Involvement of PD-1+CD4+ T cells in the development of traumatic tracheal stenosis by regulating the IL-17/STAT3 pathway

Studies have highlighted an upregulation of PD-1 expression in CD4+ T cells, which accelerates lung fibrosis by activating the IL-17/STAT3 pathway, leading to IL-17A and TGF-β1 secretion. However, the relation with traumatic tracheal stenosis (TS) remains unexplored. Our analysis found significant increases in PD-1+CD4+ T cells, IL-17A, and TGF-β1 in the TS patients (n = 10). The cellular model used CD4+ T cells co-cultured with bronchial fibroblasts while the animal model used a nylon brush to scrape the damaged tracheal mucosa. Interventions with PD-1 and STAT3 inhibitors both in vivo (n = 5) and in vitro (n = 6) showed decreased expression of TGF-β1 and IL-17A in CD4+ T cells, decreased collagen I synthesis in vivo, and reduced tractal fibrosis in vitro. Furthermore, PD-1's modulation of the STAT3 was evident. This research unveils PD-1+CD4+ T cells' role in TS, thus suggesting a novel immunotherapeutic strategy to counteract tracheal fibrosis.

COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

Infant gut DNA bacteriophage strain persistence during the first 3 years of life

Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

Deep-branching evolutionary intermediates reveal structural origins of form I rubisco

The enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the majority of biological carbon fixation on Earth. Although the vast majority of rubiscos across the tree of life assemble as homo-oligomers, the globally predominant form I enzyme-found in plants, algae, and cyanobacteria-forms a unique hetero-oligomeric complex. The recent discovery of a homo-oligomeric sister group to form I rubisco (named form I') has filled a key gap in our understanding of the enigmatic origins of the form I clade. However, to elucidate the series of molecular events leading to the evolution of form I rubisco, we must examine more distantly related sibling clades to contextualize the molecular features distinguishing form I and form I' rubiscos. Here, we present a comparative structural study retracing the evolutionary history of rubisco that reveals a complex structural trajectory leading to the ultimate hetero-oligomerization of the form I clade. We structurally characterize the oligomeric states of deep-branching form Iα and I'' rubiscos recently discovered from metagenomes, which represent key evolutionary intermediates preceding the form I clade. We further solve the structure of form I'' rubisco, revealing the molecular determinants that likely primed the enzyme core for the transition from a homo-oligomer to a hetero-oligomer. Our findings yield new insight into the evolutionary trajectory underpinning the adoption and entrenchment of the prevalent assembly of form I rubisco, providing additional context when viewing the enzyme family through the broader lens of protein evolution.

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and a TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12s. In eukaryotes, TnpB homologs occur as two distinct types, Fanzor1s and Fanzor2s. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, which revealed that both Fanzor1s and Fanzor2s stem from a single lineage of IS607 TnpBs with unusual active site arrangement. The widespread nature of Fanzors implies that the properties of this particular lineage of IS607 TnpBs were particularly suited to adaptation in eukaryotes. Biochemical analysis of an IS607 TnpB and Fanzor1s revealed common strategies employed by TnpBs and Fanzors to co-evolve with their cognate transposases. Collectively, our results provide a new model of sequential evolution from IS607 TnpBs to Fanzor2s, and Fanzor2s to Fanzor1s that details how genes of prokaryotic origin evolve to give rise to new protein families in eukaryotes.

Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria

IMPORTANCE

Here, we profiled putative phages of Saccharibacteria, which are of particular importance as Saccharibacteria influence some human oral diseases. We additionally profiled putative phages of Gracilibacteria and Absconditabacteria, two Candidate Phyla Radiation (CPR) lineages of interest given their use of an alternative genetic code. Among the phages identified in this study, some are targeted by spacers from both CPR and non-CPR bacteria and others by both bacteria that use the standard genetic code as well as bacteria that use an alternative genetic code. These findings represent new insights into possible phage replication strategies and have relevance for phage therapies that seek to manipulate microbiomes containing CPR bacteria.

[Prevalence and influencing factors of abnormal spinal curvature in primary and secondary school students in Shandong Province in 2020]

In 2020, the prevalence of abnormal spinal curvature among 54 079 students in Shandong Province was 1.54%. The multivariate logistic regression model analysis showed that, compared with those in primary school, economically underdeveloped areas, and non-residential schools, students in middle and high schools, economically average areas, and residential schools had a higher risk of abnormal spinal curvature, with OR (95%CI) values of 2.029 (1.662-2.476), 2.746 (2.208-3.416), 2.237 (1.740-2.875) and 2.057 (1.705-2.483), respectively. Compared with those in economically underdeveloped areas, who were underweight, who had seat adjustments≤1 time per academic year, and who had physical education classes≤1 per week, students in economically developed areas, who were normal weight, overweight, and obese, who had seat adjustments≥2 times per academic year, and who had physical education classes 2-3 or≥4 per week, had a lower risk of abnormal spinal curvature, with OR (95%CI) values of 0.690 (0.521-0.915), 0.722 (0.546-0.955), 0.535 (0.389-0.735), 0.383 (0.274-0.535), 0.835 (0.711-0.980), 0.561 (0.474-0.663) and 0.491 (0.315-0.766), respectively.

Correlation between nocturnal intermittent hypoxemia and mild cognitive impairment in the older adult and the role of BDNF Val66Met polymorphism: a hospital-based cross-sectional study

PURPOSE

To explore the prevalence of nocturnal intermittent hypoxemia (NIH) in a tertiary hospital geriatric department and the relationship between NIH and mild cognitive impairment (MCI) in older adults, and to examine the role of brain-derived neurotrophic factor (BDNF) Val66Met polymorphism.

METHODS

Older adults aged ≥ 60 were enrolled. NIH and cognitive assessments were conducted. BDNF concentrations and BDNF Val66Met polymorphism were detected for a preliminary exploration of the possible mechanism of the process.

RESULTS

Of 325 older adults enrolled, 157 (48%) had NIH and were further divided into mild, moderate, and severe NIH groups according to their oxygen desaturation of ≥ 4% per hour of sleep (ODI4). MCI detection rate in the four groups gradually increased, and the differences were statistically significant (chi-square = 4.457, P = 0.035). ODI4 was negatively correlated with MoCA score in all participants (r =  - 0.115, P = 0.039) and patients with NIH (r =  - 0.199, P = 0.012). After adjusting for sex, age, and cardiovascular risk factors, NIH and MCI remained independently associated (OR = 3.13, 95% CI 1.03-9.53, P = 0.045). BDNF levels were positively correlated with MoCA score (r = 0.169, P = 0.028) and negatively correlated with nocturnal average oxygen saturation in patients with NIH (r =  - 0.288, P = 0.008). Older adults with different BDNF Val66Met genotypes did not show significant differences in MCI rate and BDNF levels (P > 0.05).

CONCLUSION

The older adults with NIH have a higher MCI detection rate. BDNF levels may be a potential biomarker for cognitive dysfunction in patients with NIH.

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12. In eukaryotes and their viruses, TnpB homologs occur as two distinct types, Fanzor1 and Fanzor2. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, revealing that a clade of IS607 TnpBs with unusual active site arrangement found primarily in Cyanobacteriota likely gave rise to both types of Fanzors. The wide-spread nature of Fanzors imply that the properties of this particular group of IS607 TnpBs were particularly suited to adaptation and evolution in eukaryotes and their viruses. Experimental characterization of a prokaryotic IS607 TnpB and virally encoded Fanzor1s uncovered features that may have fostered coevolution between TnpBs/Fanzors and their cognate transposases. Our results provide insight into the evolutionary origins of a ubiquitous family of RNA-guided proteins that shows remarkable conservation across domains of life.

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.

O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters

The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S₂O₃^2-] via the complete Sox pathway coupled to O₂. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO₃^-, resulting in higher [S₂O₃^2-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.

[Clinical and pathological analysis of 35 cases of ocular adnexal solitary fibrous tumor]

Objective: To analyze the clinical and pathological characteristics and prognosis of 35 cases of solitary fibrous tumor of ocular adnexal (SFT). Methods: This was a retrospective case series study. The clinical data of 35 cases of ocular adnexal SFT was collected in Tianjin Eye Hospital from January 2000 to December 2020. The clinical manifestations, imaging examination results, pathological characteristics, treatment of patients were analyzed, and patients were followed up. All cases were classified according to the 2013 classification of World Health Organization of tumors of soft tissue and bone. Results: There were 21 males (60.0%) and 14 females (40.0%). The age range was 17 to 83 years, and the median age was 44 (35, 54)years. All patients were unilateral, with 23 (65.7%) in the right eye and 12 (34.3%) in the left eye. The course of disease ranged from 2 months to 11 years, with an a median duration of 12(6,36)months. Clinical manifestations included exophthalmos, limited eye movements, diplopia, and tearing. All patients underwent surgical treatment of complete resection of the tumor. Ocular adnexal SFT mostly occurred in the upper orbit (19 cases, 73.1%). On imaging examination, the tumor showed well-circumscribed space occupying lesion that heterogeneously enhanced with contrast, and abundant blood flow signals in the tumors. MRI showed isointensity or low signal on T1WI, and significantly enhanced on T2WI, presenting intermediate-to-high heterogeneous signals. The tumor diameter was 2.1 (1.5, 2.6) cm. There were 23 cases (65.7%) of classic subtype, 2 cases (5.7%) of giant cell subtype, 8 cases (22.9%) of myxoid subtype, and 2 cases (5.7%) of malignancy. Immunohistochemical staining showed that Vimentin, CD34 and STAT6 were positively expressed in all patients. Twenty-one cases (60.0%) showed positive expression of BCL-2, and Ki-67 positive index ranged from 1.0% to 10.0%. Tumors in this group were all low-risk according to the Demicco risk stratification. Follow-up was available for 25 patients with a duration of 2 years to 14 years and 7 months, and the median follow-up time was 88 (61, 124) months. Two patients relapsed, and no distant metastasis or death was observed. Conclusions: Ocular adnexal SFT mainly presents as a painless, slow-growing mass. And most of them are typical SFT. The imaging manifestations are varied Ocular adnexal SFT generally follows a benign course, with a good prognosis after complete excision. Recurrence could occur many years after surgery which requiring careful and long-term follow-up.

[Study on the reliability and validity of the Chinese Criteria of Health Scale for the elderly people]

Objective: To evaluate the reliability and validity of the Chinese Criteria of Health Scale for the elderly people. Methods: A cross-sectional study was performed among older adults of Meiyuan Community in Haidian District, Beijing and Nanwangkong Village in Qingzhou City,Shandong Province during July 2021. Using a cluster sampling method, totally 667 elderly people were investigated by face-to-face interview, using the scale which was formulated after two rounds of the Delphi method and pilot study. The overall scale includes physical health, mental health and social health subscales, including 9, 52 and 15 items, respectively. Four weeks after the survey, 56 elderly people were randomly selected and repeated the survey with the same method. The test-retest reliability, split-half reliability and internal consistency reliability of the scale were evaluated, and the validity was evaluated at the same time, including construct validity and content validity. Results: A total of 710 questionnaires were distributed and 667 valid questionnaires were obtained, with a total effective rate of 93.94%. The score of the overall scale was 79.79±16.22, the scores of the physical health, mental health, social health sub-scores were 41.64±9.76, 26.82±3.92 and 11.34±5.19, respectively. The scale had excellent reliability. In the test-retest reliability, the intraclass correlation coefficient (ICC) of the overall scale and each subscale were 0.766-0.861, and the weighted Kappa values were 0.762-0.817. The Spearman-Brown coefficient of the overall scale and each subscale in the split-half reliability were 0.722-0.855 (all P<0.001). The Cronbach's α coefficients of the overall scale of internal consistency reliability and each subscale were 0.748-0.899, and the Cronbach's α coefficients of each dimension were from 0.709 to 0.963(all P<0.001). At the same time, the scale had good construct validity and content validity. The correlation coefficients between the score of each dimension and its sub-scale were larger, from 0.641 to 0.873 (all P<0.05). The cumulative variance contribution rates of the scale and three subscales were all more than 50% of the approved standard. A total of 11 common factors were extracted, and all the load values of each item on the corresponding factors were ≥0.04. Conclusion: The Chinese Criteria of Health Scale for the elderly people has good validity and excellent reliability. It can be used as a basis for the scientific division of the health status of the elderly, the formulation of relevant policies by the government and the provision of appropriate health services for the elderly.

Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication

The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins, and some hypothetical proteins. Based on CRISPR spacer targeting, the predominance of bacterial taxonomic affiliations of phage genes with those from Bacteroidetes, and the high sequence similarity of the phage bS21 genes and those from Bacteroidetes classes of Flavobacteriia, Cytophagia and Saprospiria, these phages are predicted to infect diverse Bacteroidetes species that inhabit a range of depths in freshwater lakes. Thus, bS21 phages have the potential to impact microbial community composition and carbon turnover in lake ecosystems. The transcriptionally active bS21-encoding phages were likely in the late stage of replication when collected, as core structural genes and bS21 were highly expressed. Thus, our analyses suggest that the phage bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects preferentially for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.

[Research advances of real world study in the field of chronic wound]

In recent years, as a powerful supplement to the randomized controlled trial (RCT), real world study (RWS) has received more and more attention. However, in the field of chronic wounds, most of the patients have complex condition, and the strict inclusion and exclusion criteria of RCT were lack of practical application values. The RWS provides data closer to the real medical environment in clinical medical practice, drug and medical device supervision, and health technology evaluation. However, RWS has some problems that need to be resolved, such as inconsistent diagnostic criteria and unclear research endpoints. In addition, RWS in chronic wound research in China seems to have not really started yet, and institutions at all levels need to work together to promote the development of RWS.

Detection and enumeration of Lak megaphages in microbiome samples by endpoint and quantitative PCR

Lak megaphages are prevalent across diverse gut microbiomes and may potentially impact animal and human health through lysis of Prevotella. Given their large genome size (up to 660 kbp), Lak megaphages are difficult to culture, and their identification relies on molecular techniques. Here, we present optimized protocols for identifying Lak phages in various microbiome samples, including procedures for DNA extraction, followed by detection and quantification of genes encoding Lak structural proteins using diagnostic endpoint and SYBR green-based quantitative PCR, respectively.

For complete details on the use and execution of this protocol, please refer to Crisci et al., (2021).

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Optimized DNA extraction procedure for use with various microbiome samples

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Amplification of Lak phage structural protein genes for detection and sequencing

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Quantification of major capsid protein genes to estimate Lak phage abundance

[Relationship between nutritional factors and clinical outcome in children with tuberculous meningitis]

Objective: To investigate the relationship between nutritional risk status and clinical outcome in children with tuberculous meningitis (TBM). Methods: The clinical data (basic information, clinical symptoms and laboratory test results) of 112 patients with TBM, who were admitted to Department of Pediatric Infectious Diseases of West China Second Hospital of Sichuan University,from January 2013 to December 2020 were retrospectively analyzed. The patients were divided into the nutritional risk group and the non-nutritional risk group according to the assessment of the nutritional risk by the STRONGkids Scale. The variables of basic information, clinical symptoms and laboratory test measurements etc. were compared between the two groups by using Student t test, Rank sum test or Chi-square test. Multivariate Logistic regression analysis were used to analyze nutritional risk factors. Results: Among 112 patient with TBM, 55 were males and 57 females. There were 62 cases in the nutritional risk group and 50 cases in the non-nutritional risk group. The proportion of cases with nutritional risk was 55.4% (62/112). Patients in the nutritional risk who lived in rural areas, had symptoms of brain nerve damage, convulsions, emaciation and anorexia, with a diagnosis time of ≥21 days, and the level of cerebrospinal fluid (CSF) protein were all higher than those in the non-nutritional risk group ((50 cases (80.6%) vs. 32 cases (64.0%), 20 cases (32.3%) vs.8 cases (16.0%), 33 cases (53.2%) vs. 15 cases (30.0%), 30 cases (48.4%) vs. 2 cases (4.0%), 59 cases (95.2%) vs. 1 case (2.0%),41 cases (66.1%) vs.18 cases (36.0%), 1 406 (1 079, 2 068) vs. 929 (683, 1 208) mg/L, χ²=3.91, 3.90, 6.10, 26.72, 98.58, 10.08, Z=4.35, all P<0.05). The levels of serum albumin,hemoglobin,lymphocyte count, white blood cell count, and CSF glucose were significantly lower in patients with nutritional risk ((36±5) vs. (41±4) g/L, (110±17) vs. (122±14) g/L, 1.4 (1.0, 2.0)vs. 2.3 (1.6, 3.8)×10⁹/L, 7.8 (6.3, 10.0)×10⁹ vs. 10.0 (8.3, 12.8)×10⁹/L, 1.0 (0.8, 1.6) vs. 2.1 (1.3, 2.5) mmol/L, t=-6.15, -4.22, Z=-4.86, -3.92, -4.16, all P<0.05).Increased levels of serum albumin (OR=0.812, 95%CI:0.705-0.935, P=0.004) and lymphocyte count (OR=0.609, 95%CI:0.383-0.970, P=0.037) may reduce the nutritional risk of children with TBM; while convulsions (OR=3.853, 95%CI:1.116-13.308, P=0.033) and increased level of CSF protein (OR=1.001,95%CI:1.000-1.002, P=0.015) may increase the nutritional risk of children with TBM. Similarly, the rate of complications and drug-induced liver injury was higher in the nutritional risk group (47 cases (75.8%) vs. 15 cases(30.0%), 31 cases (50.0%) vs.8 cases (16.0%), χ²=23.50, 14.10, all P<0.05). Moreover, the length of hospital stay was also longer in the nutritional risk group ((27±13) vs. (18±7) d, t=4.38, P<0.05). Conclusions: Children with TBM have a high incidence of nutritional risk. Convulsive, the level of serum albumin, the level of lymphocyte count and CSF protein may affect the nutritional risk of children with TBM. The nutritional risk group has a high incidence of complications and heavy economic burden.It is necessary to carry out nutritional screening and nutritional support for children with TBM as early as possible.

Alum Addition Triggers Hypoxia in an Engineered Pit Lake

Here, we examine the geobiological response to a whole-lake alum (aluminum sulfate) treatment (2016) of Base Mine Lake (BML), the first pilot-scale pit lake established in the Alberta oil sands region. The rationale for trialing this management amendment was based on its successful use to reduce internal phosphorus loading to eutrophying lakes. Modest increases in water cap epilimnetic oxygen concentrations, associated with increased Secchi depths and chlorophyll-a concentrations, were co-incident with anoxic waters immediately above the fluid fine tailings (FFT) layer post alum. Decreased water cap nitrate and detectable sulfide concentrations, as well as increased hypolimnetic phospholipid fatty acid abundances, signaled greater anaerobic heterotrophic activity. Shifts in microbial community to groups associated with greater organic carbon degradation (i.e., SAR11-LD12 subclade) and the SRB group Desulfuromonodales emerged post alum and the loss of specialist groups associated with carbon-limited, ammonia-rich restricted niches (i.e., MBAE14) also occurred. Alum treatment resulted in additional oxygen consumption associated with increased autochthonous carbon production, watercap anoxia and sulfide generation, which further exacerbate oxygen consumption associated with on-going FFT mobilized reductants. The results illustrate the importance of understanding the broader biogeochemical implications of adaptive management interventions to avoid unanticipated outcomes that pose greater risks and improve tailings reclamation for oil sands operations and, more broadly, the global mining sector.

[Relationships between lead-induced learning and memory impairments and gut microbiota disturbance in mice]

Objective: To explore the effect of lead exposure on the neurobehavior and gut microbiota community structure in mice. Methods: In August 2019, 64 C57BL/6 mice were randomly divided into 4 groups: control group (0 ppm) , low lead exposure group (20 mg/l) , medium lead exposure group (100 mg/l) and high lead exposure group (500 mg/l) . During the experiment, they were free to eat and drink. The drinking water of the lead exposure group was mixed with lead acetate, and sodium acetate was added in the control group. After 10 weeks of exposure, the Morris water maze was used to test the learning and memory ability of each group of mice, and then they were sacrificed for sampling. ICP-MS was used to detect lead content in whole blood and brain tissue. ELISA was used to determine the level of IL-1β in mouse serum. 16S rRNA sequencing was used to detect the structural diversity of the intestinal flora in feces, and then the correlation between the flora and behavior indicators was analyzed. Results: In the Morris water maze experiment, compared with the control group, there was no significant difference in the body weight and swimming speed of the mice in the lead exposure groups. The escape latency of the mice in the 100 mg/l and 500 mg/l dose groups was prolonged, and the number of platform crossings decreased (P<0.05) ; meanwhile, the staying time of the mice in the 500 mg/l Pb-treated group in the target quadrant was lower than that of the control group, and the difference was statistically significant (P<0.05) . Compared with the control group, the blood lead content of the mice in each lead exposure group was significantly increased, and the brain lead content of mice in the 500 mg/l dose group was significantly elevated (P<0.05) . The serum IL-1β levels of mice in each lead exposure group were higher than those of the control group (P<0.05) . At the phylum level, the relative abundance of the Proteobacteria phylum in all of Pb-treated groups was significantly increased (P<0.05) ; at the genus level, Allobaculum, Desulfovibrio, Lachnospiraceae_NK4A136_group, Turicibacter and Ureaplasma were significantly increased (P<0.05) . Among them. The relative abundance of Desuffaoibrio, Turici bacter, and Ureaplasma was negatively correlated with the residence time of mice in the quadrant of the platform (r=-0.32, -0.29, -0.44, P<0.05) . Conclusion: Lead exposure induced learning and memory impairments in mice, which may be related to the disturbance of the gut microbiota.

[Mental health status and its influencing factors of nurses in geriatric department after workplace violence]

Objective: To investigate the mental health status and influencing factors of geriatric nurses after workplace violence. Methods: From February 2019 to January 2020, 102 geriatric nurses who suffered workplace violence in three hospitals in Shaoxing were collected as the observation group and 100 geriatric nurses who did not suffer workplace violence in the same period as the control group. The general data of nurses in the two groups were investigated, the workplace violence was investigated with the hospital workplace violence questionnaire, the mental disorders and mental diseases were investigated with the symptom checklist 90 (SCL-90) , the symptoms of post-traumatic stress disorder were investigated with the symptom checklist of post-traumatic stress disorder (pcl-c) , and the psychological elasticity was investigated with the psychological elasticity scale, Social support was investigated with social support scale (SSRs) . Results: The total average score of symptom checklist 90 (SCL-90) of nurses with workplace violence was (1.49 ± 0.48) . Compared with the control group, the total average score of SCL-90, somatization, obsessive-compulsive symptoms, depression, anxiety and fear factors in the observation group were significantly increased (P<0.05) . The total score of post-traumatic stress disorder symptom list (pcl-c) in the observation group was (34.51±9.87) . Compared with the control group, the total average score of pcl-c, re experience, avoidance and vigilance factors in the observation group were significantly increased (P<0.05) . The total average score of SCL-90 of nurses with workplace violence was positively correlated with psychological elasticity and social support (P<0.05) . Multivariate linear analysis showed that psychological elasticity, tenacity and control, optimism, social support and subjective support were the main factors affecting nurses＇mental health. Conclusion: Geriatric nurses suffering from workplace violence are prone to mental health problems and post-traumatic stress disorder, which should be improved by improving their psychological elasticity and social support.

Closely related Lak megaphages replicate in the microbiomes of diverse animals

Lak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-Western diet, baboons, and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic polymerase chain reaction and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation.

[Clinical and pathological analysis of ocular adnexal diffuse large B-cell lymphoma]

Objective: To summarize the clinical and pathological characteristics of diffuse large B-cell lymphoma of ocular adnexal (OA-DLBCL). Methods: A retrospective case series study. Twenty-three cases of OA-DLBCL were collected in Tianjin Eye Hospital from January 2005 to December 2018. The clinical manifestations and imaging examination results were analyzed. The pathological characteristics and immune subtypes were analyzed with hematoxylin and eosin staining and immunohistochemistry. Eighteen patients completed the follow-up. Overall survival (OS) time was from the date of diagnosis to the date of death or the final follow-up (April 30, 2020). Clinical stages were analyzed by the Ann Arbor classification; Kaplan-Meier plots were used to visualize survival outcomes. The different risk groups were compared using Log-rank test. Results: There were 13 males and 10 females. The median age was 65 years (range, 43 to 82 years). Twenty-two patients had unilateral lymphoma (14 left eyes, 8 right eyes), and one patient had bilateral lymphoma. The OA-DLBCL was in the orbit in 14 patients, in the lacrimal gland in two patients, in both the lacrimal gland and the orbit in three patients, in both the lacrimal sac and the orbit in one patient, in the conjunctiva in one patient, in both the conjunctiva and the orbit in one patient, and in the skin of eyelids in one patient. Imaging examinations showed the tumors were of irregular soft tissue density. MRI showed the tumors were close to the extraocular muscles or ectocinerea. Centroblastic morphology was present in 21 specimens, and 2 specimens had immunoblastic morphology. Six patients were of germinal center B cell-like (GCB) type, and 17 were of non-GCB type. There were 2 patients with double expression of cellular-myelocytomatosis viral oncogene and B-cell lymphoma 2. The follow-up time ranged from 25 to 156 months, and the median follow-up time was 48 months. Five of them had primary OA-DLBCL, and 13 patients had secondary OA-DLBCL. Five patients were at the Ann Arbor clinical stage ⅠE, one was at stage ⅢE, and 12 were at stage ⅣE. During the follow-up, 8 patients survived, and 10 died. The 1-, 3-, and 5-year OS rates were 88.9%, 71.4% and 41.7%, respectively. Log-rank analysis indicated that the Ann Arbor clinical stage and age were related to the OS of OA-DLBCL (χ²=7.448, 8.804; both P<0.01). The gender, tumor size, molecular typing, Ki-67 index, and bone invasion were not related to the OS of OA-DLBCL (all P>0.05). Conclusions: OA-DLBCL mainly occurrs in the elderly population, unilaterally, and in the orbit. Most molecular types are non-GCB subtypes. The Ann Arbor clinical stage and age are associated with prognosis. (Chin J Ophthalmol, 2021, 57: 366-371).

Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

Optimal reference genes for real-time quantitative PCR and the expression of sigma factors in Acidithiobacillus caldus under various conditions

AIMS

Acidithiobacillus caldus is an important sulphur-oxidizing bacterium that plays crucial roles in the bioleaching industry. This study aims to analyse the optimal reference gene for real-time quantitative PCR (RT-qPCR) under different conditions and investigate the transcription levels of the sigma factor genes in the stress response.

METHODS AND RESULTS

We selected six housekeeping genes and analysed them via RT-qPCR using two energy resources, under four stress conditions. Three statistical approaches BestKeeper, geNorm, and NormFinder were utilized to determine transcription stability of these reference genes. The gapdH gene was the best internal control gene using elemental sulphur as an energy resource and under heat stress, map was the best internal control gene under pH and osmotic stress, era was the best internal control gene for the K₂ S₄ O₆ energy resource, and rpoC was the best internal control gene under Cu²⁺ stress. Furthermore, the expressional levels of 11 sigma factors were analysed by RT-qPCR in the stress response.

CONCLUSIONS

Stable internal control genes for RT-qPCR analysis of A. caldus were determined, and the expression patterns of sigma factor genes of A. caldus were investigated.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification of the optimal reference gene and analysis of transcription levels of sigma factors in A. caldus can provide clues for reference gene selection and the study of sigma factor function.

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

INTRODUCTION

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life.

RESULTS

Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

CONCLUSIONS

Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

[Assessment of computed tomographic angiographysinus development combined with occipitalbone marks for the location of transverse sigmoid sinus junction]

Objective: To introduce and evaluate a technique to precisely localize the transverse-sigmoid sinus junction (TSSJ) in retrosigmoid craniotomy. Methods: This was a single-center prospective randomized controlled study. Sixty-three patients, 29 male and 34 female, who would undergo retrosigmoid craniotomy admitted to Department of Neurosurgery, the First Affiliated Hospital of Xinjiang Medical Universityfrom March to October 2019 were enrolled in the study and were divided into trial group and control group according to the computer-generated random numbers. Preoperative venous computed tomographic angiography (CTA) combined with 3-dimensional computed tomography computed tomography (3D CT) was randomly given to the patients(n=32). Asterion was used for identification of the TSSJ in the controls (n=31). The main outcome measures as postoperative complications and relevant intraoperative indicators were compared. Results: Incision length, craniotomy time, bone window sizein trial group were shorter or smaller than those of the controls, as(6.8±0.5) cm vs (8.0±1.5) cm, (37±8) min vs (45±15) min, (8.7±1.2) cm(2) vs (10.2±2.4) cm(2) respectively, with statistical significance (all P<0.05). No statistical significance was found in bleeding amount, incidence of sinus injury and cerebrospinal fluid leakage. While incidence of neck pain was lower in case group (15.63% vs 38.71%; P=0.04) and the remission time of incisional pain in case group was shorter [(6±1) d vs (9±2) d; P=0.01]. Conclusion: While the technique is used, the center of the keyhole should be located at transitional place of the lateral part of the occipitomastoid suture, the retromastoid ridge and the superior nuchal line. Compared with the traditional craniotomy method marked by asterion, it has great advantages in reducing incidence of postoperative complications, craniotomy time, and the remission time of incisional pain.

Large freshwater phages with the potential to augment aerobic methane oxidation

There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

PI3K/Akt and ERK1/2 pathways are responsible for sodium butyrateinduced inhibition of neuronal apoptosis in rats with cerebral infarction

The aim of this study was to elucidate the neuronal protection effect of sodium butyrate (NaB) on neuronal apoptosis in rats with cerebral infarction (CI), and the involvement of the phosphatidilinositol 3-kinase/protein kinase B (PI3K/Akt) and extracellular-signal-regulated kinase 1/2 (ERK1/2) pathways. MI model in rats was performed by middle cerebral artery occlusion (MCAO). Three hours after reperfusion, gastric administration of 5 or 10 mg/kg NaB was performed. Neurological deficit score, infarct size and brain edema were evaluated in rats after 24 h of reperfusion. Enzyme-linked immunosorbent assay (ELISA) was conducted to determine contents of oxidative stress factors. Lactate dehydrogenase (LDH) activity, cell viability and apoptosis in extracted neurons were determined. Moreover, expression levels of Bcl-2, Bax, Akt and ERK1/2 were examined. NaB treatment markedly reduced infarct size and brain edema content in CI rats, and NaB treatment improved viability, decreased LDH activity and reversed contents of malondialdehyde (MDA) and superoxide dismutase (SOD) in a dose-dependent manner. In addition, NaB treatment dose-dependently reduced apoptotic rate and Bax level, as well as enhanced Bcl-2 level. Protein levels of Akt and ERK1/2 were markedly upregulated in NaB-treated neurons. NaB treatment alleviates neuronal apoptosis via the PI3K/Akt and ERK1/2 pathways in CI rats, thus protecting the deterioration of CI.

Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog

Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

Clades of huge phages from across Earth's ecosystems

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO₂-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria.IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.

Soliton superlattices in twisted hexagonal boron nitride

Properties of atomic van der Waals heterostructures are profoundly influenced by interlayer coupling, which critically depends on stacking of the proximal layers. Rotational misalignment or lattice mismatch of the layers gives rise to a periodic modulation of the stacking, the moiré superlattice. Provided the superlattice period extends over many unit cells, the coupled layers undergo lattice relaxation, leading to the concentration of strain at line defects - solitons - separating large area commensurate domains. We visualize such long-range periodic superstructures in thin crystals of hexagonal boron nitride using atomic-force microscopy and nano-infrared spectroscopy. The solitons form sub-surface hexagonal networks with periods of a few hundred nanometers. We analyze the topography and infrared contrast of these networks to obtain spatial distribution of local strain and its effect on the infrared-active phonons of hBN.

[The clinicopathological features and HPV detection of conjunctival actinic keratosis]

Objective: To describe the clinicopathological features of conjunctival actinic keratosis (AK) and relation to the infection of human papillomavirus (HPV). Method: Retrospective case series study. Eighteen cases (18 eyes) of conjunctival AK were obtained in Tianjin Eye Hospital and Institute (2005-2018). The clinical and histopathological features were studied. HPV was detected by a modified general primer HPV polymerase chain reaction (PCR) system in all formalin-fixed, paraffin-embedded specimens. Results: The male to female ratio was 5∶1. The mean age at diagnosis was 60 years (range: 43-79 years). Sixteen cases were located in the nasal interpalpebral region, and two cases were located in the temporal interpalpebral region. All cases were located in corneal limbus, and the mean distance of corneal invasion was 2 mm (range, 1-4 mm). The mean diameter was 4.6 mm (range, 2.0-8.0 mm). Clinically, most lesions (16 cases) appeared as a white or milky, flat plaque with clear borderline and conjunctival hyperemia; a few lesions (2 cases) showed a brown-black mass, partially white. Pathologically, conjunctival AK was a proliferation of epithelium with prominent parakeratosis or hyperkeratosis, stratum spinosm thickening and basal cell proliferation. Many AKs show solar elastosis and a mild inflammatory infiltrate of lymphocytes and plasma cells in the stroma. Most lesions (15 cases) were hypertrophic type, two cases were pigmented type, and one case was acantholytic type. HPV was negative in 18 cases. All case were removed by complete surgical excision. The rage of follow-up period was 1.0-10.4 years, ten cases were recorded, and no case recurred after surgical excision. Conclusions: Conjunctival AK is epithelial precancerous lesion that occurs in the keratoconjunctival margin. HPV infection might not be a causative factor in conjunctival AK. (Chin J Ophthalmol, 2019, 55: 531-535).

[Mid-to-long term outcomes and influence factors of postoperative concurrent chronic ankle instability and posterior ankle impingement]

OBJECTIVE

To investigate the mid-to-long-term efficacy of patients with chronic ankle instability combined with posterior impingement syndrome after 3-9 years of follow-up, and to analyze the influencing factors.

METHODS

From February 2010 to December 2015, 46 patients underwent concurrent lateral ankle ligament repair with posterior ankle arthroscopic surgery at the Institute of Sports Medicine, Peking University Third Hospital. The patient was first placed in a prone position and underwent arthroscopic debridement for the posterior impingement. After finishing the posterior arthroscopy, the surgeon and assistants first translated the patient to the affected side, then turned to the healthy side, and changed the position to the supine position. During the turning over, another assistant held the arthroscope and the instrument to ensure that it was sterile and could be used without replacement. The anterior ankle arthroscopy was operated if necessary and the lateral ankle ligament repair was anatomic repaired with anchors. The 42 patients were followed up, including 26 males and 16 females. The average age was (28.9±10.0) years. The patient's clinical symptoms, joint stability, mobility and motor function were compared by questionnaire and physical examination. The preoperative and postoperative visual analogue scale (VAS) scores, American Orthopaedic Foot and Ankle Society (AOFAS) scores, Tegner scores were compared, and the clinical scores and the patient age, gender, height and weight were compared. The correlations between body mass index (BMI), preoperative duration, surgery duration, and cartilage injury were analyzed.

RESULTS

The mean follow-up time was (71.8±22.8) months. The postoperative VAS scores (1.0 vs. 5.0, P<0.001), AOFAS scores (92 vs. 80, P<0.001), and Tegner scores (6.5 vs. 2, P<0.001) were significantly superior to the preoperative levels. The excellent and good rate was 97.6%. The postoperative VAS score (t=2.719, P=0.10), AOFAS score (t=-2.853, P=0.10), Tegner score (t=-3.443, P=0.001) and time to return exercise (t=2.814, P=0.008) were negatively correlated with the patient age, and the postoperative VAS score was negatively correlated with cartilage injury (Z=-2.195, P=0.028).

CONCLUSION

The mid-to-long-term clinical outcomes of the chronic ankle ligament instability combined with the posterior impingement were good. The age of the patients was negatively correlated with the clinical outcome. The combined cartilage injury could aggravate the postoperative pain.

Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems

The Candidate Phyla Radiation (CPR) comprises a huge group of bacteria that have small genomes that rarely encode CRISPR-Cas systems for phage defense. Consequently, questions remain about their mechanisms of phage resistance and the nature of phage that infect them. The compact CRISPR-CasY system (Cas12d) with potential value in genome editing was first discovered in these organisms. Relatively few CasY sequences have been reported to date, and little is known about the function and activity of these systems in the natural environment. Here, we conducted a genome-resolved metagenomic investigation of hot spring microbiomes and recovered CRISPR systems mostly from Roizmanbacteria that involve CasY proteins that are divergent from published sequences. Within population diversity in the spacer set indicates current in situ diversification of most of the loci. In addition to CasY, some Roizmanbacteria genomes also encode large type I-B and/or III-A systems that, based on spacer targeting, are used in phage defense. CRISPR targeting identified three phage represented by complete genomes and a prophage, which are the first reported for bacteria of the Microgenomates superphylum. Interestingly, one phage encodes a Cas4-like protein, a scenario that has been suggested to drive acquisition of self-targeting spacers. Consistent with this, the Roizmanbacteria population that it infects has a CRISPR locus that includes self-targeting spacers and a fragmented CasY gene (fCasY). Despite gene fragmentation, the PAM sequence is the same as that of other CasY reported in this study. Fragmentation of CasY may avoid the lethality of self-targeting spacers. However, the spacers may still have some biological role, possibly in genome regulation. The findings expand our understanding of CasY diversity, and more broadly, CRISPR-Cas systems and phage of CPR bacteria.

[New opportunity of management strategy of diagnosis and treatment of chronic wound: emerging technology]

Along with the development of society and the change of disease spectrum, chronic wound is gradually becoming the core of burn and plastic surgery field. Although there have been some progresses in the diagnosis and treatment technology, the management strategy of chronic wound is still in the traditional mode stage. The development of internet of things, cloud computing, big data, artificial intelligence, and other emerging technologies is changing with each passing day, and they have rapidly penetrated into the health care field. To explore the application prospect of emerging technology in the diagnosis and treatment management of chronic wound and to plan its strategy and mode in the diagnosis and treatment of chronic wound can further promote development of discipline of burns.

Discordance Between Resident and Active Bacterioplankton in Free-Living and Particle-Associated Communities in Estuary Ecosystem

Bacterioplankton are the major driving force for biogeochemical cycles in estuarine ecosystems, but the communities that mediate these processes are largely unexplored. We sampled in the Pearl River Estuary (PRE) to examine potential differences in the taxonomic composition of resident (DNA-based) and active (RNA-based) bacterioplankton communities in free-living and particle-associated fractions. MiSeq sequencing data showed that the overall bacterial diversity in particle-associated fractions was higher than in free-living communities. Further in-depth analyses of the sequences revealed a positive correlation between resident and active bacterioplankton communities for the particle-associated fraction but not in the free-living fraction. However, a large overlapping of OTUs between free-living and particle-associated communities in PRE suggested that the two fractions may be actively exchanged. We also observed that the positive correlation between resident and active communities is more prominent among the abundant OTUs (relative abundance > 0.2%). Further, the results from the present study indicated that low-abundance bacterioplankton make an important contribution towards the metabolic activity in PRE.

[Clinical characteristics and renal uric acid excretion in early-onset gout patients]

Objective: To investigate clinical characteristics and renal uric acid excretion in early-onset gout patients. Methods: Consecutive inpatients with primary gout were recruited between 2013 and 2017. The patients with gout onset younger than 30 were defined as early-onset group while the others were enrolled as control group. Clinical characteristics and uric acid (UA) indicators were compared between two groups. Results: Among 202 recruited patients, the early-onset group included 36 patients (17.8%). Compared with control group, the early-onset group presented more patients with obesity [13 patients (36.1%) vs. 22 patients (13.3%), P<0.05], significantly higher serum UA level [(634±124)μmol/L vs.(527±169)μmol/L] and glomerular load of UA[(7.2±2.8)mg·min(-1)·1.73m(-2) vs. (4.4±2.2)mg·min(-1)·1.73m(-2)] and estimated glomerular filtration rate (GFR) [(83±21)ml·min(-1)·1.73m(-2) vs. (67±21)ml·min(-1)·1.73m(-2)] (all P<0.05), lower fractional excretion of UA [4.4% (3.4%,6.1%) vs. 7.2% (5.2%,9.6%),P<0.05], whereas 24h urinary UA excretion was comparable [(2 788±882)μmol/1.73m(2) vs. (2 645±1 140)μmol/1.73m(2), P=0.274]. Subgroup analysis of patients without chronic kidney disease showed significantly lower fractional excretion of UA in the early-onset group [4.5%(3.3%,6.1%) vs. 6.7% (5.1%,8.7%),P<0.05]. Logistic regression analysis showed that obesity (OR=3.25) and fractional excretion of UA less than 7% (OR=9.01, all P<0.05) were risk factors of gout early onset. Conclusion: The gout patients with early-onset younger than 30 present high serum and glomerular load of uric acid which might be due to obesity and relative under-excretion of renal uric acid.

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

Solvent-free nanofluid with three structure models based on the composition of a MWCNT/SiO2 core and its adsorption capacity of CO2

A series of core/shell nanoparticle organic/inorganic hybrid materials (NOHMs) with different weight ratios of two components, consisting of multi-walled carbon nanotubes (MWCNTs) and silicon dioxide (SiO₂) as the core were synthesized. The NOHMs display a liquid-like state in the absence of solvent at room temperature. Five NOHMs were categorized into three kinds of structure states based on different weight ratio of two components in the core, named the power strip model, the critical model and the collapse model. The capture capacities of these NOHMs for CO₂ were investigated at 298 K and CO₂ pressures ranging from 0 to 5 MPa. Compared with NOHMs having a neat MWCNT core, it was revealed that NOHMs with the power strip model show better adsorption capacity toward CO₂ due to its lower viscosity and more reactive groups that can react with CO₂. In addition, the capture capacities of NOHMs with the critical model were relatively worse than the neat MWCNT-based NOHM. The result is attributed to the aggregation of SiO₂ in these samples, which may cause the consumption and hindrance of reactive groups. However, the capture capacity of NOHMs with the collapse model was the worst of all the NOHMs, owing to its lowest content of reactive groups and hollow structure in MWCNTs. In addition, they presented non-interference of MWCNTs and SiO₂ without aggregation state.

[Study of the effects of three luteal phase supporting strategies on clinical outcomes of intrauterine insemination]

OBJECTIVE

To explore the effects of three luteal phase supporting strategies on clinical outcomes of intrauterine insemination (IUI).

METHODS

1 779 subjects who underwent IUI at the Center of Reproductive Medicine, Peking University Third Hospital from November 2014 to June 2015 were enrolled in this retrospectively study.According to the luteal phase supporting strategies, all the subjects were divided into three groups: subjects receiving Dydrogesterone were group A; subjects receiving oral micronized progesterone were group B; subjects receiving vaginal micronized progesterone were group C. The pregnancy outcomes, including clinical pregnancy rate, early miscarriage rate, biochemical pregnancy rate and ectopic pregnancy rate were compared in the three groups.

RESULTS

There was no significant difference in the three groups in constituent ratio, average IUI times, rate of the natural cycle, rate ofovulation cycle and dropout rate(P>0.05). Similarly, there was also no significant difference in pregnancy outcomes in all groups.Subsequent stratified analysis demonstrated that pregnancy outcomes in subjects of natural cycle and ovulation cycle still showed no significant difference(P>0.05).

CONCLUSION

Our study suggested that the effects of three luteal phase supporting strategies on clinical outcomes of IUI were similar.The medication in clinic should be individualized.

Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps

Results of this study showed that the bacterial composition in vagina (V) greatly differed from intrauterine microbiome (I). Microbiomes were present in all intrauterine samples of healthy women (Group H (I)) and patients with endometrial polyps (EP) (including Group EP (I) and Group EP/chronic endometritis (CE) (I)). Indeed, the intrauterine bacteria population in Group EP/CE (I) were more diverse than those in Groups EP (I) and H (I). The result also confirmed the bacterial composition differences between vagina and uterus as well as the intrauterine microbiome alteration in the patients, compared to the healthy. Although bacteria of Proteobacteria, Firmicutes and Actinobacteria, dominated the intrauterine microbiome in all samples, however, proportions of Firmicutes from Group EP/CE (I) and Group EP (I) were much higher than that from Group H (I), in contrast, the proportions of Proteobacteria were far lower than the healthy. At the genus level, compared to Group H (I), it is found that proportions of Lactobacillus, Gardnerella, Bifidobacterium, Streptococcus, and Alteromonas were significantly higher, and that of Pseudomonas were significantly lower in Group EP/CE (I) or Group EP (I). In addition, lower proportions of Enterobacter and Sphingomonas and a higher proportion of Prevotella were also observed in Group EP/CE (I). In conclusion, uterine microbiomes between patients with EP and the healthy are significantly different and all the potentially important variation of uterine microbes may cause EP, but not definitively related to CE. Further experiments should be performed to test these relationships to endometritis occurrence.

Comparison of antioxidant activities of different parts from snow chrysanthemum (Coreopsis tinctoria Nutt.) and identification of their natural antioxidants using high performance liquid chromatography coupled with diode array detection and mass spectrometry and 2,2'-azinobis(3-ethylbenzthiazoline-sulfonic acid)diammonium salt-based assay

Snow chrysanthemum (Coreopsis tinctoria Nutt.), a world-widely well-known flower tea material, has attracted more and more attention because of its beneficial health effects such as antioxidant activity and special flavor. In this study, a high performance liquid chromatography coupled with diode array detection and mass spectrometry (HPLC-DAD-MS) and 2,2'-azinobis(3-ethylbenzthiazoline-sulfonic acid)diammonium salt (ABTS) based assay was employed for comparison and identification of antioxidants in different samples of snow chrysanthemum. The results showed that snow chrysanthemum flowers possessed the highest while stems presented the lowest antioxidant capacities. Fourteen detected peaks with antioxidant activity were temporarily identified as 3,4',5,6,7-pentahydroxyflavanone-O-hexoside, chlorogenic acid, 2R-3',4',8-trihydroxyflavanone-7-O-glucoside, flavanomarein, flavanocorepsin, flavanokanin, quercetagitin-7-O-glucoside, 3',5,5',7-tetrahydroxyflavanone-O-hexoside, marein, maritimein, 1,3-dicaffeoylquinic acid, coreopsin, okanin and acetyl-marein by comparing their UV spectra, retention times and MS data with standards or literature data. Antioxidants existed in snow chrysanthemum are quite different from those reported in Chrysanthemum morifolium, a well-known traditional beverage in China, which indicated that snow chrysanthemum may be a promising herbal tea material with obvious antioxidant activity.

Genomic full-length sequence of two HLA-A alleles, A*02:07:01 and A*02:10, identified by cloning and sequencing

We report the sequences of 5' promoter and 3' untranslated region (UTR) of A*02:07:01 and A*02:10 for the first time.

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.