Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China.

A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.

Post-synthetic modification (PSM) of MOFs with an ionic polymer for efficient adsorptive removal of methylene blue from water.

UiO-66-NH2 was functionalized with an ionic polymer poly(2-acrylamido-2-methylpropane sulfonic acid) (PAMPS) through a post-synthetic modification (PSM) strategy. Due to the excellent dispersibility in water and the existence of abundant active binding sites, the obtained UiO-66-PAMPS shows significantly improved adsorption capability toward methylene blue (MB) in aqueous solution.

Effects of hierarchical nursing management in patients with acute pulmonary embolism.

BACKGROUND: Acute pulmonary embolism (acute PE) is the most serious manifestation of venous thromboembolism. Hierarchical nursing management is an improved option for nursing, but no study that indicated the effects of hierarchical nursing management in patients with acute PE could be found. This study aimed to explore the effects of hierarchical nursing management on the quality of nursing care and the prognosis of patients with acute PE. Methods From January 2020 to January 2022, 92 patients with acute PE were recruited and divided into the study group and the control group. The study group was designated with our hierarchical nursing care and the control group was designated with a conventional nursing care. The data of general characteristics, nursing quality, the improvement of clinical symptoms, the job satisfaction of nursing was collected and compared. Results The door-to-needle time, the thrombectomy time and length of emergency staying the study group were shorter than those in the control group (P < 0.005). The rate of complications in the study group was lower than that in the control group (P = 0.158). The scores of the nursing quality and the nursing satisfaction levels in the study group were remarkably higher than that in the control group. Conclusion For acute PE patients, the using of hierarchical nursing management can shorten the rescue time, reduce the rate of complications and improve the nursing quality of nursing care.

The application of pre-hospital first aid mode in patients with acute stroke: meta-analysis.

To systematically evaluate the application effect of pre-hospital and in-hospital emergency mode in patients with acute stroke. The study was conducted by systematic search of Chinese (CNKI, Wanfang and VIP) and English (PubMed, EMBASE and Cochrane Library) databases. The case-control studies comparing the role of pre-hospital and in-hospital emergency mode for patients with acute stroke were included in this study. Outcome indicators included the time from admission to thrombolytic therapy (DNT), the time from calling for help to receiving professional treatment, the first aid effect (effective rate, disability rate and mortality), complications and prognosis. Meta-analysis was performed using RevMan 5.3. Seventeen studies were included in the final analysis. Compared with traditional emergency measures, pre-hospital and in-hospital emergency measures can significantly reduce DNT (mean difference [MD] = -22.63, p < 0.00001), time from call to professional treatment (MD: -13.22, p < 0.00001), disability rate (RR = 0.88, p = 0.004), fatality rate (RR = 0.58, p < 0.00001), central cerebral fever (RR = 0.44, p = 0.0009), and gastrointestinal bleeding (RR = 0.44, p = 0.002). In addition, daily living ability (MD = 16.56, p < 0.00001) and emergency response rate (RR = 1.50, p < 0.00001) were significantly improved. The pre-hospital and in-hospital emergency mode has a significant emergency effect in patients with acute stroke, which is a protective factor. This emergency mode can be widely used in clinical practice.

DNA Motifs and an Accessory CRISPR Factor Determine Cas1 Binding and Integration Activity in Sulfolobus islandicus.

CRISPR-Cas systems empower prokaryotes with adaptive immunity against invasive mobile genetic elements. At the first step of CRISPR immunity adaptation, short DNA fragments from the invaders are integrated into CRISPR arrays at the leader-proximal end. To date, the mechanism of recognition of the leader-proximal end remains largely unknown. Here, in the Sulfolobus islandicus subtype I-A system, we show that mutations destroying the proximal region reduce CRISPR adaptation in vivo. We identify that a stem-loop structure is present on the leader-proximal end, and we demonstrate that Cas1 preferentially binds the stem-loop structure in vitro. Moreover, we demonstrate that the integrase activity of Cas1 is modulated by interacting with a CRISPR-associated factor Csa3a. When translocated to the CRISPR array, the Csa3a-Cas1 complex is separated by Csa3a binding to the leader-distal motif and Cas1 binding to the leader-proximal end. Mutation at the leader-distal motif reduces CRISPR adaptation efficiency, further confirming the in vivo function of leader-distal motif. Together, our results suggest a general model for binding of Cas1 protein to a leader motif and modulation of integrase activity by an accessory factor.

LDHA promotes osteoblast differentiation through histone lactylation.

Osteoblast cells tend to metabolize glucose to lactate via aerobic glycolysis during osteogenic differentiation. However, the function of lactate in this process is still elusive. As a newly discovered protein posttranslational modification, lactate-derived histone lactylation has been found to play important roles in gene regulation and have profound effects on diverse biological processes. Here, we found that the expression of lactate dehydrogenase A (LDHA), intracellular lactate, and histone lactylation levels were all gradually increased during osteogenic differentiation. Knockdown of LDHA impaired the formation of mineralized nodules and ALP activity. RNA-sequencing and subsequent validation experiments showed that JunB expression was decreased in LDHA knockdown cells. Mechanistically, knockdown of LDHA decreased histone lactylation mark enrichment on JunB promoter, and exogenous lactate treatment rescued this effect. Our study revealed a non-canonical function of lactate during osteogenic differentiation.

Successful Application of Extracorporeal Membrane Oxygenation in an Acute Tonsillitis Patient Complicated with Acute Respiratory Distress Syndrome: A Case Report.

Cases of acute tonsillitis, a common disease in the emergency department, are mostly mild and those complicated by severe pneumonia and acute respiratory distress syndrome are rarely reported.

CRISPR-mediated host genomic DNA damage is efficiently repaired through microhomology-mediated end joining in Zymomonas mobilis.

CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against mobile genetic elements (MGEs) through uptake of invader-derived spacers. De novo adaptation samples spacers from both invaders and hosts, whereas primed adaptation shows higher specificity to sample spacers from invaders in many model systems as well as in the subtype I-F system of Zymomonas mobilis. Self-derived spacers will lead to CRISPR self-interference. However, our in vivo study demonstrated that this species used the microhomology-mediated end joining (MMEJ) pathway to efficiently repair subtype I-F CRISPR-Cas system-mediated DNA breaks guided by the self-targeting spacers. MMEJ repair of DNA breaks requires direct microhomologous sequences flanking the protospacers and leads to DNA deletions covering the protospacers. Importantly, CRISPR-mediated genomic DNA breaks failed to be repaired via MMEJ pathway in presence of higher copies of short homologous DNA. Moreover, CRISPR-cleaved exogenous plasmid DNA was failed to be repaired through MMEJ pathway, probably due to the inhibition of MMEJ by the presence of higher copies of the plasmid DNA in Z. mobilis. Our results infer that MMEJ pathway discriminates DNA damages between in the host chromosome versus mobile genetic element (MGE) DNA, and maintains genome stability post CRISPR immunity in Z. mobilis.

CRISPR-Associated Factor Csa3b Regulates CRISPR Adaptation and Cmr-Mediated RNA Interference in Sulfolobus islandicus.

Acquisition of spacers confers the CRISPR-Cas system with the memory to defend against invading mobile genetic elements. We previously reported that the CRISPR-associated factor Csa3a triggers CRISPR adaptation in Sulfolobus islandicus. However, a feedback regulation of CRISPR adaptation remains unclear. Here we show that another CRISPR-associated factor, Csa3b, binds a cyclic oligoadenylate (cOA) analog (5'-CAAAA-3') and mutation at its CARF domain, which reduces the binding affinity. Csa3b also binds the promoter of adaptation cas genes, and the cOA analog enhances their binding probably by allosteric regulation. Deletion of the csa3b gene triggers spacer acquisition from both plasmid and viral DNAs, indicating that Csa3b acted as a repressor for CRISPR adaptation. Moreover, we also find that Csa3b activates the expression of subtype cmr-α and cmr-ß genes according to transcriptome data and demonstrate that Csa3b binds the promoters of cmr genes. The deletion of the csa3b gene reduces Cmr-mediated RNA interference activity, indicating that Csa3b acts as a transcriptional activator for Cmr-mediated RNA interference. In summary, our findings reveal a novel pathway for the regulation of CRISPR adaptation and CRISPR-Cmr RNA interference in S. islandicus. Our results also suggest a feedback repression of CRIPSR adaptation by the Csa3b factor and the cOA signal produced by the Cmr complex at the CRISPR interference stage.

Clinical study on a skin stretching technique with adjustable external fixators to treat skin defects.

The aim of this study was to determine the effectiveness of a skin stretching technique with adjustable external fixators in treating skin defects.Eighteen patients treated with a skin-stretching technique with adjustable external fixators for skin defects from April 2017 to October 2019 were included. Visual Analogue Scale (VAS) scores were collected during therapy. The skin defects gradually became smaller until they were completely resolved according to the blood flow of the affected limb and wound skin (the color, temperature, elasticity, and capillary response). The defect sizes ranged from 4 cm × 2 cm to 20 cm × 6 cm.The 18 adjustable external fixators were dismantled in 2 to 9 days (mean, 4.05 days) after the operation, and the defects were completely closed and the sutures were removed after 2 to 3 weeks. The average VAS score was 5.97. The follow-up period was 4 to 12 months (mean, 6.3 months); 17 patients healed well with linear small scar, and no infections or patients of necrosis were observed. Sensory recovery was assessed using the Medical Research Council scale, and all the sensation scores were S3+. Eight patients were healed after the first stage. Nine patients were closed totally while small sinus or skin defect were observed after sutures were removed; 3 patients were healed after the second debridement, and 6 patients finally healed after the dressings were changed. Patellar osteomyelitis recurred in 1 patient who was transferred to the Orthopedic Department for further treatment, and a flap graft procedure was performed.The operation was simple and obviously reduced the course of the disease, the costs, and the damage to the donor site, and it is also significantly superior to skin graft or flap transplantation procedures in terms of the resulting skin sensation, color, texture, elasticity, and appearance.

Cas4 Nucleases Can Effect Specific Integration of CRISPR Spacers.

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems incorporate short DNA fragments from invasive genetic elements into host CRISPR arrays in order to generate host immunity. Recently, we demonstrated that the Csa3a regulator protein triggers CCN protospacer-adjacent motif (PAM)-dependent CRISPR spacer acquisition in the subtype I-A CRISPR-Cas system of Sulfolobus islandicus However, the mechanisms underlying specific protospacer selection and spacer insertion remained unclear. Here, we demonstrate that two Cas4 family proteins (Cas4 and Csa1) have essential roles (i) in recognizing the 5' PAM and 3' nucleotide motif of protospacers and (ii) in determining both the spacer length and its orientation. Furthermore, we identify amino acid residues of the Cas4 proteins that facilitate these functions. Overexpression of the Cas4 and Csa1 proteins, and also that of an archaeal virus-encoded Cas4 protein, resulted in strongly reduced adaptation efficiency, and the former proteins yielded a high incidence of PAM-dependent atypical spacer integration or of PAM-independent spacer integration. We further demonstrated that in plasmid challenge experiments, overexpressed Cas4-mediated defective spacer acquisition in turn potentially enabled targeted DNA to escape subtype I-A CRISPR-Cas interference. In summary, these results define the specific involvement of diverse Cas4 proteins in in vivo CRISPR spacer acquisition. Furthermore, we provide support for an anti-CRISPR role for virus-encoded Cas4 proteins that involves compromising CRISPR-Cas interference activity by hindering spacer acquisition.IMPORTANCE The Cas4 family endonuclease is an essential component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. The CrenarchaeotaSulfolobus islandicus REY15A carries two cas4 genes (cas4 and csa1) linked to the CRISPR arrays. Here, we demonstrate that Cas4 and Csa1 are essential to CRISPR spacer acquisition in this organism. Both proteins specify the upstream and downstream conserved nucleotide motifs of the protospacers and define the spacer length and orientation in the acquisition process. Conserved amino acid residues, in addition to those recently reported, were identified to be important for these functions. More importantly, overexpression of the Sulfolobus viral Cas4 abolished spacer acquisition, providing support for an anti-CRISPR role for virus-encoded Cas4 proteins that inhibit spacer acquisition.

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin.

Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin.