Objective To determine the pathogen of a local dengue fever outbreak in Shenzhen city in 2010,and to analyze the molecular characteristics of the epidemic dengue virus strain as well as explore the possible origin.Methods The serum samples collected from the suspect dengue fever cases were detected for IgM, IgG by enzyme-linked immunosorbent assay ( ELISA ),immunochromatography and dengue virus nucleic acid by real-time polymerase chain reaction (PCR).Serum samples from patients with early stage dengue fever were used to isolate virus with C6/36 and BHK-21 cell lines.The type of isolated virus strain was determined by RT-semi-nested-PCR and realtime PCR.E gene of isolated virus strain was amplified by RT-PCR and sequenced.Homology and phylogenetic tree of E gene of Shenzhen dengue virus with the strains isolated from other areas were constructed.Results IgM,IgG and RNA of type 1 dengue virus were detected in serum samples from dengue fever suspected patients.Type 1 dengue virus named DEV1-SZ1029 was successfully isolated from the serum sample.The homology of nucleotide sequence of E gene of SZ1029 strain with standard type 1 dengue virus HAWAII 45,Fj231/04,GD14/97 and GD05/99 were 94.8％,99.6％,97.7％ and 98.5 ％,respectively.The phylogenetic tree indicated that SZ1029 had the greatest similarity with the D1/Malaysia/36000/05 strain,SG(EHI)DED142808 strain and Fj231/04 strain and they lied in the same branch of the phylogenetic tree.The isolated dengue virus type 1 belonged to genetype Ⅰ with GZ/80,Taiwan87,All patients lived in a certain construction site in Shenzhen and had no recent travel history outside the area in one month before infection.Conclusions The virological,serological and molecular features all identify that the local dengue fever outbreak in Shenzhen in 2010 is caused by type 1 dengue virus and SZ1029 strain may be transferred from Southeast Asian region,and there may be a plague focus in Shenzhen.

Objectivde To explore the efficacy of i-GMS applied to the diabetes patient outside the hospital.Methods Totally 80 type 2 diabetes mellitus patients were divided into an experiment group (Group A) and a control group (Group B).Group A executed blood glucose monitoring by Glucose Management App and intelligent blood glucose meter (personal version),and Group B completed monitoring by some portable blood glucose meter.Telephone follow-up was performed once a week,and the two groups were compared on glycated albumin (GA) value 3 weeks after discharging,values of HbA1c,FPG and PG2h 3 months after,the times of blood glucose monitoring and hypoglycaemia as well as the patient satisfaction over the glucose management.Results Group A had the values of GA,HbA1c,FPG and PG2h significantly lower than those of Group B (P＜ 0.05).The times of glucose monitoring and patient satisfaction in Group A were statistically higher than those of Group B,while the incidence rate of hypoglycaemia of the former was lower than that of the latter (P＜0.05).Conclusion I-GMS proves efficient when used for glucose self monitoring and management of the type 2 diabetes mellitus patient.

Objective To perform laboratory detection and molecular traceability analysis on a case of imported kala-azar in Shenzhen to determine the infection strain. Methods Bone marrow puncture fluid and blood samples from a case of kala-azar in Shenzhen were collected for laboratory tests. The patient's bone marrow puncture fluid smears were stained with Giemsa and examined under a microscope. Blood samples were examined for antibodies using the rk39 visceral leishmania rapid diagnostic reagent. Whole blood DNA was extracted, and the ITS-1 sequence was amplified by PCR, sequenced and aligned, and a phylogenetic tree was constructed based on the ITS-1 sequence. Results Microscopic examination of the patient's bone marrow smears revealed a large number of Leishmania amastigotes without flagella, confirming the diagnosis of kala-azar. The patient's blood was tested positive with the rk39 rapid diagnostic reagent, and PCR amplification yielded an ITS-1 gene product sequence that matched the expected size. Sequence alignment with the NCBI database showed 100% sequence similarity with the ITS-1 gene sequence of Leishmania infantum, confirming the infecting strain as Leishmania infantum. Phylogenetic tree construction of the amplified ITS-1 sequence revealed clustering into a clade with Leishmania infantum , and close to KC347299, one of the reference sequence selected. Conclusions The case of kala-azar in Shenzhen was caused by Leishmania infantum. Kala-azar still occurs in China, so the diagnostic technology of medical personnel in non-epidemic areas should be strengthened so that they can actively use new diagnostic technologies to assist in diagnosis, thus improving their prevention and control ability of Leishmania parasites.

Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. CoBRA provides a comprehensive state-of-the-art ChIP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience. This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference database, and pathway analysis. CoBRA is publicly available online at https://bitbucket. org/cfce/cobra.

BRAF is a serine/threonine kinase that harbors activating mutations in ∼7% of human malignancies and ∼60% of melanomas. Despite initial clinical responses to BRAF inhibitors, patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma, we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors. To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas, we integrate expression, ATAC-seq, and CRISPR screen data. We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6, which together enable resistance to BRAF inhibitors in melanoma cells. Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720, providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.

Objective To investigate the prevalence and risk predictors of depressive tendency in type 2 diabetic patients with peripheral neuropathy.Methods From May 2017 to December 2017,150 diabetic patients with peripheral neuropathy and 150 diabetic patients without peripheral neuropathy in the First Affiliated Hospital of Harbin Medical University were collected.The general clinical data,including age,sex,diabetic duration,height,weight,body mass index (BMI),fasting blood glucose (FBG),fasting insulin (FINS),homeostasis modal assessment-insulin resistance index(HOMA-IR),glycated hemoglobin(HbA1c),blood lipid and blood pressure were collected.The motor nerve and sensory nerve conduction velocity of lower limbs were measured by electromyograph.Zung depression self-rating scale(SDS) was used for self-rating of depression syndrome.Results There were 46 cases(30.67％) suffered from depression(SDS ＞50) in the neuropathic group,and 25 cases(16.67％) suffered from depression in the non-neuropathic group.The incidence rate of depression in the neuropathic group was significantly higher than that in the non-neuropathic group and tended to be severe (x2 =12.732,P =0.005).Non-conditional Logistic multivariate stepwise regression analysis showed that sex,the course of diabetes and low density lipoprotein (LDL) were associated with depressive tendency (x2 =3.994,P =0.049;x2 =5.334,P =0.032;x2 =6.172,P =0.020).Conclusion The prevalence of depression in diabetic patients with peripheral neuropathy is higher and tends to be severe.Sex,the course of diabetes and LDL are risk factors of depressive tendency.

Targeted protein degradation(TPD)has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell's endogenous protein degrada-tion machinery.However,the susceptibility of proteins for targeting by TPD approaches,termed"degradability",is largely unknown.Here,we developed a machine learning model,model-free anal-ysis of protein degradability(MAPD),to predict degradability from features intrinsic to protein tar-gets.MAPD shows accurate performance in predicting kinases that are degradable by TPD compounds[with an area under the precision-recall curve(AUPRC)of 0.759 and an area under the receiver operating characteristic curve(AUROC)of 0.775]and is likely generalizable to inde-pendent non-kinase proteins.We found five features with statistical significance to achieve optimal prediction,with ubiquitination potential being the most predictive.By structural modeling,we found that E2-accessible ubiquitination sites,but not lysine residues in general,are particularly associated with kinase degradability.Finally,we extended MAPD predictions to the entire proteome to find 964 disease-causing proteins(including proteins encoded by 278 cancer genes)that may be tractable to TPD drug development.

Proteins usually associate with other molecules physically to execute their functions. Identifying these interactions is important for the functional analysis of proteins. Previously, we reported the parallel analysis of translated ORFs (PLATO) to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the "bait" molecules, followed by the deep sequencing analysis of mRNA. However, the sample processing, from extraction of precipitated mRNA to generation of DNA libraries, includes numerous steps, which is tedious and may cause the loss of materials. Barcoded PLATO (PLATO-BC), an improved platform was further developed to test its application for protein interaction discovery. In this report, we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis (IBM). Tripartite motif containing 21 (TRIM21) was identified as a potentially new IBM autoantigen. We also expanded the application of PLATO-BC to identify protein interactions for JQ1, single ubiquitin peptide, and NS5 protein of Zika virus. From PLATO-BC analyses, we identified new protein interactions for these "bait" molecules. We demonstrate that Ewing sarcoma breakpoint region 1 (EWSR1) binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4. RIO kinase 3 (RIOK3), a newly identified ubiquitin-binding protein, is preferentially associated with K63-ubiquitin chain. We also find that Zika NS5 protein interacts with two previously unreported host proteins, par-3 family cell polarity regulator (PARD3) and chromosome 19 open reading frame 53 (C19orf53), whose attenuated expression benefits the replication of Zika virus. These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of "bait" molecules.

The mammalian epididymis not only plays a fundamental role in the maturation of spermatozoa, but also provides protection against various stressors. The foremost among these is the threat posed by oxidative stress, which arises from an imbalance in reactive oxygen species and can elicit damage to cellular lipids, proteins, and nucleic acids. In mice, the risk of oxidative damage to spermatozoa is mitigated through the expression and secretion of glutathione peroxidase 5 (GPX5) as a major luminal scavenger in the proximal caput epididymidal segment. Accordingly, the loss of GPX5-mediated protection leads to impaired DNA integrity in the spermatozoa of aged Gpx5

The TEA domain (TEAD) family proteins (TEAD1‒4) are essential transcription factors that control cell differentiation and organ size in the Hippo pathway. Although the sequences and structures of TEAD family proteins are highly conserved, each TEAD isoform has unique physiological and pathological functions. Therefore, the development and discovery of subtype selective inhibitors for TEAD protein will provide important chemical probes for the TEAD-related function studies in development and diseases. Here, we identified a novel TEAD1/3 covalent inhibitor (DC-TEADin1072) with biochemical IC