and their production was subsequently quantified. The exosome secretion-related pathways in IPFP-MSCs were evaluated through high-throughput transcriptome sequencing analysis, q-PCR and western blot analysis before and after TNF-α preconditioning. Furthermore, exosomes derived from TNF-α preconditioned IPFP-MSCs (IPFP-MSC-EXOsTNF−α) were administered intra-articularly in an OA mouse model, and subsequent evaluations were conducted to assess joint pathology and gait alterations. The expression of proteins involved in the maintenance of cartilage homeostasis within the exosomes was determined through proteomic analysis.ResultsThe preconditioning with TNF-α significantly enhanced the exosome secretion of IPFP-MSCs compared to unpreconditioned MSCs. The potential mechanism involved the activation of the PI3K/AKT signaling pathway in IPFP-MSCs by TNF-α precondition, leading to an up-regulation of autophagy-related protein 16 like 1(ATG16L1) levels, which subsequently facilitated exosome secretion. The intra-articular administration of IPFP-MSC-EXOsTNF−α demonstrated superior efficacy in ameliorating pathological changes in the joints of OA mice. The preconditioning of TNF-α enhanced the up-regulation of low-density lipoprotein receptor-related protein 1 (LRP1) levels in IPFP-MSC-EXOsTNF−α, thereby exerting chondroprotective effects.ConclusionTNF-α preconditioning constitutes an effective and promising method for optimizing the therapeutic effects of IPFP-MSCs derived exosomes in the treatment of OA.Graphical

Assessment of microbial diversity in various saline soils driven by salt content

The Yellow River Delta, as an important reserve land resource area, faces soil salinization problems. Understanding the bacterial community composition in saline soils is an important foundation for control and utilization of saline soils. However, few studies have been conducted on the composition of bacterial communities in soils with different degrees of salinization. Thus, saline soils categorized into low-salinity (LS), medium-salinity (MS), and high-salinity (HS) based on electrical conductivity (EC) were collected. The 16S rRNA high-throughput sequencing analysis was performed to analyze the effects of salinities on soil bacterial community patterns, as well as the relationships between soil bacterial communities and environmental factors. The results showed that Actinobacteriota, Proteobacteria, Chloroflexi, Firmicutes, Acidobacteriota, Gemmatimonadota and Bacteroidota accounted for almost 90 % of all the bacterial community. The linear discriminant analysis effects (LDA > 3.7) showed that 6, 5 and 3 biomarkers were present in LS, MS and HS soils, respectively, which indicated EC was an important factor influencing the saline soil bacterial community patterns. Redundancy analysis further revealed that the primary environmental parameters impacting the bacterial community were pH, EC, nitrate nitrogen, available phosphorus, total phosphorus, and soil organic matter. According to network analysis, the microbial network complexity was increased steadily with increasing of soil salinity. These findings together revealed that bacterial communities could serve as a reliable way to assess and improve the quality of salinized soils.

Feeding ecology of Lagocephalus spadiceus in the Beibu Gulf by high-throughput sequencing and stable isotope analyses

Feeding ecology of Lagocephalus spadiceus in the Beibu Gulf by high-throughput sequencing and stable isotope analyses

High-Throughput Sequencing Analysis of Microbiota and Enzyme Activities in Xiaoqu from Seven Provinces in Southern China.

Xiaoqu, a pivotal starter in baijiu fermentation, provides the most microflora and enzymes to initiate and maintain baijiu brewing. This study aims to explore the differences in microbiota and enzyme activities among Xiaoqu samples from seven provinces in southern China using high-throughput sequencing, plate isolation, and activity detection. The analyses revealed significant differences in bacterial and fungal communities across the samples. A total of 22 bacterial species and 17 target fungal species were isolated and identified. Predominant bacteria included Bacillus (Bacillus subtilis) and lactic acid bacteria (LABs), while the fungal communities were primarily composed of yeasts (Saccharomyces cerevisiae) and various molds. The activities of α-amylase and glucoamylase varied significantly among the samples, and samples from HN1 and GZ2 exhibited the highest activities. Correlation analyses highlighted the pivotal role of LABs in maintaining acidity and the importance of molds and yeasts in the saccharification and fermentation processes. These findings shed light on the microbial composition and diversity of Xiaoqu and the critical role of microbes in baijiu production. Moreover, they suggested potential microbial resources for developing artificial Xiaoqu via synthetic microbial community in the future, enhancing baijiu fermentation efficiency and overall product quality.

Revealing Interactions of Gut Microbiota and Metabolite in Confined Environments Using High-Throughput Sequencing and Metabolomic Analysis.

A confined environment is a special kind of extreme working environment, and prolonged exposure to it tends to increase psychological stress and trigger rhythmic disorders, emotional abnormalities and other phenomena, thus seriously affecting work efficiency. However, the mechanisms through which confined environments affect human health remain unclear. Therefore, this study simulates a strictly controlled confined environment and employs integrative multi-omics techniques to analyze the alterations in gut microbiota and metabolites of workers under such conditions. The aim is to identify metabolic biomarkers and elucidate the relationship between gut microbiota and metabolites. High-throughput sequencing results showed that a confined environment significantly affects gut microbial composition and clusters subjects' gut microbiota into two enterotypes (Bla and Bi). Differences in abundance of genera Bifidobacterium, Collinsella, Ruminococcus_gnavus_group, Faecalibacterium, Bacteroides, Prevotella and Succinivibronaceae UCG-002 were significant. Untarget metabolomics analyses showed that the confined environment resulted in significant alterations in intestinal metabolites and increased the activity of the body's amino acid metabolism and bile acid metabolism pathways. Among the metabolites that differed after confined environment living, four metabolites such as uric acid and beta-PHENYL-gamma-aminobutyric acid may be potential biomarkers. Further correlation analysis demonstrated a strong association between the composition of the subjects' gut microbiota and these four biomarkers. This study provides valuable reference data for improving the health status of workers in confined environments and facilitates the subsequent proposal of targeted prevention and treatment strategies.

Comparative Analysis of Gut Microbiota Composition in Yaks Across Different Geographical Region

Background: Despite the significance of gut microbiota in in determining the health and adaptability of the host, limited information exists regarding the influence of diverse geographic conditions on the intestinal microbiota of yaks. The study aimed at undertaking comprehensive comparison of microbiota composition in yaks originating from distinct geographic regions. Methods: 15 fecal samples were collected from yaks inhabiting 5 regions in China: Madoi, Nagqu and Deqin Shangri-la, Lhasa and Yushu. Through rigorous high-throughput sequencing analysis, the alpha diversity using metrics such as Shannon, ACE and Chao indices were assessed. Result: Notably, the Shangri-la samples exhibited the highest alpha diversity. Principal coordinate analysis revealed substantial variations in the composition of the intestinal microbiota across different regions. Firmicutes and Bacteroidetes emerged as the dominant phyla, with Ruminococcaceae being the most abundant family. Particularly, the genus Ruminococcaceae_UCG-005 demonstrated prominence, exhibiting higher abundance in Yushu samples compared to others. However, intriguingly, the predicted functional gene composition of the gut microbiota exhibited remarkable similarity across diverse geographical regions.

Long Non-coding RNAs Influence Aging Process of Sciatic Nerves in SD Rats.

To investigate the long non-coding RNAs (lncRNAs) changes in the sciatic nerve (SN) in Sprague Dawley (SD) rats during aging. Eighteen healthy SD rats were selected at the age of 1 month (1M) and 24 months (24M) and SNs were collected. High-throughput transcriptome sequencing and bioinformatics analysis were performed. Protein-protein interaction (PPI) networks and competing endogenous RNA (ceRNA) networks were established according to differentially expressed genes (DEGs). As the length of lncRNAs increased, its proportion to the total number of lncRNAs decreased. A total of 4079 DElncRNAs were identified in Con vs. 24M. GO analysis was primarily clustered in nerve and lipid metabolism, extracellular matrix, and vascularization-related fields. There were 17 nodes in the PPI network of the target genes of up-regulating genes including Itgb2, Lox, Col11a1, Wnt5a, Kras, etc. Using quantitative RT-PCR, microarray sequencing accuracy was validated. There were 169 nodes constructing the PPI network of down-regulated target genes, mainly including Col1a1, Hmgcs1, Hmgcr. CeRNA interaction networks were constructed. Lipid metabolism, angiogenesis, and ECM fields might play an important role in the senescence process in SNs. Col3a1, Serpinh1, Hmgcr, and Fdps could be candidates for nerve aging research.

The salivary microbiome and oral health status in HBeAg-negative chronic hepatitis B

Background/purposeDysbiosis of oral microbiota has been reported in late stage of chronic hepatitis B (CHB) infection with cirrhosis. CHB is characterized by the constant virus-induced liver injury which may lead to liver cirrhosis and hepatocellular carcinoma (HCC). However, some patients show normal liver function without antiviral treatment, associating with favourable prognosis. The oral microbiota composition and oral health status in these patients is unidentified. Materials and methodsThe study focuses on the composition of oral microbiota and oral health status in individuals with CHB and HBV vaccinees as controls. The CHB patients were hepatitis B 'e' antigen (HBeAg)-negative, with or without elevated liver enzyme increase at time of sampling, The 16S rRNA high-throughput sequencing and bioinformatic analysis were applied to investigate oral bacterial diversity, and oral examination including decay-missing-filled teeth (DMFT) index, probing depth (PD) and mucosal status was performed, along with oral health questionnaire, to assess the oral health status in CHB patients and healthy controls. ResultsOur results indicate that their oral microbiome compositions are not significantly different though some have increased ALT/AST liver enzyme levels at the time of sampling, compared to the healthy control participants who are vaccinated e.g. protected from this viral disease. CHB patients here bore a good oral health status and life-style habits as comparing to healthy controls. ConclusionThese findings suggest that a health-associated salivary microflora is present in CHB without severe liver injury. Continued regular dental health and lifestyle support in liver disease patients is therefore justified.

SEV-mediated lipid droplets transferred from bone marrow adipocytes promote ferroptosis and impair osteoblast function

Osteoporosis is linked to increased bone marrow adipocyte (BMAd) proliferation, which displaces bone-forming cells and alters the local environment. The impact of BMAd lipid droplets on bone health and osteoblast function remains unclear. This study investigates the interplay between BMAd-derived lipid droplets and osteoblast functionality, focusing on ferroptosis pathways. Osteoblast cultures were treated with conditioned media from adipocytes to simulate in vivo conditions. High-throughput mRNA sequencing and Western blot analysis were used to profile changes in gene expression and protein levels related to ferroptosis, oxidative phosphorylation, and osteogenic markers. Cellular assays assessed the direct impact of lipid droplets on osteoblast activity. Results showed that osteoblasts exposed to adipocyte-conditioned media had increased intracellular lipid droplet accumulation, upregulation of ferroptosis-related genes and proteins, and downregulation of oxidative phosphorylation and osteoblast differentiation markers. Treatment with ferroptosis inhibitors reversed the detrimental effects on osteoblasts, indicating the functional relevance of this pathway in osteoporosis. BMAd-derived lipid droplets contribute to osteoblast dysfunction through ferroptosis induction. Inhibiting ferroptosis could preserve osteoblast function and combat osteoporosis-related bone issues, suggesting that modulating lipid metabolism and redox balance in bone cells may be promising for future treatments.

Effects of gradual increase of ciprofloxacin and cefotaxime on nitrogen and phosphorus removal and microbial community in moving bed biofilm reactor

To clarify the effects of trace amount of antibiotics in wastewater on biofilm reactor, this study explored the effects of gradual increase of ciprofloxacin (CIP) and cefotaxime (CTX) ranging from 100 to 1000 ng·L−1 on the nitrogen and phosphorus removal and microbial community in a moving bed biofilm reactor (MBBR). Under different phases of CIP and CTX gradual increase, the resilience of culturable functional bacteria including ammonifying bacteria, nitrite oxidizing bacteria, aerobic denitrifying bacteria and phosphorus accumulating organisms in the biofilm was analyzed. High-throughput sequencing analysis was used to reveal the microbial community structure and species composition of functional bacteria. The results indicated that the treatment performance of MBBR was temporarily affected by trace CIP and CTX and returned to its original level within 1–2 days. Ammonifying bacteria exhibited strong resilience in trace CIP and CTX stress environments. Trace CIP and CTX altered the microbial community structure in biofilm, but the performance of nitrogen and phosphorus removal in MBBR was slightly affected. This might attribute to the rapid proliferation of Thauera, Dechloromonas and Candidatus_Accumulibacter on the carrier biofilm. The research results help to deepen the understanding of the impact of trace antibiotics on the MBBR and to provide a reference for the development of microbial germplasm resources for biological nitrogen and phosphorus removal from wastewater under antibiotic stress conditions.

Microbial succession and flavor impact during natural fermentation of Tartary buckwheat sourdough

In this study, the succession process and driving mechanisms of microbial communities during the fermentation of Tartary buckwheat sourdough were explored using high-throughput sequencing and microbiome co-occurrence network analysis. A gas chromatograph–mass spectrometer (GC–MS) was used to monitor the dynamic evolution of flavor compounds in Tartary buckwheat sourdough at different fermentation stages. Using GC–MS and principal component analysis, 47 volatile compounds were identified as the main differential volatile compounds during fermentation. The predominant bacterial genera observed in the natural fermentation of Tartary buckwheat sourdough included Enterococcus, Weissella, Cronobacter, Lactococcus, and Pediococcus. Among fungi, Alternaria, Botrytis, Trichothecium, and Vishniacozyma were the dominant genera. The correlation analysis results revealed that Weissella, Pediococcus, Lactobacillus, Acinetobacter, and Vishniacozyma were the core functional microbes involved in flavor formation. Organic acids were the primary driving force for microbial succession. This study provides a better understanding of the relationship between microbial communities and volatile components in the natural fermentation process of Tartary buckwheat sourdough as well as useful information for improving the flavor quality of Tartary buckwheat sourdough products, thereby helping to choose starter cultures with flavor modulation ability.

The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals.

The Australian Biosecurity Genomic Database (ABGD) is a curated collection of reference viral genome sequences based on the Australian National Notifiable Disease List of Terrestrial Animals. It was created to facilitate the screening of high-throughput sequencing (HTS) data for the potential presence of viruses associated with notifiable disease. The database includes a single verified sequence (the exemplar species sequence, where relevant) for each of the 60 virus species across 21 viral families that are associated with or cause these notifiable diseases, as recognized by the World Organisation for Animal Health. The open-source ABGD on GitHub provides usage guidance documents and is intended to support building a culture in Australian HTS communities that promotes the use of quality-assured, standardized, and verified databases for Australia's national biosecurity interests. Future expansion of the database will include the addition of more strains or subtypes for highly variable viruses, viruses causing diseases of aquatic animals, and genomes of other types of pathogens associated with notifiable diseases, such as bacteria. Database URL: https://github.com/ausbiopathgenDB/AustralianBiosecurityGenomicDatabase.

Tetramethylpyrazine ameliorates LPS-induced acute lung injury via the miR-369-3p/DSTN axis

Acute lung injury (ALI) is a severe clinical respiratory condition characterized by high rates of mortality and morbidity, for which effective treatments are currently lacking. In this study, lipopolysaccharide (LPS) was used to induce ALI mice, demonstrating the efficacy of tetramethylpyrazine (TMP) in ameliorating ALI. Subsequent we perfored high-throughput sequencing analysis and used Targetscan 8.0 and miRWalk 3.0 databases to predict the interaction between microRNAs and destrin (DSTN), ultimately identifying miR-369-3p as the focus of the investigation. The adenovirus carrying miR-369-3p was administered one week prior to LPS-induced in order to assess its potential efficacy in ameliorating ALI in mice. The findings indicated that the overexpression of miR-369-3p resulted in enhanced lung function, reduced pulmonary edema, inflammation, and permeability in LPS-induced ALI mice, while the suppression of miR-369-3p exacerbated the damage in these mice. Furthermore, the beneficial effects of TMP on LPS-induced ALI were negated by the downregulation of miR-369-3p. The results of our study demonstrate that TMP mitigates LPS-induced ALI through upregulation of miR-369-3p. Consequently, the findings of this study advocate for the clinical utilization of TMP in ALI treatment, with miR-369-3p emerging as a promising target for future ALI interventions.

Distribution of Carbon-Sequestering Microbes in Different Habitats and the Interaction with Habitat Factors in a Natural Karst Cave

The distributional characteristics of microorganisms in karst cave ecosystems have been widely studied. However, in such a dark, humid, and oligotrophic habitat, studies on the differences in carbon-sequestering bacteria in multiple habitats are limited. Therefore, to learn the distribution characteristics of carbon-sequestering colonies in cave habitats and their correlation with habitat factors (e.g., pH, Ca2+, Mg2+, etc.), samples from five cave habitats (weathered rock walls, underground river water, drips, sediments, and air) were collected from the twilight and dark zones of Shiziyan Cave (CO2 concentration 5385 ppm). The results of high-throughput sequencing and statistical analyses showed that there were significant differences in the distribution of communities in different habitats, with higher abundance in sediments habitat and underground river water habitat, and the dominant phyla of Pseudomonadota (30.53%) and Cyanobacteria (75.11%) in these two habitats. The microbial diversity of the carbon-sequestering microbial community was higher in sediments than in underground river water. The pH, and Ca2+, SO42−, and NO3− concentrations can alter the diversity of carbon-sequestering microbes, thereby affecting carbon cycling in caves. Carbon metabolism analyses suggest that microbes in the habitat can cooperate and coexist by participating in different carbon metabolic pathways. These results expanded our understanding of carbon-sequestering microbial communities in cave systems and their responses to the environment.

Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants.

Assessing the pathogenicity of genetic variants is a critical aspect of genomic medicine and precision healthcare. Over the last decades, the identification of genetic variants and their characterization has become simpler (advent of high-throughput sequencing technologies, analysis, and visualization support tools, etc.). However, the quality of assessments to distinguish benign from pathogenic variants is critical to inform clinical decision-making and improve patient outcomes. In this article, we investigate the relationships using correlation tests between the characterization of genetic variants in the literature and their pathogenicity scores computed by two state-of-the-art assessment tools (SIFT and PolyPhen-2).

Targeting Nrf2/PHKG2 axis to enhance radiosensitivity in NSCLC

While ferroptosis shows promise in anti-cancer strategy, the molecular mechanisms behind this process remain poorly understood. Our research aims to highlight the regulation of radiotherapy-induced ferroptosis in non-small cell lung cancer (NSCLC) via the NRF2/PHKG2 axis-mediated mechanism. To identify ferroptosis-associated genes associated with radioresistance in NSCLC, this study employed high-throughput transcriptome sequencing and Lasso risk regression analysis. Clinical samples were analyzed to confirm PHKG2 expression changes before and after radiotherapy. The study further examined ferritinophagy-related factors, intracellular iron levels, mitochondrial function, and ferroptosis in NSCLC cells undergoing radiation exposure to explore the effect of PHKG2 on radiosensitivity or radioresistance. The research also demonstrated the transcriptional inhibition of PHKG2 by NRF2 and created in situ transplantation tumor models of NSCLC to examine the role of NRF2/PHKG2 axis in NSCLC radiosensitivity and resistance in vivo. The Lasso risk regression model that incorporated ferroptosis-associated genes effectively predicted the prognosis of patients with NSCLC. Radiotherapy-sensitive tissues exhibited an increased expression of PHKG2. Overexpression of PHKG2 led to elevated intracellular iron levels by promoting ferritinophagy and increased mitochondrial stress-dependent ferroptosis induced by radiotherapy. PHKG2 transcription repression was achieved through NRF2. The FAGs-Lasso risk regression model can accurately predict the prognosis of NSCLC patients. Targeting Nrf2 upregulates the expression of PHKG2 and reverses radiotherapy resistance in NSCLC by promoting iron autophagy and inducing mitochondrial dysfunction, thereby increasing radiotherapy sensitivity.