The variation and evolution of complete human centromeres

Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.

Association of serum 25-hydroxyvitamin d concentrations with all-cause and cause-specific mortality among individuals with depression: A cohort study

BACKGROUND

Limited evidence exists on the relationship between vitamin D status and mortality in depressed patients.

METHODS

This study investigates serum 25-hydroxyvitamin D [25(OH)D] concentrations in 8417 adults with depression among the National Health and Nutrition Examination Survey (NHANES, 2005-2018). Mortality outcomes were assessed through National Death Index records up to December 31, 2019. Cox proportional risk models estimated risk ratios (HR) and 95 % confidence intervals (CI) for all-cause, cardiovascular disease (CVD), and cancer mortality. Restricted cubic spline analyses explored the nonlinear association of serum 25(OH)D levels with mortality, using the likelihood ratio test for nonlinearity.

RESULTS

The weighted mean serum 25(OH)D level was 66.40 nmol/L (95 % CI: 65.8, 67.0), with 36.3 % having deficient vitamin D (<50 nmol/L [20 ng/mL]). Over an average 7.16-year follow-up, 935 deaths were documented, including 296 CVD deaths and 191 cancer deaths. Higher serum 25(OH)D levels were associated with reduced all-cause mortality (HRs 0.55-1.00, p trend = 0.006) and cancer-specific mortality (HRs 0.36-1.00, p trend = 0.015) after multivariate adjustment. The relationship between serum 25(OH)D and all-cause mortality exhibited a nonlinear pattern (P for nonlinearity <0.001), with a 34 % lower risk for each unit increase in natural log-transformed 25(OH)D levels. Significant interactions were observed with age, antidepressant use, and diabetes status.

CONCLUSIONS

Higher serum 25(OH)D levels were associated with decreased all-cause and cancer-specific mortality in depressed adults, particularly among younger individuals and those using antidepressants or without diabetes. Further research is essential to understand mechanisms and interventions related to vitamin D in depression.

Comparative genomics of macaques and integrated insights into genetic variation and population history

The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta) and crab-eating macaques ( M. fascicularis)

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques ( Macaca mulatta, MMU) and crab-eating macaques ( M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Structurally divergent and recurrently mutated regions of primate genomes

We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.

TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation

Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.

The complete and fully-phased diploid genome of a male Han Chinese

Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.

Comprehensive analysis of m6A regulators characterized by the immune microenvironment in Duchenne muscular dystrophy

BACKGROUND

Duchenne muscular dystrophy (DMD) is an X-linked, incurable, degenerative neuromuscular disease that is exacerbated by secondary inflammation. N⁶-methyladenosine (m⁶A), the most common base modification of RNA, has pleiotropic immunomodulatory effects in many diseases. However, the role of m⁶A modification in the immune microenvironment of DMD remains elusive.

METHODS

Our study retrospectively analyzed the expression data of 56 muscle tissues from DMD patients and 26 from non-muscular dystrophy individuals. Based on single sample gene set enrichment analysis, immune cells infiltration was identified and the result was validated by flow cytometry analysis and immunohistochemical staining. Then, we described the features of genetic variation in 26 m⁶A regulators and explored their relationship with the immune mircoenvironment of DMD patients through a series of bioinformatical analysis. At last, we determined subtypes of DMD patients by unsupervised clustering analysis and characterized the molecular and immune characteristics in different subgroups.

RESULTS

DMD patients have a sophisticated immune microenvironment that is significantly different from non-DMD controls. Numerous m⁶A regulators were aberrantly expressed in the muscle tissues of DMD and inversely related to most muscle-infiltrating immune cell types and immune response-related signaling pathways. A diagnostic model involving seven m⁶A regulators was established using LASSO. Furthermore, we determined three m⁶A modification patterns (cluster A/B/C) with distinct immune microenvironmental characteristics.

CONCLUSION

In summary, our study demonstrated that m⁶A regulators are intimately linked to the immune microenvironment of muscle tissues in DMD. These findings may facilitate a better understanding of the immunomodulatory mechanisms in DMD and provide novel strategies for the treatment.

Ink Drop Displacement Model-Based Direct Binary Search

A novel statistical ink drop displacement (IDD) printer model for the direct binary search (DBS) halftoning algorithm is proposed. It is intended primarily for pagewide inkjet printers that exhibit dot displacement errors. The tabular approach in the literature predicts the gray value of a printed pixel based on the halftone pattern in some neighborhood of that pixel. However, memory retrieval time and the complexity of memory requirements hamper its feasibility in printers that have a very large number of nozzles and produce ink drops that affect a large neighborhood. To avoid this problem, our IDD model embodies dot displacements by moving each perceived ink drop in the image from its nominal location to its actual location, rather than manipulating the average gray values. This enables DBS to directly compute the appearance of the final printout without retrieving values from a table. In so doing, the memory issue is eliminated and the computation efficiency is enhanced. The deterministic cost function of DBS is replaced by the expectation over the ensemble of the displacements for the proposed model such that the statistical behavior of the ink drops is accounted for. Experimental results show significant improvement in the quality of the printed image over the original DBS. Besides, the image quality obtained by the proposed approach appears to be slightly better than that obtained by the tabular approach.

Amine-Assisted Simultaneous CO2 Absorption and Mineral Carbonation: Effect of Different Categories of Amines

The hybrid technology of CO₂ capture-mineral carbonation (CCMC) using alkaline streams has emerged in recent years. However, thus far, there has been no comprehensive study revealing the mechanisms of the simultaneous CCMC process regarding the choice of amine types and sensitivity of parameters. Combining with the analysis of multistep reaction mechanisms for different amines, we investigated a representative from each category in CCMC using calcium chloride to simulate the alkaline resource after leaching, i.e., primary (ethanolamine, MEA), secondary (diisopropanolamine, DIPA), tertiary (diethylethanolamine, DEAE), and triamine (diethylenetriamine, DETA), respectively. In the adsorption step, increasing the amine concentration beyond 2 mol/L reduced the absorption efficiency of DEAE due to the hydration mechanism, motivating a rational choice of concentration. In CCMC sections, when the amine concentration increased, only DEAE exhibited an increased carbonation efficiency of up to 100%, while DETA showed the lowest conversion. The carbonation of DEAE demonstrated the least sensitivity to temperature. The crystal transformation experiments suggested that over time, the produced vaterite could completely transform to calcite or aragonite, except those from DETA. Thus, with rationally chosen conditions, DEAE was demonstrated ideal for CCMC. These findings obtained in this work provided a theoretical foundation for designing future CCMC processes.

Characterization of large-scale genomic differences in the first complete human genome

BACKGROUND

The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet.

RESULTS

Here, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution.

CONCLUSION

Our study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.

Exploring the promotion of green technology innovation in the new energy vehicle industry: An evolutionary game analysis

This paper aims to explore how to promote green technology innovation (GTI) among new energy vehicle (NEV) manufacturers and the strategic changes among the government, manufacturers, and consumers. From the perspective of evolutionary game theory, a tripartite evolutionary game model is established to analyze the influence of key factors on the tripartite strategies in the context of the government's willingness to subsidize gradually decreases. The main findings are as follows: (1) government subsidies provided to manufacturers better promote their willingness to participate in GTI. The relationship between government subsidies and GTI is not linear, and the government cannot blindly increase the level of subsidies. (2) The willingness of NEV manufacturers to engage in GTI is influenced by price and consumer purchase preferences. The higher the price of new energy vehicle using green technology (NEVG) is not better, and lowering the price of NEVGs can promote manufacturers' participation in GTI and consumers' purchase of NEVGs. (3) Increasing the mileage of NEVGs and consumers' green consumption preferences will effectively increase consumers' willingness to purchase. Accordingly, this study suggests that to enhance manufacturers' participation in GTI, the government should increase subsidies and encourage green consumption among consumers. In addition, manufacturers should focus on improving the mileage of NEVGs and reducing their prices to make them more accessible to consumers.

The variation and evolution of complete human centromeres

We completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find that centromere single-nucleotide variation can increase by up to 4.1-fold relative to other genomic regions, with the caveat that up to 45.8% of centromeric sequence, on average, cannot be reliably aligned with current methods due to the emergence of new α-satellite higher-order repeat (HOR) structures and two to threefold differences in the length of the centromeres. The extent to which this occurs differs depending on the chromosome and haplotype. Comparing the two sets of complete human centromeres, we find that eight harbor distinctly different α-satellite HOR array structures and four contain novel α-satellite HOR variants in high abundance. DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by at least 500 kbp-a property not readily associated with novel α-satellite HORs. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan, and macaque genomes. Comparative analyses reveal nearly complete turnover of α-satellite HORs, but with idiosyncratic changes in structure characteristic to each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the p- and q-arms of human chromosomes and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.

Association of serum alkaline phosphatase and depression in US adults: a population-based cross-sectional study

Background

Depression, a serious public health disorder, is increasingly prevalent worldwide. An association between alkaline phosphatase (ALP) and neurological disorders has been reported. However, data on ALP and depression risk are scarce, which warrants attention.

Methods

We assessed the association between ALP and risk of depression in adults from the 2007-2014 National Health and Nutrition Examination Survey (NHANES). Depression was assessed using the Patient Health Questionnaire-9. Univariate and multivariate logistic regression were used to assess the association between ALP and risk of depression, and subgroup analyses were also performed.

Results

A total of 17,485 participants were included. The prevalence of depression was 9.3% (1,631/17,485) and ALP was significantly associated with the risk of depression when ALP was a categorical variable (quadratic or categorized by 79 U/L) in a multivariate logistic regression model after adjusting for confounding factors (≥79 U/L vs. <79 U/L, adjusted OR, 1.15; 95%CI, 1.02-1.29). Each 1-unit increase in ALP (log₂) was associated with a 20% increase in depression prevalence (adjusted OR, 1.20; 95%CI, 1.06-1.36) when ALP was used as a continuous variable. Subgroup analysis showed that ALP was positively associated with the risk of depression with different characteristics.

Conclusion

Our findings suggest that higher alkaline phosphatase levels, even within the normal range, are significantly associated with a higher risk of depression in US adults. Such findings require further prospective studies to provide more evidence.

Structurally divergent and recurrently mutated regions of primate genomes

To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs, ABCD7, OLAH) and new lineage-specific genes are generated (e.g., CKAP2, NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g., RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.

TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find that only 14% of all human TAD boundaries are shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.

The relationship between slack resources and organizational resilience: The moderating role of dual learning

Slack resources and organizational learning are key elements in building organizational resilience. This paper constructs an impact model of organizational resilience and investigates the impact of slack resources on organizational resilience using data from Chinese-listed companies, as well as verifying the moderating effect of organizational dual learning through hierarchical analysis. The findings show that: Firstly, both absorbed slack resources and unabsorbed slack resources promote organizational resilience. Secondly, organizational learning has a moderating effect on the relationship between slack resources and organizational resilience, where organizational exploitative learning positively moderates the relationship between unabsorbed slack resources and organizational resilience, while organizational exploitative learning negatively moderates the relationship between absorbed slack resources and organizational resilience. Accordingly, organizations should pay attention to the composition of slack resources and the coordination between slack resources and organizational dual learning in order to improve organizational resilience.

Relationship between depressive disorders and biochemical indicators in adult men and women

BACKGROUND

Depression is a psychiatric disorder with global public health concerns. Although a number of risk factors have been identified for depression, there is no clear relationship between biochemistry and depression. In this study, we assessed whether depressive disorders are significantly associated with biochemical indicators.

METHODS

Our study included 17,561 adults (age ≥ 18 years) participating in the 2009-2018 National Health and Nutrition Examination Survey (NHANES). The relationship between depression and biochemical and obesity indicators was analyzed by logistic regression.

RESULTS

As compared to the control group, men with depression showed significantly higher levels of gamma-glutamyl transferase, glucose, and triglycerides, and lower levels of albumin and total bilirubin. The depressed group had higher levels of alkaline phosphatase, bicarbonate, and sodium than the control group.

CONCLUSION

Several biochemical and anthropometric indices were associated with depression in this study. It would be interesting to further analyze their cause-effect relationship.

LIMITATIONS

This study is a cross-sectional study. The population is less restricted and does not exclude people with diabetes, pregnancy, etc., so it is less significant for a specific population. Dietary information was not included, as diet plays an important role in many indicators.

Development and validation of a novel M1 macrophage-related gene prognostic signature for lung cancer

Background

Lung cancer (LC) is the most common cancer. Using data from The Cancer Genome Atlas (TCGA), we analyzed the functional roles of M1 macrophage status in LC patients.

Methods

Clinical and transcriptome data of LC patients were obtained from the TCGA dataset. We identified M1 macrophage-related genes in LC patients and investigated the underlying molecular mechanisms of these genes in LC patients. After performing a least absolute shrinkage and selection operator (LASSO) Cox regression analysis, the LC patients were divided into two subtypes, and the underlying mechanism of the association between them was further explored. A comparison of immune infiltration was conducted between the two subtypes. Based on gene set enrichment analysis (GSEA), the key regulators associated with subtypes were further explored.

Results

M1 macrophage-related genes were identified using TCGA data, and these genes might be related to the activation of the immune response and cytokine-mediated signaling pathways in LC. A seven M1 macrophage-related gene signature (including STAT1, TAP1, UBE2L6, TAP2, CXCR6, PSMB8 and CD2) was identified in LC using LASSO Cox regression analysis. Two subtypes (low risk and high risk) of LC patients were created based on the seven M1 macrophage-related gene signature. Univariate and multivariate survival analyses further confirmed that the subtype classification was an effective independent prognostic factor. Moreover, the two subtypes were correlated with immune infiltration, and GSEA revealed that the pathways of tumor cell proliferation and immune-related biological processes (BPs) might play an important role in LC in the high-risk group and low-risk group, respectively.

Conclusions

M1 macrophage-related subtypes of LC were identified and were closely associated with immune infiltration. The gene signature involved in M1 macrophage-related genes could help make a distinction and predict prognosis for LC patients.

Recycling the High-Salinity Textile Wastewater by Quercetin-Based Nanofiltration Membranes with Minimal Water and Energy Consumption

Effective recovery of dyes and salts from textile wastewater by nanofiltration (NF) remains a serious challenge due to the high consumption of water and energy caused by the limited performance of the available membranes. Herein, a novel strategy is described to prepare loose polyester NF membranes by using renewable quercetin as the aqueous monomer for fractionation of high salinity textile wastewater with minimal water and energy consumption. Compared with NF270, taken as the reference membrane, the QE-0.2/TMC-0.2 membrane significantly improved the efficiency for dye/salt fractionation by 288%. The water consumption was also decreased by 42.9%. The efficiency is attributed to an ultrahigh water permeance of 198 ± 2.1 L^-1 m^-2 h^-1 bar^-1 with a high selectivity of 123 (extremely low NaCl rejection of 1.6% and high Congo red rejection of 99.2%). The optimal quercetin-based membrane had an ultrathin separation layer of about 39 ± 1.2 nm with good hydrophilicity and negative charge density. Moreover, this work includes a novel method of comparison with a theoretically ideal membrane, which shows that both the energy and water consumption are near their theoretical minimum. This strategy is expected to save energy and minimize carbon emissions for membrane-based wastewater treatment systems.

Association between serum calcium and in-hospital mortality in critical patients with multiple myeloma: a cohort study

BACKGROUND

Elevated serum calcium levels may serve as a useful clinical biomarker of mortality in patients with multiple myeloma(MM). However, the clinical significance of the relationship between serum calcium levels and in-hospital mortality in MM patients admitted to the Intensive Care Unit (ICU) remains unclear.

OBJECTIVES

This study aimed to explore the association between serum calcium levels and in-hospital mortality in patients with MM in the ICU.

METHODS

Patients with MM were identified from the Medical Information Mart for Intensive Care IV(MIMIC-IV) database. The outcome was in-hospital mortality. Multivariable-adjusted Cox regression analysis, curve fitting, and threshold effects analysis were used to assess the relationship between serum calcium levels and in-hospital mortality in patients with MM in the ICU.

RESULTS

Our study included 262 patients with MM with a mean age of 72.3 ± 11.0 years, 63.4% of whom were male. The in-hospital mortality was 19.5% (51/262). The relationship between serum calcium levels and in-hospital mortality was nonlinear. The effect size on the left and right sides of the inflection point, were 0.270 (HR: 0.270, 95% CI 0.106-0.687, P < 0.05) and 2.104 (HR: 2.104, 95% CI 1.069-4.142, P < 0.05), respectively. The results of the sensitivity analysis remained stable.

CONCLUSION

Our findings show that a nonlinear relationship exists between serum calcium levels and in-hospital mortality in critically ill patients with MM. A serum calcium level of approximately 8.40 mg/dL was associated with the lowest risk of in-hospital mortality, which increases with rising serum calcium levels, and should be of concern to ICU physicians.

Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders

Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] < 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance (P < 3.64e-7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense (n = 41) or truncating (n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden (DDX3X, MECP2, WDR45, and HDAC8). This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.

Association Between Dietary Fiber Intake and Risk of Depression in Patients With or Without Type 2 Diabetes

BACKGROUND

Depression and type 2 diabetes (T2D) are both serious public health problems, with morbidity and mortality in people increasing year by year, resulting in a heavy economic burden. A correlation between dietary fiber and both has been reported. Nevertheless, few data are available concerning dietary fiber and the risk of depression with or without T2D, which deserve further attention.

MATERIALS AND METHODS

We assessed the relationship between dietary fiber intake and risk of depression with or without T2D in the 2007-2014 National Health and Nutrition Examination Survey (NHANES) population. A 24-h dietary review was used to assess fiber intake. The Patient Health Questionnaire-9 was used to assess depression. Stability of the results was assessed using restricted cubic spline models and logistic regression, as well as sensitivity analyses.

RESULTS

A total of 17,866 adults aged 20 years and older with a mean age of 49.3 ± 17.7 years were included in this study, of whom 49.5% were male. After adjusting for covariates, the association of dietary fiber intake with the risk of depression appeared to differ between non-T2D group and T2D group (OR, 0.987; 95% CI, 0.979-0.995 vs. OR, 1.003; 95% CI, 0.988-1.017). Furthermore, when dietary fiber was converted to a categorical variable, there was evidence of interaction between T2D status and fiber intake on decreasing the prevalence of depression (P-value for interaction = 0.015). Sensitivity analysis showed stable results.

CONCLUSION

Our findings indicated that whether a patient has T2D may affect the relationship between dietary fiber intake and the risk of depression, which still needs to be confirmed by further randomized controlled trials.

Inherited and acquired causes renal vein thrombosis in an 11-year-old boy who was relieved after piperacillin-tazobactam and rivaroxaban treatment: a case report

BACKGROUND

Physiological hypercoagulability is a well-known condition in older populations, whereas thrombosis, especially in renal veins, is a rare occurrence in teenagers. This paper presents a pediatric case of renal venous infarction and thrombosis.

CASE DESCRIPTION

We report the case of an 11-year-old Chinese boy who presented with low back discomfort and was afraid to walk. Computed tomography (CT) revealed thrombosis in his renal veins and inferior vena cava. He was being treated for severe refractory mycoplasma pneumoniae pneumonia (MPP). He was treated with rivaroxaban and urokinase for thrombosis, and azithromycin for MPP. On day 2 after admission, his symptoms improved. Therefore, the dosage of rivaroxaban was decreased from 10 to 5 mg twice per day. On day 3 after admission, enhanced CT revealed new thromboses in the bilateral pulmonary trunks and arteries, inferior cava, right renal veins, bilateral common iliac veins, and internal iliac vein. The ultrasonography showed a strip hypoecho at the pulmonary artery bifurcation. All the above imaging suggested that antithrombotic therapy was insufficient. His plasma antithrombin (AT) III activity remained consistently low during hospitalization. The family history was re-examined and revealed that both his father and grandfather had experienced spontaneous pulmonary thrombosis around the age of 30. He was diagnosed with acquired and inherited thrombosis and inherited AT III deficiency. Following a medication regimen of piperacillin-tazobactam for 1 week and rivaroxaban (10 mg, twice daily), he was discharged and no thrombosis and other side effects or complications occurred in the following 3 months.

CONCLUSIONS

This is a rare case of a teenager with inherited and acquired hypercoagulability. For refractory MPP pediatric patients with thrombosis, clinicians should consider whether hereditary factors, such as inherited AT III deficiency, are involved in thrombosis.

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Typical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers. In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation-a process we refer to as genome inference. Compared with mapping-based approaches, PanGenie is more than 4 times faster at 30-fold coverage and achieves better genotype concordances for almost all variant types and coverages tested. Improvements are especially pronounced for large insertions (≥50 bp) and variants in repetitive regions, enabling the inclusion of these classes of variants in genome-wide association studies. PanGenie efficiently leverages the increasing amount of haplotype-resolved assemblies to unravel the functional impact of previously inaccessible variants while being faster compared with alignment-based workflows.

Associations between urea nitrogen and risk of depression among subjects with and without type 2 diabetes: A nationwide population-based study

BACKGROUND

Depression and type 2 diabetes (T2D) are serious public health problems with irreversible health consequences and a significant economic burden on the healthcare system. Previous studies have suggested that blood urea nitrogen (BUN) was inversely longitudinally associated with incidence of diabetes and depression in adults, but few well-designed studies have examined the effects of status of T2D on the full range of relationship between BUN and depression.

METHODS

The analysis sample consisted of adults aged≥20 years from the 2007-2014 National Health and Nutrition Examination Survey (NHANES) who completed the Patient Health Questionnaire-9 (PHQ-9), involving 19,005 participants. By stratifying participants according to T2D status, we further assessed the difference between BUN and risk of depression in participants with and without T2D using multivariate logistic regression (interaction test).

RESULTS

In this cross-sectional study, the association between BUN and depression prevalence appeared to differ between the T2D and non-T2D groups (OR: 1.00, 95% Cl: 0.95-1.05 vs. OR: 0.89, 95% Cl: 0.85-0.93). In addition, there was evidence of an interaction between BUN levels and T2D status in reducing the risk of depression (P value for interaction = 0.032.) The relationship between BUN and depressive symptoms was significant in non-T2D subjects (P < 0.001), but not in T2D (P = 0.940).

CONCLUSIONS

Our findings suggest that there is a significant relationship between BUN and depression, and T2D status may influence the association between BUN and the risk of depression. Such findings require further prospective studies to provide more evidence.

A high-quality bonobo genome refines the analysis of hominid evolution

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation^1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes^1,3–5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.

A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

An evolutionary driver of interspersed segmental duplications in primates

BACKGROUND

The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human-ape gene families, nuclear pore interacting protein (NPIP).

RESULTS

Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis.

CONCLUSIONS

LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution.

Enhancement of lysozyme crystallization under ultrasound field

With the increasing demand for biopharmaceuticals, a method to crystallize biomolecule products with high quality, high yield and uniform size distribution as well as regular crystal habit is needed. In this work, ultrasound was used as a nucleation accelerator to decrease the energy barrier for lysozyme crystal formation. Crystallization experiments on egg-white lysozyme were carried out with and without ultrasound. The effect of ultrasound on induction time, metastable zone width, crystal size and morphology and process yield was investigated in detail. The nucleation-promoting effect produced by ultrasound is illustrated by the reduction of metastable zone width and induction time. By inducing faster nucleation, ultrasound leads to protein crystals grow at lower supersaturation levels with shorter induction time. It was found that ultrasound could result in uniform size distribution of the product due to the preventing of aggregation. However, long time continuous application of ultrasound could result in smaller particle size. Hence, ultrasonic-stop method was found to be a more appropriate strategy to enhance the crystallization process of proteins such as lysozyme.

TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user-friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python-TREEasy-that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ-Tree), species inference from concatenated data (with IQ-Tree and RaxML-NG), species tree inference from gene trees (with ASTRAL, MP-EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the "WGD clade" of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy).

Partial Oxidation Strategy to Synthesize WS2/WO3 Heterostructure with Enhanced Adsorption Performance for Organic Dyes: Synthesis, Modelling, and Mechanism

In this work, a facile oxidation strategy was developed to prepare novel tungsten disulfide/tungsten trioxide (WS₂/WO₃) heterostructures for adsorbing organic dyes efficiently by combining the hydrophilic property of WO₃ and the superior dye affinity of WS₂. The structural and elemental properties of the synthesized hybrid materials were systematically investigated, and the results demonstrated the retained flower-like morphology of the primitive WS₂ and the successful introduction of WO₃. Furthermore, surface properties such as a superior hydrophilicity and negative-charged potential were also demonstrated by a water contact angle characterization combined with a Zeta potential analysis. The performance of the obtained WS₂/WO₃ hybrid materials for removing Rhodamine B (RhB) from wastewater was evaluated. The results showed that the maximum adsorption capacity of the newly synthesized material could reach 237.1 mg/g. Besides, the adsorption isotherms were also simulated by a statistical physics monolayer model, which revealed the non-horizontal orientation of adsorbates and endothermic physical interaction. Finally, the adsorption mechanism and the recyclability revealed that the partial oxidation strategy could contribute to a higher adsorption capacity by modulating the surface properties and could be applied as a highly efficient strategy to design other transition metal dichalcogenides (TMDs) heterostructures for removing organic dyes from wastewater.

[A multicenter, retrospective study of pathogenic bacteria distribution and drug resistance in febrile neutropenic patients with hematological diseases in Shanghai]

目的

了解上海地区中性粒细胞缺乏（粒缺）伴发热血液病患者致病细菌的分布及耐药情况。

方法

回顾性分析2012年1月至2014年12月上海市12家医院血液科粒缺伴发热住院患者的临床分离菌株，用纸片扩散法进行药敏试验，WHONET 5.6软件分析病原菌分布及药敏数据。

结果

从上海地区粒缺伴发热患者中共分离出1 260株细菌，其中革兰阳性菌420株（33.3%），革兰阴性菌840株（66.7%）。排在前七位的分别是肺炎克雷伯菌158株（12.5%）、嗜麦芽窄食单胞菌120株（9.5%）、大肠埃希菌115株（9.1%）、铜绿假单胞菌109株（8.7%）、鲍曼不动杆菌83株（6.6%）、金黄色葡萄球菌70株（5.6%）和屎肠球菌63株（5.0%）。呼吸道分泌物标本中，非发酵菌占56.2%（350/623）。其中嗜麦芽窄食单胞菌占15.3%（95/623）。血液标本中，肠杆菌科细菌占42.3%（104/246），凝固酶阴性葡萄球菌占34.6%（85/246）。脓液标本中肠杆菌科细菌占39.4%（76/193），肠球菌属细菌占28.5%（55/193）。耐甲氧西林金黄色葡萄球菌葡萄球菌（MRSA）和耐甲氧西林凝固酶阴性葡萄球菌（MRCNS）的检出率分别为54.3%和82.5%，未发现耐利奈唑胺、万古霉素、替考拉宁葡萄球菌属菌株，耐万古霉素屎肠球菌的检出率为8.9%，肠球菌属未检出耐利奈唑胺的菌株。肠杆菌科细菌对碳青霉烯类药物高度敏感。铜绿假单胞菌对亚胺培南和美罗培南的耐药率已分别达34.1%和15.8%。嗜麦芽窄食单胞菌对米诺环素、左氧氟沙星、复方磺胺甲恶唑等药物敏感。鲍曼不动杆菌仅对头孢哌酮/舒巴坦的耐药率低于10.0%。肺炎克雷伯菌、嗜麦芽窄食单胞菌、铜绿假单胞菌、鲍曼不动杆菌等革兰阴性菌对大多常用抗菌药物的耐药率低于CHINET监测的数据。

结论

粒缺伴感染患者常见感染部位致病菌株分布有其特点，细菌耐药率整体低于CHINET全国医院大样本监测。

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.

The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals

Reef-building corals provide the structural basis for one of Earth's most spectacular and diverse-but increasingly threatened-ecosystems. Modern Indo-Pacific reefs are dominated by species of the staghorn coral genus Acropora, but the evolutionary and ecological factors associated with their diversification and rise to dominance are unclear. Recent work on evolutionary radiations has demonstrated the importance of introgression and ecological opportunity in promoting diversification and ecological success. Here, we analyze the genomes of five staghorn coral species to examine the roles of introgression and ecological opportunity in the rise to dominance of Acropora. We found evidence for a history marked by a major introgression event as well as recurrent gene flow across species. In addition, we found that genes with topologies mismatching the species tree are evolving faster, which is suggestive of a role for introgression in spreading adaptive genetic variation. Demographic analysis showed that Acropora lineages profited from climate-driven mass extinctions in the Plio-Pleistocene, indicating that Acropora exploited ecological opportunity opened by a new climatic regime favoring species that could cope with rapid sea-level changes. Collectively, the genomes of reef-building corals have recorded an evolutionary history shaped by introgression and climate change, suggesting that Acropora-among most vulnerable corals to stressors-may be critical for understanding how reefs track the impending rapid sea-level changes of the Anthropocene.

Polymorphism of the androgen receptor gene CAG repeat sequence and male climacteric syndrome

The aim of this study was to analyze the association between polymorphism of the androgen receptor (AR) gene CAG repeat sequence and the climacteric syndrome in men. The study was performed in 103 males with climacteric syndrome and 111 males without the clinical syndrome of climacteric, aged between 40 and 70 years. DNA sequencing of the CAG repeat sequence in the N-terminal domain of the first exon of the AR gene was analyzed. The AR allele length ranged from 18-34 CAG repeats in males with climacteric syndrome. The average value of CAG repeat was 24.7±2.58. However, the corresponding values ranged from 15-24 CAG repeat in control group and the average value of CAG repeat was 21.25±2.63. There was a significant difference of the number of CAG repeat between the two groups. The occurrence of male climacteric syndrome was related to the CAG repeat number of androgen receptor gene, and the male patients with more CAG repeats had higher risk of clinical syndrome of climacteric. The detection of CAG repeat number of AR gene might be helpful for the prediction of clinical syndrome of climacteric.

Oxidative stress induced necroptosis activation is involved in the pathogenesis of hyperoxic acute lung injury

Necroptosis has been found to be involved in the pathogenesis of some lung diseases, but its role in hyperoxic acute lung injury (HALI) is still unclear. This study aimed to investigate contribution of necroptosis to the pathogenesis of HALI induced by hyperbaric hyperoxia exposure in a rat model. Rats were divided into control group, HALI group, Nec-1 (necroptosis inhibitor) group and edaravone group. Rats were exposed to pure oxygen at 250 kPa for 6 h to induce HALI. At 30 min before hyperoxia exposure, rats were intraperitoneally injected with Nec-1 or edaravone, and sacrificed at 24 h after hyperoxia exposure. Lung injury was evaluated by histology, lung water to dry ratio (W/D) and bronchoalveolar lavage fluid (BALF) biochemistry; the serum and plasma oxidative stress, expression of RIP1, RIP3 and MLKL, and interaction between RIP1 and RIP3 were determined. Results showed hyperoxia exposure significantly caused damage to lung and increased necroptotic cells and the expression of RIP1, RIP3 and MLKL. Edaravone pre-treatment not only inhibited the oxidative stress in HALI, but also reduced necroptotic cells, decreased the expression of RIP1, RIP3 and MLKL and improved lung pathology. Nec-1 pretreatment inhibited necroptosis and improved lung pathology, but had little influence on oxidative stress. This study suggests hyperoxia exposure induces oxidative stress may activate necroptosis, involving in the pathology of HALI, and strategies targeting necroptosis may become promising treatments for HALI.

Roles of transforming growth factor β in hyperoxia-induced lung injury

Hyperoxia induced lung injury (HILI) refers to the acute lung injury secondary to prolonged exposure to hyperoxia at elevated partial pressure. With the advent of efficient systems for delivery of high concentrations of oxygen in hospitals, the population at risk for this condition has been markedly increased. Although numerous studies have been conducted to investigate the pathogenesis of HILI, the specific mechanism is still poorly understood and some hypotheses have been proposed. Transforming growth factor β (TGF-β) is a secreted protein that controls proliferation, cellular differentiation and other functions in most cells and is a type of cytokine that plays a role in many diseases. In this mini-review, we summarize the role of TGF-β in HILI according to its relationships with reactive oxygen species (ROS), pro-inflammatory cytokines, cell apoptosis and pulmonary fibrosis. We hope it may help the understanding of pathogenesis of HILI and provide a greater understanding for the target therapy of HILI.

Helium preconditioning protects against neonatal hypoxia-ischemia via nitric oxide mediated up-regulation of antioxidases in a rat model

This study aimed to investigate the role of nitric oxide (NO) in the neuroprotective effects of helium preconditioning (He-PC) in a neonatal hypoxia/ischemia (HI) rat model. Seven-day old rat pups were divided into normal control group, He-PC group, HI group, He-PC+HI group, L-NAME+HI group and L-NAME+He-PC+HI group. HI was induced by exposure to 80% oxygen for 90 min. He-PC was conducted with 70% helium-30% oxygen for three 5-min periods. Three hours after He-PC, animals in control group and He-PC group were sacrificed, and the brain was collected for the detection of NO content. At 24h after HI, animals in control group, HI group, He-PC+HI group, and L-NAME+He-PC+HI group were sacrificed, and the brain was collected for detection of infarct ratio, antioxidases (SOD, HO-1 and Nrf2), DNA binding activity of Nrf2 and TUNEL staining. Three weeks later, the neurological function and brain atrophy were determined. Results showed pretreatment with L-NAME alone failed to exert protective effect on HI. He-PC significantly increased NO content, reduced the brain infarct area, increased anti-oxidases expression and DNA binding activity of Nrf2, decreased the apoptotic cells, and improved the neurological function and brain atrophy. In addition, this protection was markedly inhibited by L-NAME (a non-selective NOS inhibitor). These findings suggest that the He-PC may induce NO production to activate Nrf2, exerting neuroprotective effect on neonatal HI.

Case Report Serious pulmonary infection in a splenectomized patient with adult type 1 Gaucher disease

A 49-year-old man with a history of Gaucher disease type 1, resulting in serious splenomegaly and eating disorder, was referred to our department and underwent a splenectomy under general anesthesia. Gaucher disease is very rare, and its first signs are unexplained splenomegaly and hypersplenism. On preoperative examination, the patient's platelet count was slightly low, and his other test results were normal. Surprisingly, on the first postoperative day, the patient developed a lung infection. This gradually progressed to acute respiratory distress syndrome with respiratory failure, requiring intubation and mechanical ventilation. The patient eventually recovered, and he was discharged after receiving antibiotics and other treatments to enhance immunity. However, his postoperative lung infection led to a significantly prolonged and expensive hospital stay. This case suggests that we must pay close attention to the immune dysfunction of patients with Gaucher disease type 1. Anesthesia and surgery with accompanying post-traumatic stress can weaken patients' immunity and cause susceptibility to severe lung infections. Pulmonary signs and functions should be monitored closely during the perioperative period, and, if necessary, gamma globulin and thymosin should be administered early in the preoperative or postoperative period to enhance immunity.

Monitoring tissue blood oxygen saturation in the internal jugular venous area using near infrared spectroscopy

Central venous blood oxygen saturation (ScvO2) is an important monitoring index of fluid resuscitation. However, monitoring of ScvO2 is not continuous and invasive. Near infrared spectroscopy (NIRS) is an optical technology for the noninvasive detection of hemodynamic changes, with advantages of being real-time, continuous, low-cost, and portable. The present study aimed to determine whether a correlation exists between the tissue blood oxygen saturation in the internal jugular venous area (StO2) data obtained with NIRS and the ScvO2 and whether these two quantities are equivalent. Data were collected from 13 patients. We used ultrasound to locate the placement site for the NIRS light source outside the internal jugular vein. Meanwhile, a sample for blood gas analysis was obtained through the central venous catheter. A correlation analysis between the StO2 and ScvO2 of 13 samples was performed (Pearson correlation coefficient), suggesting a high correlation between them (r = 0.906, StO2 =1.0018 ScvO2 +2.8524). Bland-Altman analysis was also performed between the StO2 and ScvO2. Results were as follows: 100% of monitored points fell within the range of the mean ± 1.96 SD of the difference between the StO2 and ScvO2; range of the mean ± 1.96 SD of the difference between the StO2 and ScvO2 was 3 ± 10.2; confidence interval of the difference between the StO2 and ScvO2 was -7.2 to 13.2%. The StO2 monitored with NIRS correlated highly with the ScvO2 measured in the internal jugular vein. Therefore, the StO2 can be used for directing clinical treatment with further research.

Pre-treatment with Cobra venom factor alleviates acute lung injury induced by intestinal ischemia-reperfusion in rats

BACKGROUND

Previous studies have shown that complement activation is required for intestinal ischemia-reperfusion (IIR)-induced tissue damage. Cobra venom factor (CVF), a structural and functional homolog to the activated form of C3 (the central component of the complement system), can cause exhaustive activation of the alternative pathway and deplete the complement components.

AIM

This study aims to investigate the effect of CVF pretreatment on acute lung injury induced by IIR in rats.

MATERIALS AND METHODS

Lung injury was induced by clamping superior mesenteric artery (SMA) for 60 min followed by 4 h of reperfusion. CVF was given via the tail vein 24 h before the operation.

RESULTS

Histological results as well as lung edema determination and permeability assay showed the severe damages were induced in the lungs of rats in the IIR group, accompanying with the increases in the levels of pulmonary malondialdehyde (MDA), myeloperoxidase (MPO) activity, intercellular adhesion molecule-1 (ICAM-1), interleukin (IL)-8. Remarkably, CVF pretreatment significantly attenuated the morphological lung injury, lung edema and lung permeability, reduced the increase of the levels of MDA, MPO, ICAM-1 and IL-8 induced by IIR. In addition, the severe damage of intestinal and elevation of plasma diamine oxidase activity in the IIR rats were significantly alleviated by CVF pretreatment.

CONCLUSIONS

CVF pretreatment could significantly reduce the acute lung injury induced by IIR. The mechanism might include, at least in part, the inhibition of oxidant generation, infiltration of neutrophils, ICAM-1 expression and IL-8 release. CVF might be an efficient reagent for preventing the IIR injuries in clinical condition.

Predominant porB1A and porB1B genotypes and correlation of gene mutations with drug resistance in Neisseria gonorrhoeae isolates in Eastern China

BACKGROUND

Variations of porB1A and porB1B genes and their serotypes exist in Neisseria gonorrhoeae isolates from different geographical areas, and some site mutations in the porB1B gene correlate with drug resistance.

METHODS

The β-lactamase production of N. gonorrhoeae isolates was determined by paper acidometric test and nitrocefin discs. The porB1A and porB1B genes of 315 non-penicillinase-producting N. gonorrhoeae (non-PPNG) strains were amplified by PCR for sequencing to determine serotypes and site mutations. A duplex PCR was designed to simultaneously detect both porB1A and porB1B genes. Penicillin and tetracycline resistance was assessed by an in vitro drug sensitivity test.

RESULTS

Of the N. gonorrhoeae isolates, 31.1% tested positive for porB1A and 68.9% for porB1B genes. All the 98 porB1A+ isolates belonging to IA6 serotype with either no mutation at the 120 and 121 sites (88.8%) or a D120G (11.2%) mutation and were no resistance to both penicillin and tetracycline. Among the 217 porB1B+ isolates, 26.7%, 22.6% and 11.5% belonged to IB3, IB3/6 and IB4 serotypes, respectively. Particularly, two novel chimeric serotypes, IB3/6-IB2 and IB2-IB4-IB2, were found in 77 and 8 porB1B+ isolates. Two hundred and twelve (97.7%) of the porB1B+ isolates were presented G120 and/or A121 mutations with 163 (76.9%) at both sites. Interestingly, within the 77 porB1B+ isolates belonging to IB3/6-IB2 serotype, 15 were discovered to possess novel deletions at both A121 and N122 sites. All the replacement mutations at these sites in PorB1B were correlated with resistance and the deletion mutation showed the highest resistance.

CONCLUSION

N. gonorrhoeae isolates circulating in Eastern China include a sole PorB1A serotype (IA6) and five PorB1B serotypes. Multiple mutations in porB1B genes, including novel A121 and N122 deletions, are correlated with high levels of penicillin and tetracycline resistance.

Characterization of the ompL1 gene of pathogenic Leptospira species in China and cross-immunogenicity of the OmpL1 protein

Background

The usefulness of available vaccine and serological tests for leptospirosis is limited by the low cross-reactivity of antigens from numerous serovars of pathogenic Leptospira spp. Identification of genus-specific protein antigens (GP-Ag) of Leptospira would be important for development of universal vaccines and serodiagnostic methods. OmpL1, a transmembrane porin of pathogenic leptospires, was identified as a possible GP-Ag, but its sequence diversity and immune cross-reactivity among different serovars of pathogenic leptospires remains largely unknown.

Results

PCR analysis demonstrated that the ompL1 gene existed in all 15 official Chinese standard strains as well as 163 clinical strains of pathogenic leptospires isolated in China. In the standard strains, the ompL1 gene could be divided into three groups (ompL1/1, ompL1/2 and ompL1/3) according to their sequence identities. Immune electron microscopy demonstrated that all products of the different gene types of ompL1 are located on the surface of leptospires. The microscopic agglutination test revealed extensive yet distinct cross-immunoagglutination among the antisera against recombinant OmpL1 (rOmpL1) and leptospiral strains belonging to different ompL1 gene types. These cross-immunoreactions were further verified by ELISAs using the OmpL1 proteins as the coated antigens in serum samples from 385 leptospirosis patients. All the antisera against rOmpL1 proteins could inhibit L. interrogans strain Lai from adhering to J774A.1 cells. Furthermore, immunization of guinea pigs with each of the rOmpL1 proteins could cause cross-immunoprotection against lethal challenge with leptospires from different ompL1 gene types.

Conclusion

Three types of the ompL1 gene are present in pathogenic leptospires in China. OmpL1 is an immunoprotective GP-Ag which should be considered in the design of new universal vaccines and serodiagnostic methods against leptospirosis.