Benchmarking multi-platform sequencing technologies for human genome assembly.

Genome assembly is a computational technique that involves piecing together deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a comprehensive and precise representation of the entire genome. Generating a high-quality human reference genome is a crucial prerequisite for comprehending human biology, and it is also vital for downstream genomic variation analysis. Many efforts have been made over the past few decades to create a complete and gapless reference genome for humans by using a diverse range of advanced sequencing technologies. Several available tools are aimed at enhancing the quality of haploid and diploid human genome assemblies, which include contig assembly, polishing of contig errors, scaffolding and variant phasing. Selecting the appropriate tools and technologies remains a daunting task despite several studies have investigated the pros and cons of different assembly strategies. The goal of this paper was to benchmark various strategies for human genome assembly by combining sequencing technologies and tools on two publicly available samples (NA12878 and NA24385) from Genome in a Bottle. We then compared their performances in terms of continuity, accuracy, completeness, variant calling and phasing. We observed that PacBio HiFi long-reads are the optimal choice for generating an assembly with low base errors. On the other hand, we were able to produce the most continuous contigs with Oxford Nanopore long-reads, but they may require further polishing to improve on quality. We recommend using short-reads rather than long-reads themselves to improve the base accuracy of contigs from Oxford Nanopore long-reads. Hi-C is the best choice for chromosome-level scaffolding because it can capture the longest-range DNA connectedness compared to 10× linked-reads and Bionano optical maps. However, a combination of multiple technologies can be used to further improve the quality and completeness of genome assembly. For diploid assembly, hifiasm is the best tool for human diploid genome assembly using PacBio HiFi and Hi-C data. Looking to the future, we expect that further advancements in human diploid assemblers will leverage the power of PacBio HiFi reads and other technologies with long-range DNA connectedness to enable the generation of high-quality, chromosome-level and haplotype-resolved human genome assemblies.

M1AP interacts with the mammalian ZZS complex and promotes male meiotic recombination.

Following meiotic recombination, each pair of homologous chromosomes acquires at least one crossover, which ensures accurate chromosome segregation and allows reciprocal exchange of genetic information. Recombination failure often leads to meiotic arrest, impairing fertility, but the molecular basis of recombination remains elusive. Here, we report a homozygous M1AP splicing mutation (c.1074 + 2T > C) in patients with severe oligozoospermia owing to meiotic metaphase I arrest. The mutation abolishes M1AP foci on the chromosome axes, resulting in decreased recombination intermediates and crossovers in male mouse models. M1AP interacts with the mammalian ZZS (an acronym for yeast proteins Zip2-Zip4-Spo16) complex components, SHOC1, TEX11, and SPO16. M1AP localizes to chromosomal axes in a SPO16-dependent manner and colocalizes with TEX11. Ablation of M1AP does not alter SHOC1 localization but reduces the recruitment of TEX11 to recombination intermediates. M1AP shows cytoplasmic localization in fetal oocytes and is dispensable for fertility and crossover formation in female mice. Our study provides the first evidence that M1AP acts as a copartner of the ZZS complex to promote crossover formation and meiotic progression in males.

Polygenic adaptation of a cosmopolitan pest to a novel thermal environment.

The fluctuation in temperature poses a significant challenge for poikilothermic organisms, notably insects, particularly in the context of changing climatic conditions. In insects, temperature adaptation has been driven by polygenes. In addition to genes that directly affect traits (core genes), other genes (peripheral genes) may also play a role in insect temperature adaptation. This study focuses on two peripheral genes, the GRIP and coiled-coil domain containing 2 (GCC2) and karyopherin subunit beta 1 (KPNB1). These genes are differentially expressed at different temperatures in the cosmopolitan pest, Plutella xylostella. GCC2 and KPNB1 in P. xylostella were cloned, and their relative expression patterns were identified. Reduced capacity for thermal adaptation (development, reproduction and response to temperature extremes) in the GCC2-deficient and KPNB1-deficient P. xylostella strains, which were constructed by CRISPR/Cas9 technique. Deletion of the PxGCC2 or PxKPNB1 genes in P. xylostella also had a differential effect on gene expression for many traits including stress resistance, resistance to pesticides, involved in immunity, trehalose metabolism, fatty acid metabolism and so forth. The ability of the moth to adapt to temperature via different pathways is likely to be key to its ability to remain an important pest species under predicted climate change conditions.

USP7 reduction leads to developmental failure of mouse early embryos.

As a member of Ubiquitin-specific protease subfamily, ubiquitin specific protease 7 (USP7) has been reported to participate in a variety of cellular processes, including cell cycle, apoptosis, DNA damage response, and epigenetic modification. However, its function in preimplantation embryos is still obscure. To investigate the functions of USP7 during preimplantation embryo development, we used siRNA to degrade endogenous USP7 messenger RNA. We found that USP7 knockdown significantly decreased the development rate of mouse early embryos. Moreover, depletion of USP7 induced the accumulation of the DNA lesions and apoptotic blastomeres in early embryos. In addition, USP7 knockdown caused an abnormal H3K27me3 modification in 2-cell embryos. Overall, our results indicate that USP7 maintains genome stability perhaps via regulating H3K27me3 and DNA damage, consequently controlling the embryo quality.

Speech preprocessing and enhancement based on joint time domain and time-frequency domain analysis.

Speech enhancement aims to make noisy speech signals clearer. Traditional time-frequency domain methods struggle to differentiate between speech and noise, leading to a risk of speech distortion. This paper introduces an approach that combines the time domain and time-frequency domain using the W-net module to suppress noise at the front end. The module is an improved version of Wave-U-Net, called TTF-W-Net. We conducted experiments using the TIMIT speech and NOISEX-92 noise datasets to evaluate the enhancement performance achieved by integrating preprocessing networks, specifically Wave-U-Net and our TTF-W-Net, into the baseline methods: Phase, FullSubNet+, and DB-AIAT. Experimental results show that TTF-W-Net outperforms the baseline Wave-U-Net by 15.7% on the PESQ metric and the effect of the network by using our preprocessing method is improved. Consequently, the TTF-W-Net preprocessing Net offers effective speech enhancement.

A Monte Carlo simulation-based health risk assessment of heavy metals in soils of the tropical region in southern China.

The disturbance of ecological stability may take place in tropical regions due to the elevated biomass density resulting from heavy metal and other contaminant pollution. In this study, 62 valid soil samples were collected from Sanya. Source analysis of heavy metals in the area was carried out using absolute principal component-multiple linear regression receptor modelling (APCS-MLR); the comprehensive ecological risk of the study area was assessed based on pollution sources; the Monte-Carlo model was used to accurately predict the health risk of pollution sources in the study area. The results showed that: The average contents of soil heavy metals Cu, Ni and Cd in Sanya were 5.53, 6.56 and 11.66 times higher than the background values of heavy metals. The results of soil geo-accumulation index (Igeo) showed that Cr, Mo, Mn and Zn were unpolluted to moderately polluted, Cu and Ni were moderately polluted, and Cd was moderately polluted to strongly polluted. The main sources of heavy metal pollution were natural sources (57.99%), agricultural sources (38.44%) and traffic sources (3.57%). Natural and agricultural sources were jointly identified as priority control pollution sources and Cd was the priority control pollution element for soil ecological risk. Heavy metal content in Sanya did not pose a non-carcinogenic risk to the population, but there was a carcinogenic risk to children. The element Zn had a high carcinogenic risk to children, and was a priority controlling pollutant element for the risk of human health, with agricultural sources as the priority controlling pollutant source.

Biallelic HFM1 variants cause non-obstructive azoospermia with meiotic arrest in humans by impairing crossover formation to varying degrees.

STUDY QUESTION: Do variants in helicase for meiosis 1 (HFM1) account for male infertility in humans? SUMMARY ANSWER: Biallelic variants in HFM1 cause human male infertility owing to non-obstructive azoospermia (NOA) with impaired crossover formation and meiotic metaphase I (MMI) arrest. WHAT IS KNOWN ALREADY: HFM1 encodes an evolutionarily conserved DNA helicase that is essential for crossover formation and completion of meiosis. The null mutants of Hfm1 or its ortholog in multiple organisms displayed spermatogenic arrest at the MMI owing to deficiencies in synapsis and severe defects in crossover formation. Although HFM1 variants were found in infertile men with azoospermia or oligozoospermia, the causal relationship has not yet been established with functional evidence. STUDY DESIGN, SIZE, DURATION: A Pakistani family, having two infertile brothers born to consanguineous parents, and three unrelated Chinese men diagnosed with NOA were recruited for pathogenic variants screening. PARTICIPANTS/MATERIALS, SETTING, METHODS: All the patients were diagnosed with idiopathic NOA and, for the Chinese patients, meiotic defects were confirmed by histological analyses and/or immunofluorescence staining on testicular sections. Exome sequencing and subsequent bioinformatic analyses were performed to screen for candidate pathogenic variants. The pathogenicity of identified variants was assessed and studied in vivo in mice carrying the equivalent mutations. MAIN RESULTS AND THE ROLE OF CHANCE: Six variants (homozygous or compound heterozygous) in HFM1 were identified in the three Chinese patients with NOA and two brothers with NOA from the Pakistani family. Testicular histological analysis revealed that spermatogenesis is arrested at MMI in patients carrying the variants. Mice modeling the HFM1 variants identified in patients recapitulated the meiotic defects of patients, confirming the pathogenicity of the identified variants. These Hfm1 variants led to various reductions of HFM1 foci on chromosome axes and resulted in varying degrees of synapsis and crossover formation defects in the mutant male mice. In addition, Hfm1 mutant female mice displayed infertility or subfertility with oogenesis variously affected. LIMITATIONS, REASONS FOR CAUTION: A limitation of the current study is the small sample size. Owing to the unavailability of fresh testicular samples, the defects of synapsis and crossover formation could not be detected in spermatocytes of patients. Owing to the unavailability of antibodies, we could not quantify the impact of these variants on HFM1 protein levels. WIDER IMPLICATIONS OF THE FINDINGS: Our findings provide direct clinical and in vivo functional evidence that HFM1 variants cause male infertility in humans and also suggest that HFM1 may regulate meiotic crossover formation in a dose-dependent manner. Noticeably, our findings from mouse models showed that HFM1 variants could impair spermatogenesis and oogenesis with a varying degree of severity and might also be compatible with the production of a few spermatozoa in men and subfertility in women, extending the phenotypic spectrum of patients with HFM1 variants. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the National Natural Science Foundation of China (31890780, 32070850, 32061143006, 32000587 and 31900398) and the Fundamental Research Funds for the Central Universities (YD2070002007 and YD2070002012). The authors declare no potential conflicts of interest. TRIAL REGISTRATION NUMBER: N/A.

A high neutrophil to lymphocyte ratio is associated with poor nutritional status in chronic kidney disease patients.

We aimed to investigate the relationship between the neutrophil to lymphocyte ratio (NLR) and nutritional parameters in chronic kidney disease (CKD) patients. In this cross-sectional study, 187 non-dialysis CKD patients were enrolled. Daily dietary energy intake (DEI) and daily dietary protein intake (DPI) were assessed by 3-d dietary records. Protein-energy wasting (PEW) was defined as Subjective Global Assessment (SGA) class B and C. Spearman correlation analysis, logistic regression analysis and receiver operating characteristic (ROC) curve analysis were performed. The median NLR was 2·51 (1·83, 3·83). Patients with CKD stage 5 had the highest NLR level. A total of 19·3 % (n 36) of patients suffered from PEW. The NLR was positively correlated with SGA and serum P, and the NLR was negatively correlated with BMI, waist and hip circumference, triceps skinfold thickness, mid-arm muscle circumference, DPI and Hb. Multivariate logistic regression analysis adjusted for DPI, DEI, serum creatinine, blood urea nitrogen, uric acid and Hb showed that a high NLR was an independent risk factor for PEW (OR = 1·393, 95 % CI 1·078, 1·800, P = 0·011). ROC analysis showed that an NLR ≥ 2·62 had the ability to identify PEW among CKD patients, with a sensitivity of 77·8 %, a specificity of 62·3 % and an AUC of 0·71 (95 % CI 0·63, 0·81, P < 0·001). The NLR was closely associated with nutritional status. NLR may be an indicator of PEW in CKD patients.

Cross-sectional study on the drug utilization and evaluation indicator of antibiotics used in pediatric population.

BACKGROUND: The lack of medication standards is a serious problem in paediatrics mainly because of age-related differences in organ development and physiological functions in children. Consequently, dosage measurement becomes inaccurate. For this reason, methods for evaluating and monitoring rational paediatric medications should be developed. Drug use indicators, such as those similar to the drug utilisation index (DUI) based on the Anatomical Therapeutic Chemical/Defined Daily Dose (DDD) and widely used for the assessment of appropriate dosage in adults, should be explored in terms of their applicability to children. METHODS: A total of 5,538 prescriptions of antibiotics selected from a general teaching hospital were included. Drug, dose, frequency and treatment duration were obtained from each prescription. The prescription daily dose (PDD) of each antibiotic drug was calculated as the average of the daily doses. Underdose and overdose were determined in terms of the PDD/DDD ratio for each prescription. Children's DUI (cDUI) was explored in terms of the appropriate dosage for children as follows: the meaning of children's DDD (cDDD) and the evaluation of paediatric drug dosage. RESULTS: The top five antibiotics and their utilisation rates were as follows: cefmetazole sodium injection (18.47 %), erythromycin lactobionate injection (15.07 %), amoxicillin/clavulanate potassium injection (10.72 %), ceftriaxone sodium injection (9.50 %) and azithromycin dry suspension (8.02 %). The ratio of cDUI and PDD/cDDD was mostly not close to 1. CONCLUSIONS: The establishment of a cDUI system is an effective means of paediatric dosage evaluation. In addition to DDDs, cDUI and PDD/cDDD should be used to analyse the utilisation of antibiotics in children.

Coding mutations in NUS1 contribute to Parkinson's disease.

Whole-exome sequencing has been successful in identifying genetic factors contributing to familial or sporadic Parkinson's disease (PD). However, this approach has not been applied to explore the impact of de novo mutations on PD pathogenesis. Here, we sequenced the exomes of 39 early onset patients, their parents, and 20 unaffected siblings to investigate the effects of de novo mutations on PD. We identified 12 genes with de novo mutations (MAD1L1, NUP98, PPP2CB, PKMYT1, TRIM24, CEP131, CTTNBP2, NUS1, SMPD3, MGRN1, IFI35, and RUSC2), which could be functionally relevant to PD pathogenesis. Further analyses of two independent case-control cohorts (1,852 patients and 1,565 controls in one cohort and 3,237 patients and 2,858 controls in the other) revealed that NUS1 harbors significantly more rare nonsynonymous variants (P = 1.01E-5, odds ratio = 11.3) in PD patients than in controls. Functional studies in Drosophila demonstrated that the loss of NUS1 could reduce the climbing ability, dopamine level, and number of dopaminergic neurons in 30-day-old flies and could induce apoptosis in fly brain. Together, our data suggest that de novo mutations could contribute to early onset PD pathogenesis and identify NUS1 as a candidate gene for PD.

Prices, availability, and affordability of national essential medicines in public primary hospitals: A cross-sectional survey in poverty-stricken rural areas in China.

INTRODUCTION: This study aimed to determine the prices, availability, and affordability of national essential medicines in public primary hospitals in poverty-stricken areas of Anhui province, China. METHODS: A cross-sectional study was conducted in 143 public primary hospitals in Anhui province, eastern China. Data on access to 44 essential medicines was evaluated using the standardized methodology available in the World Health Organization and Health Action International manual. RESULTS: Median price rates show that 46.51% (21 of 44) of the lowest price generics and 100% of the originator brands were more expensive than the international reference price. The median availability of the 44 medicines was 31.47%, and 65.91% (29 of 44) of the medicines had less than 50% availability. The majority of the medicines were affordable as they would cost less than a day's income in sample areas. Suppliers could respond to 88.27% of the procuring orders raised by the 143 hospitals in the study, but this ranged from 43.96% to 99.86%. CONCLUSIONS: There is poor availability and non-ideal response rate of medicine delivery in public primary hospitals in poverty-stricken areas in eastern China. Further implementation of national essential medicine policy needs to focus on improving both availability and distribution efficiency in these areas.

A homozygous FANCM frameshift pathogenic variant causes male infertility.

PURPOSE: Fanconi anemia (FA) genes play important roles in spermatogenesis. In mice, disruption of Fancm impairs male fertility and testicular integrity, but whether FANCM pathogenic variants (PV) similarly affect fertility in men is unknown. Here we characterize a Pakistani family having three infertile brothers, two manifesting oligoasthenospermia and one exhibiting azoospermia, born to first-cousin parents. A homozygous PV in FANCM (c.1946_1958del, p.P648Lfs*16) was found cosegregating with male infertility. Our objective is to validate that FANCM p.P648Lfs*16 is the PV causing infertility in this family. METHODS: Exome and Sanger sequencing were used for PV screening. DNA interstrand crosslink (ICL) sensitivity was assessed in lymphocytes from patients. A mouse model carrying a PV nearly equivalent to that in the patients (FancmΔC/ΔC) was generated, followed by functional analysis in spermatogenesis. RESULTS: The loss-of-function FANCM PV increased ICL sensitivity in lymphocytes of patients and FancmΔC/ΔC spermatogonia. Adult FancmΔC/ΔC mice showed spermatogenic failure, with germ cell loss in 50.2% of testicular tubules and round-spermatid maturation arrest in 43.5% of tubules. In addition, neither bone marrow failure nor cancer/tumor was detected in all the patients or adult FancmΔC/ΔC mice. CONCLUSION: These findings revealed male infertility to be a novel phenotype of human patients with a biallelic FANCM PV.

Correction: A homozygous FANCM frameshift pathogenic variant causes male infertility.

Hao Win, Hui Ma and Sajjad Hussain were incorrectly affiliated to 'Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA'. These authors should only have been affiliated to 'Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China'. They were also not noted as contributing equally to the paper. Both these errors have now been corrected in the PDF and HTML versions of the paper.

Bi-allelic recessive loss-of-function mutations in FIGLA cause premature ovarian insufficiency with short stature.

Premature ovarian insufficiency (POI) is a group of heterogeneous disorders characterized by decreased ovarian reserve and increased follicle stimulating hormone (FSH) levels. It is rarely associated with short stature. FIGLA mutations with POI are identified with regard to heterozygosity; till date, only one affected family has been identified with homozygous mutations in FIGLA but without functional evaluation. Here, we described two POI patients from a consanguineous family from China. An 18-year-old girl and her sister presented with primary amenorrhea and increased FSH and luteinizing hormone levels, but the sister also presented with short stature and bone age delay. Whole-genome sequencing analysis identified a recurrent homozygous mutation in the FIGLA gene, c.2 T > C (p.Met1Thr), in this family member with POI; this variant was segregated within the pedigree. This change was absent in 382 control subjects, and we did not detect any mutations in 39 other idiopathic POI patients. in vitro functional analysis indicates that the p.Met1Thr mutation does not affect the transcription of the FIGLA gene, but blocks the synthesis of the full-length FIGLA protein. Our results support the notion that bi-allelic recessive loss-of-function effects of FIGLA contribute to POI patients with short stature and expand the FIGLA-related phenotypic spectrum.

Influencing factors of physicians' prescription behavior in selecting essential medicines: a cross-sectional survey in Chinese county hospitals.

BACKGROUND: To explore the key factors affecting prescription practices of essential medicines in Chinese county hospital. National essential medicine policy (NEMP) plays important roles in health care system, especially in developing countries. As a fundamental component in the Chinese health system reform, NEMP was implemented in primary health care institutions during the first stage of reform. As it is rolled out, priority usage and zero-mark-up policy of essential medicines are to be applied in every government-run healthcare institution. However, the intention and influence factors of physicians on priority selecting essential medicine remains unclear. METHODS: Based on the theory of planned behavior, a cross-sectional questionnaire survey was conducted to analyze physicians' intention, attitude, subjective norms (SNs) and perceived behavioral control (PBC) on prescrictions and their actual behavior on selection of essential medicines. RESULTS: Two hundred eighty-two physicians participated in the structural questionnaire interview. The final structural equation model reflected influencing factors affecting physicians' prescribing behavior (χ2/df = 1.32, GFI = 0.99, IFI = 0.99). Structural equation model analysis showed that attitude, other influencers and institutional environment, and PBC significantly affected behavioral intention. However, the control extent of cognition behavior of physicians prescribing had no significant positive effect on the priority usage of essential medicines. CONCLUSION: Investigation results demonstrate physicians are unaware of NEMP design and implementation plans. To help enhance rational use of essential medicines we suggest educating physicians on the value of NEMP, and integrating the drug shortage report into the essential medicine (EM) bidding system seamless communication with pharmaceutical manufacturers' credit information system.

Trends analysis for drug utilization in county public hospitals: a sample study of the pilot area of health care reform in China.

BACKGROUND: Changes in the national drug policy always have impact on the drug utilization. In the context of China health care reform, what changes had happened in the trend of drug utilization in public hospitals? Has this change met the expectations of policy design? This study was conducted to explore the trend of medicine consumption in county public hospitals before and after health care reform, and to provide real-world evidence to help assess the effectiveness of national drug policy. METHODS: A cross-sectional study was performed to investigate the drug utilization trends of 6 county public hospitals in Anhui Province, which is the first pilot area of China health care reform. Data were collected before and after the implementation of the China National Essential Medicine Policy (NEMP) to analyse the drug utilization indicators, such as the drug utilization constituent ratio, the rate of essential medicine usage and the rate of antibiotic consumption. RESULTS: Chemicals are used most frequently and account for 60%~ 70%, followed by oral agents of proprietary Chinese medicine. The results also show increased consumption of Chinese medicine injections (χ2 = 28.428, P < 0.01). The top 3 chemical medicines consumed were anti-infective drugs (12.92%), cardiovascular system drugs (11.61%), and digestive system drugs (8.42%). For Chinese traditional medicine, the top 3 drugs consumed were internal medicine drugs (66.03%), surgical drugs (8.45%), and gynaecological drugs (7.70%). The total sales amounts of drugs covered by medical insurance are at a high level (all above 80%), whereas essential medicines are less than 50% at almost all county-level medical institutions. CONCLUSIONS: This study uncovered the changing tendency of medicine usage under the implementation of the reform. Chinese medicine injections and anti-infective drugs have always been a sustained concern of pharmacovigilance. It is noteworthy that although essential medicines are advocated for as a priority for use in the government-run hospital, the consumption proportion of these medicines is lower than expected.

Association between circulating leptin levels and multiple sclerosis: a systematic review and meta-analysis.

AIM: Leptin, synthesised by adipocytes, has been identified as a hormone that can influence inflammatory activity. Several studies have investigated leptin levels in patients with multiple sclerosis (MS), but the results are not consistent. This study aims to derive a more precise evaluation on the relationship between circulating leptin levels and MS. DESIGN: A comprehensive literature searched up to July 2017 was conducted to evaluate the association of circulating leptin levels and MS. The random-effect model was applied to calculate pooled standardised mean difference (SMD) and its 95% CI. MAIN OUTCOME MEASURES: Circulating leptin levels of patients with MS and healthy controls. RESULTS: Of 2155 studies identified, 33 met eligibility criteria and 9 studies with 645 patients with MS and 586 controls were finally included in the meta-analysis. Meta-analysis revealed that, compared with the healthy control group, the MS group had significantly higher plasma/serum leptin levels, with the SMD of 0.70% and 95% CI (0.24 to 1.15). Subgroup analyses suggested that the leptin levels of patients with MS were associated with region, age, study sample size, measurement type, gender and blood sample type. CONCLUSION: Overall, our study suggests that patients with MS have a significantly higher leptin level than in healthy controls. Further mechanism studies and longitudinal large cohort studies are still needed to further reveal the role of leptin in the pathogenesis of MS.

Phosphatase PP4 Negatively Regulates Type I IFN Production and Antiviral Innate Immunity by Dephosphorylating and Deactivating TBK1.

The effective recognition of viral infection and subsequent type I IFN production is essential for the host antiviral innate immune responses. The phosphorylation and activation of kinase TANK-binding kinase 1 (TBK1) plays crucial roles in the production of type I IFN mediated by TLR and retinoic acid-inducible gene I-like receptors. Type I IFN expression must be tightly regulated to prevent the development of immunopathological disorders. However, how the activated TBK1 is negatively regulated by phosphatases remains poorly understood. In this study, we identified a previously unknown role of protein phosphatase (PP)4 by acting as a TBK1 phosphatase. PP4 expression was upregulated in macrophages infected with RNA virus, vesicular stomatitis virus, and Sendai virus in vitro and in vivo. Knockdown of PP4C, the catalytic subunit of PP4, significantly increased type I IFN production in macrophages and dentritic cells triggered by TLR3/4 ligands, vesicular stomatitis virus, and Sendai virus, and thus inhibited virus replication. Similar results were also found in peritoneal macrophages with PP4C silencing in vivo and i.p. infection of RNA virus. Accordingly, ectopic expression of PP4C inhibited virus-induced type I IFN production and promoted virus replication. However, overexpression of a phosphatase-dead PP4C mutant abolished the inhibitory effects of wild-type PP4C on type I IFN production. Mechanistically, PP4 directly bound TBK1 upon virus infection, then dephosphorylated TBK1 at Ser(172) and inhibited TBK1 activation, and subsequently restrained IFN regulatory factor 3 activation, resulting in suppressed production of type I IFN and IFN-stimulated genes. Thus, serine/threonine phosphatase PP4 functions as a novel feedback negative regulator of RNA virus-triggered innate immunity.

Health Risk Assessment Research on Heavy Metals Ingestion Through Groundwater Drinking Pathway for the Residents in Baotou, China.

Drinking groundwater is a significant pathway for human exposure to heavy metals. To evaluate the health effect of some heavy metals ingestion through the groundwater drinking pathway, the authors collected 35 groundwater samples from the drinking water wells of local residents and the exploitation wells of waterworks in Baotou, China. The monitoring results indicate that the groundwater had been polluted by heavy metals in some regions of the study area. A health risk assessment model derived from the U.S. Environmental Protection Agency was used to determine the noncarcinogenic and carcinogenic effects to residents who drink groundwater. All the respondents in the study area were at potential risk of carcinogenic health effects from arsenic when using the lowest safe standard for carcinogenic risk (1E-06). The hazard quotient values for noncarcinogenic health risk of arsenic exceeded 1 in 14.3% of the sampling wells in the study area. The research results could provide baseline data for groundwater utilization and supervision in the Baotou plain area.

The ratio of neutrophil to lymphocyte as a potential marker of clinicopathological activity for lupus nephritis.

INTRODUCTION: The ratio of neutrophil to lymphocyte (NLR) is a novel inflammatory factor that is elevated in systemic lupus erythematosus (SLE). However, the relationship between NLR and renal pathological manifestations in patients with lupus nephritis (LN) has not been investigated. METHODS: A retrospective study included 240 SLE patients, in which 186 patients with renal involvement and 124 LN patients underwent renal biopsy, 125 healthy volunteers and 125 chronic kidney disease (CKD) controls. Patients with SLE disease activity 2000 (SLEDAI-2 K) > 9 and ≤ 9 were defined as severely active and mildly active, respectively. Clinical parameters and renal pathological data were collected from medical records. The correlations between NLR and clinicopathological features were analyzed. RESULTS: The NLR of SLE group was significantly higher than that of the sex-age matched control groups. Patients with nephritis had higher NLR levels than those without nephritis (P = 0.044). Increased NLR was observed in severely active group compared to mildly active group (P = 0.020). NLR was significantly positively related with SLEDAI score, Renal SLEDAI score, C-reactive protein (CRP), 24-h urine protein, renal activity index (AI), cellular crescents and tubular atrophy, and negatively correlated with serum albumin. NLR was significantly decreased after treatment. Based on the receiver operating characteristic (ROC) curve, the best NLR cut-off value to predict severe activity of SLE and cellular crescents in renal pathology was 2.19 and 3.16, respectively. CONCLUSION: NLR may be a non-invasive and potential inflammatory marker in evaluating clinical and renal pathological activity in LN patients.