Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about ...the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions.
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•Heavy metals were the most important factor affecting microbes.•Microbial interactions were changed in response to heavy metal contamination.•Bacteria showed diverse changes in response to heavy metal contamination.•Archaea were tolerant to heavy metals.•Microbes adapt to heavy metal contamination through their interactions.
Background
Mycobacterium tuberculosis
(MTB) is a relatively infrequent infection encountered during hematopoietic stem-cell transplantation (HSCT). The identification of MTB following HSCT remains a ...complex task, with delayed detection and misdiagnosis potentially resulting in unfavorable outcomes. Metagenomic next-generation sequencing (mNGS) represents a novel, highly sensitive, and rapid diagnostic tool in clinical settings for discerning intricate infections and detecting exceedingly rare pathogens
Methods
With the aid of mNGS, we diagnosed MTB in the lymph nodes and lungs of two patients with hematological diseases following allogeneic peripheral blood hematopoietic stem cell transplantation. Both patients presented with a fever, localized symptoms, and clinical signs. Following inconclusive results from routine tests, impractical biopsy procedures, and unsuccessful responses to empirical treatments, mNGS was employed as a final recourse, revealing DNA fragments of MTB in blood samples.
Results
The diagnoses were ultimately confirmed in conjunction with additional clinical evidence. The application of mNGS in MTB cases after allogeneic HSCT has rarely been reported. The mNGS technique can provide a prompt and highly sensitive indication leading to the definitive diagnosis of MTB in complex post-transplant scenarios.
Hydrophilic interaction chromatography (HILIC) has experienced increasing attention in recent years. Much research has been carried out in the area of HILIC separation mechanisms, column techniques ...and applications. Because of their good permeability, low resistance to mass transfer and easy preparation within capillaries, hydrophilic monolithic columns represent a trend among novel HILIC column techniques. This review attempts to present an overview of the preparation and applications of HILIC monolithic columns carried out in the past decade. The separation mechanism of various hydrophilic monolithic stationary phases is also reviewed.
Many cardioprotective pharmacological agents failed to exert their protective effects in diabetic hearts subjected to myocardial ischemia/reperfusion (MI/R). Identify the molecular basis linking ...diabetes with MI/R injury is scientifically important and may provide effective therapeutic approaches. Dynamin-related protein 1 (Drp1)-mediated mitochondrial fission plays an important role in MI/R injury under non-diabetic conditions. Importantly, recent studies indicated that Drp1-mediated mitochondrial fission is enhanced in the myocardium of diabetic mice. The above evidences suggested that Drp1 may be one critical molecule linking diabetes with MI/R injury. We hypothesized that inhibition of Drp1 may be effective to reduce MI/R injury in diabetic hearts.
High-fat diet and streptozotocin-induced diabetic mice were subjected to MI/R or sham operation. Mdivi-1 (1.2 mg/kg), a small molecule inhibitor of Drp1 or vehicle was administrated 15 min before the onset of reperfusion. Outcome measures included mitochondrial morphology, mitochondrial function, myocardial injury, cardiac function and oxidative stress.
Mitochondrial fission was significantly increased following MI/R as evidenced by enhanced translocation of Drp1 to mitochondria and decreased mitochondrial size. Delivery of Mdivi-1 into diabetic mice markedly inhibited Drp1 translocation to the mitochondria and reduced mitochondrial fission following MI/R. Inhibition of Drp1 in diabetic hearts improved mitochondrial function and cardiac function following MI/R. Moreover, inhibition of Drp1 reduced myocardial infarct size and serum cardiac troponin I and lactate dehydrogenase activities. These cardioprotective effects were associated with decreased cardiomyocyte apoptosis and malondialdehyde production and increased activities of antioxidant enzyme manganese superoxide dismutase.
Pharmacological inhibition of Drp1 prevents mitochondrial fission and reduces MI/R injury in diabetic mice. The findings suggest Drp1 may be a potential novel therapeutic target for diabetic cardiac complications.
High material cost is the biggest barrier for the industrial use of low-molecular-weight organics (i.e. lactate) as external carbon and electron source for sulfidogenic metal removal in sulfate-rich ...effluents. This study aims to provide mechanistic evidence from kinetics to microbiome analysis by batch modeling to support the possibility of decreasing the lactate input to achieve cost-effective application. The results showed that gradient COD/SO42− ratios at a low level had promising treatment performance, reaching neutralized pH with nearly total elimination of COD (91%–99%), SO42− (85%–99%), metals (80%–99%) including Cu, Zn, and Mn. First-order kinetics exhibited the best fit (R2 = 0.81–0.98) to (bio)chemical reactions, and the simulation results revealed that higher COD/SO42− accelerated the reaction rate of SO42− and COD but not suitable to that of metals. On the other hand, we found that the decreasing COD/SO42− ratio increased average path distance but decreased clustering coefficient and heterogeneity in microbial interaction network. Genetic prediction found that the sulfate-reduction-related functions were significantly correlated with the reaction kinetics changed with COD/SO42− ratios. Our study, combining reaction kinetics with microbiome analysis, demonstrates that the use of lactate as a carbon source under low COD/SO42− ratios entails significant efficiency of metal removal in sulfate-rich effluent using SRB-based technology. However, further studies should be carried out, including parameter-driven optimization and life cycle assessments are necessary, for its practical application.
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•Low COD/SO42− ratio achieved almost complete sulfate and metal removal.•Limited lactate entailed tilt advantages of sulfate reducers but confines sulfidogenic metal removal.•Microbial profile transformations caused by COD/SO42− ratio changes are narrow.•Proteobacteria and Firmicutes are leading assemblages in the ecological molecular network.•Sulfate-reduction-related genes are induced by faster lactate degradation while slower SO42− reduction.
Summary
Alicyclobacillus species inhabit diverse environments and have adapted to broad ranges of pH and temperature. However, their adaptive evolutions remain elusive, especially regarding the role ...of mobile genetic elements (MGEs). Here, we characterized the distributions and functions of MGEs in Alicyclobacillus species across five environments, including acid mine drainage (AMD), beverages, hot springs, sediments, and soils. Nine Alicyclobacillus strains were isolated from AMD and possessed larger genome sizes and more genes than those from other environments. Four AMD strains evolved to be mixotrophic and fell into distinctive clusters in phylogenetic tree. Four types of MGEs including genomic island (GI), insertion sequence (IS), prophage, and integrative and conjugative element (ICE) were widely distributed in Alicyclobacillus species. Further, AMD strains did not possess CRISPR‐Cas systems, but had more GI, IS, and ICE, as well as more MGE‐associated genes involved in the oxidation of iron and sulfide and the resistance of heavy metal and low temperature. These findings highlight the differences in phenotypes and genotypes between strains isolated from AMD and other environments and the important role of MGEs in rapid environment niche expansions.
To investigate the ecological effects of chemical and biological control methods on tobacco wildfire disease, a plot field experiment was conducted to compare the control efficiency and mechanisms of ...a chemical pesticide (kasugamycin wettable powder, KWP) and a biological control agent (BCA) through high-throughput sequencing of bacterial 16S rRNA genes.
The results showed that the BCA displayed better performance in decreasing the disease index and morbidity of tobacco than the chemical pesticide. By monitoring the endophytic community within tobacco leaves, it was found that the control effects of these two methods might be mediated by different changes in the endophytic bacterial communities and community assembly patterns. The application of either method decreased the taxonomic diversity of the leaf endophytic community. Compared to the BCA, KWP showed a more significant effect on the endophytic community structure, while the endophytic community treated with the BCA was able to return to the original state, which presented much lower disease infection. The disease control efficiency of KWP and BCA treatments might be achieved by increasing the abundance of Sphingomonas and Streptophyta, respectively. Furthermore, an analysis of the ecological processes in community assembly indicated that the BCA strengthened the homogeneous and variable selection, while KWP enhanced ecological drift.
The results suggested different control mechanisms between KWP and BCA treatments, which will help in developing diverse ecological strategies for plant disease control.
Lung adenocarcinoma (ACA) is the most common subtype of non-small-cell lung cancer. About 70%-80% patients are diagnosed at an advanced stage; therefore, the survival rate is poor. It is urgent to ...discover accurate markers that can differentiate the late stages of lung ACA from the early stages. With the development of biochips, researchers are able to efficiently screen large amounts of biological analytes for multiple purposes.
Our team downloaded GSE75037 and GSE32863 from the Gene Expression Omnibus (GEO) database. Next, we utilized GEO's online tool, GEO2R, to analyze the differentially expressed genes (DEGs) between stage I and stage II-IV lung ACA. The using the Cytoscape software was used to analyze the DEGs and the protein-protein interaction (PPI) network was further constructed. The function of the DEGs were further analyzed by cBioPortal and Gene Expression Profiling Interactive Analysis (GEPIA) online tools. We validated these results in 72 pairs human samples.
We identified 109 co-DEGs, most of which were involved in either proliferation, S phase of mitotic cell cycle, regulation of exit from mitosis, DNA replication initiation, DNA replication, and chromosome segregation. Utilizing cBioPortal and University of California Santa Cruz databases, we further confirmed 35 hub genes. Two of these genes, encoding CDC28 protein kinase regulatory subunit 2 (CKS2) and RecQ-mediated genome instability 2 (RMI2), were upregulated in lung ACA compared with adjacent normal tissues. The Kaplan-Meier curves revealed upregulation of CKS2 and RMI2 are associated with worse survival. Using CMap analysis, we discovered 10 small molecular compounds that reversed the altered DEGs, the top five are phenoxybenzamine, adiphenine, resveratrol, and trifluoperazine. We also evaluated 72 pairs resected samples, results revealed that upregulation of CKS2 and RMI2 in lung ACA were associated with larger tumor size. Our results allow the deeper recognizing of the mechanisms of the progression of lung ACA, and may indicate potential therapeutic strategies for the therapy of lung ACA.
•Significant cross-taxon congruence was found among bacteria, fungi, and zoobenthos.•Fungal community was more resistant to eutrophication compared to bacteria and zoobenthos.•Eutrophication ...decreased cross-taxon congruence in sediment biodiversity.•Bacteria worked as stabilizer in sediment ecosystem.
Eutrophication is a major problem currently affecting sediment biodiversity in different kingdoms. Surveys at different spatial scales have suggested that nutrient enrichment drove the congruence in biodiversity across different kingdoms. In this study, we examined the diversity indexes of bacteria, fungi, and zoobenthos in Dongting Lake, which is undergoing different trophic levels. The species richness and Shannon index of bacteria, fungi, and zoobenthos were all consistent with the intermediate disturbance hypothesis along the content of TN and TP, with the hysteresis of fungal group. Significant cross-taxon congruence was found in species richness between bacteria and zoobenthos, and Shannon index between bacteria and fungi. Also, the strength of congruence in biodiversity among bacteria, fungi and zoobenthos would decrease along nutrient enrichment. Multi- and single-kingdom networks found that bacterial group contained more nodes and edges compared to fungal and zoobenthos groups, and bacterial removal led to the lowest natural connectivity. And highest positive interaction proportion and lowest absolute value of natural connectivity slope were observed in zoobenthos group. These results highlighted the importance of bacteria as stabilizer in sediment ecosystem, and the most sensitive feature of zoobenthos to nutrient enrichment. Taken together, our results confirmed the cross-taxon congruence between multi-kingdoms, and the effectiveness of bacteria as a potential bioindicator of ecological change.
•DSI revealed that patients with unilateral MCA stenosis have a disrupted structural network.•Stroke-free patients with unilateral MCA stenosis have damaged white matter fibers.•The fiber disruption ...is more severe in the lesion hemisphere of patients with MCA stenosis.•The DSI technique is a noninvasive and sensitive tool that can be applied in clinical research.
We aimed to detect microstructural changes in the brains of patients with unilateral middle cerebral artery (MCA) stenosis and to assess the integrity of the fiber structure and the small-world networks using diffusion spectrum imaging (DSI).
A total of 21 healthy controls and 48 patients with unilateral MCA stenosis underwent 3.0 T MRI examination using DSI technique. Differential tractography, diffusion connectometry, and structural networks were performed by using DSI software. The correlation between the stenosis and quantitative anisotropy (QA) were analyzed using multiple regression models in the correlation tractography.
Differential tractography analysis showed that the left or right MCA stenosis group had decreased fiber connectivity in the brain network compared with the control group. The correlation tractography analysis of the patients with MCA stenosis showed that QA was negatively correlated with stenosis in the bilateral arcuate fasciculus, bilateral corticostriatal and corticothalamic pathway, bilateral corticopontine and corticospinal tract, right superior longitudinal fasciculus, right cingulum, corpus callosum, and left frontal aslant tract. Statistically significant differences were shown between the MCA stenosis groups and control group in graph density, global efficiency, network path length, and rich club coefficient.
DSI revealed that stroke-free patients with unilateral MCA stenosis have a disrupted structural network and damaged white matter fibers. Furthermore, the fiber connection disruption is more severe in the ipsilateral hemisphere and less prominent in the contralateral hemisphere in patients with unilateral MCA stenosis. Therefore, microstructural impairment has happened to patients with unilateral MCA stenosis even at a subclinical stage.
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