DeepSec: a deep learning framework for secreted protein discovery in human body fluids

Motivation: Human proteins that are secreted into different body fluids from various cells and tissues can be promising disease indicators. Modern proteomics research empowered by both qualitative and quantitative profiling techniques has made great progress in protein discovery in various human fluids. However, due to the large number of proteins and diverse modifications present in the fluids, as well as the existing technical limits of major proteomics platforms (e.g. mass spectrometry), large discrepancies are often generated from different experimental studies. As a result, a comprehensive proteomics landscape across major human fluids are not well determined. Results: To bridge this gap, we have developed a deep learning framework, named DeepSec, to identify secreted proteins in 12 types of human body fluids. DeepSec adopts an end-to-end sequence-based approach, where a Convolutional Neural Network is built to learn the abstract sequence features followed by a Bidirectional Gated Recurrent Unit with fully connected layer for protein classification. DeepSec has demonstrated promising performances with average area under the ROC curves of 0.85–0.94 on testing datasets in each type of fluids, which outperforms existing state-of-the-art methods available mostly on blood proteins. As an illustration of how to apply DeepSec in biomarker discovery research, we conducted a case study on kidney cancer by using genomics data from the cancer genome atlas and have identified 104 possible marker proteins

Establishment and application of a VP3 antigenic domain-based peptide ELISA for the detection of antibody against goose plague virus infection

The detection of antibody against goose plague virus (GPV) infection has never had a commercialized test kit, which has posed challenges to the prevention and control of this disease. In this study, bioinformatics software was used to analyze and predict the dominant antigenic regions of the main protective antigen VP3 of GPV. Three segments of bovine serum albumin (BSA) vector-coupled peptides were synthesized as ELISA coating antigens. Experimental results showed that the VP3-1 (358-392aa) peptide had the best reactivity and specificity. By using the BSA-VP3-1 peptide, a detection method for antibody against GPV infection was established, demonstrating excellent specificity with no cross-reactivity with common infectious goose pathogen antibodies. The intra-batch coefficient of variation and inter-batch coefficient of variation were both less than 7%, indicating good stability and repeatability. The dynamic antibody detection results of gosling vaccines and the testing of 120 clinical immune goose serum samples collectively demonstrate that BSA-VP3-1 peptide ELISA can be used to detect antibody against GPV in the immunized goose population and has higher sensitivity than traditional agar gel precipitation methods. Taken together, the developed peptide-ELISA based on VP3 358-392aa could be useful in laboratory viral diagnosis, routine surveillance in goose farms. The main application of the peptide-ELISA is to monitor the antibody level and vaccine efficacy for GPV, which will help the prevention and control of gosling plague

Tetra­aqua­bis(2-oxo-1,2-dihydro­quinoline-4-carboxyl­ato-κO 4)nickel(II)

In the title compound, [Ni(C10H6NO3)2(H2O)4], the central NiII atom is located on an inversion center and coordinated in a slightly distorted octa­hedral geometry by two O atoms from two 2-oxo-1,2-dihydro­quinoline-4-carboxyl­ate ligands and four water mol­ecules, all of which act as monodentate ligands. The crystal structure features an extensive network of inter­molecular hydrogen-bonding inter­actions (O—H⋯O and N—H⋯O) and offset face-to-face π–π stacking inter­actions [centroid–centroid distances = 3.525 (3) and 3.281 (5) Å]

Reactivation of hypersaline aerobic granular sludge after low-temperature storage

Chen, Y., Zhu, J. Y., Qin, Y., Zhang, Z. M., & Yuan, S. C.  (March-April, 2017). Reactivation of hypersaline aerobic  granular sludge after low-temperature storage.  Water  Technology and Sciences (in Spanish),  8 (2), 61-70.    Reactivation of hypersaline aerobic granular sludge after  low-temperature storage was studied by slowly increasing  the organic loading. Results indicated that the basic external  features of thawed hypersaline aerobic granules were still  largely intact after a six-week low temperature storage, but  the colors and internal structure changed greatly. Aerobic  granules experienced a process of particle disintegration,  fragmentary particles, filamentous bacteria-like particles,  and dense granules during the recovery process. After  more than one-month re-cultivation, the settling property,  dehydrogenase activity, and nitrification properties of  hypersaline aerobic granules returned to normal. During  the re-cultivated process, the decentralized growth pattern  of particles can be effectively controlled, and granules can  grow compactly by controlling water alkalinity, aeration rate  and reactor settling time

Effect of HNO3 treatment on the La0.6Sr0.4Co0.2Fe0.8O3-delta obtained via combined EDTA-citrate complexing process

The La0.6Sr0.4Co0.2Fe0.8O3-delta(LSCF) composite oxide was prepared via combined EDTA-citrate complexing process with concentrated nitric acid treatment. The treatment would result in the self-combustion of solid state precursors at low temperatures. The effect of preparing conditions on LSCF's catalytic properties was investigated by using decomposition of peroxide hydrogen as the model. The FT-IR results of the solid state precursor and the pH values of aqueous solution of it were studied to determine the mechanism of the thermal decomposition of organic in the precursor and of the self-combustion process. Moreover, XRD was employed to characterize the crystal structure of LSCF calcined at higher temperatures. The study shows that the treatment can depress the growth of crystallite and improve the catalysis for decomposition of peroxide hydrogen. Of the all samples, the LSCF-40-900 has the highest activity to the decomposition of peroxide hydrogen

Lack of association between the CALM1 core promoter polymorphism (-16C/T) and susceptibility to knee osteoarthritis in a Chinese Han population

<p>Abstract</p> <p>Background</p> <p><it>CALM1 </it>gene encodes calmodulin (CaM), an important and ubiquitous eukaryotic Ca²⁺-binding protein. Several studies have indicated that a deficient CaM function is likely to be involved in the pathogenesis of osteoarthritis (OA). Using a convincing genome-wide association study, a Japanese group has recently demonstrated a genetic association between the <it>CALM1 </it>core promoter polymorphism (-16C/T transition SNP, rs12885713) and OA susceptibility. However, the subsequent association studies failed to provide consistent results in OA patients of differently selected populations. The present study is to evaluate the association of the -16C/T polymorphism with knee OA in a Chinese Han population.</p> <p>Methods</p> <p>A case-control association study was conducted. The polymorphism was genotyped in 183 patients who had primary symptomatic knee OA with radiographic confirmation and in 210 matched controls. Allelic and genotypic frequencies were compared between patients and control subjects.</p> <p>Results</p> <p>No significant difference was detected in genotype or allele distribution between knee OA and control groups (all <it>P </it>> 0.05). The association was also negative even after stratification by sex. Furthermore, no association between the -16C/T SNP genotype and the clinical variables age, sex, BMI (body mass index) and K/L (Kellgren/Lawrence) score was observed in OA patients.</p> <p>Conclusion</p> <p>The present study suggests that the CALM1 core promoter polymorphism -16C/T is not a risk factor for knee OA susceptibility in the Chinese Han population. Further studies are needed to give a global view of this polymorphism in pathogenesis of OA.</p

High correlations between plant clonality and ecosystem service functions after management in a chronosequence of evergreen conifer plantations

IntroductionClimate change and mono-afforestation or mono-reforestation have continuously caused a decline in biodiversity and ecosystem services on forest plantations. Key plant functional traits in forests or plantations may affect ecosystem functions after forest management practices. Plant clonality, a key functional trait, frequently links to biodiversity and ecosystem functions and affects the biodiversity–ecosystem functioning relationship. However, little is known about how plant clonality affects ecosystem functions and services of plantations after forest management.MethodsWe conducted a field experiment to discuss the diversity and proportion of clonal plants, plant diversity of the communities, and ecosystem service functions and their relationships under 10 years of close-to-nature (CTN) management, artificial gap management, and control (i.e., without management) in the three stages of C. Lanceolata plantations.ResultsOur results showed that CTN and gap management modes significantly facilitated diversity of clonal plants, plant diversity of the communities, and parameters of ecosystem service functions in C. lanceolata plantations. Moreover, CTN management promoted plant community diversity, soil water conservation, and carbon storage the most in the earlier stand stages. Diversity of clonal plants was significantly positively correlated with ecosystem service functions after forest management. Structural equation modeling analysis indicated that forest gap or CTN management indirectly positively affected ecosystem service functions through increasing diversity of clonal woody plants and plant diversity of the communities.ConclusionOur results indicate a highly positive effect of gap or CTN management on diversity and proportion of clonal plants and on plant diversity of the communities, which link to improvements in ecosystem service functions (i.e., water and soil conservation and carbon storage). The link between forest management, diversity, and ecosystem functions suggests that key functional traits or plant functional groups should be considered to underline the mechanism of traits–ecosystem functioning relationships and the restoration of degraded plantations

ATAD2 Overexpression Identifies Colorectal Cancer Patients with Poor Prognosis and Drives Proliferation of Cancer Cells

ATPase family AAA domain-containing 2 (ATAD2) has been identified as a critical modulator involved in cell proliferation and invasion. The purpose of this study was to explore the expression of ATAD2 in CRC tissues as well as its relationship with degree of malignancy. Data containing three independent investigations from Oncomine database demonstrated that ATAD2 is overexpressed in CRC compared with normal tissue, and similar result was also found in 32 pairs of CRC tissues by qPCR. The protein expression of ATAD2 was examined in six CRC cell lines and 300 CRC specimens. The results showed that high expression of ATAD2 was significantly correlated with tumor size (P<0.001), serum CEA (P=0.012), lymph node metastasis (P=0.018), liver metastasis (P=0.025), and clinical stage (P=0.004). Kaplan-Meier method suggested that higher ATAD2 protein expression significantly associated with the overall survival (OS) of CRC patients (P<0.001) and was an independent predictor of poor OS. Functional studies showed that suppression of ATAD2 expression with siRNA could significantly inhibit the growth in SW480 and HCT116 cells. These results indicated that ATAD2 could serve as a prognostic marker and a therapeutic target for CRC

Suppress HBV by therapeutic vaccine

乙肝预防性疫苗显著减少了乙肝新发感染，但目前全球仍有约2.5亿慢性乙肝感染者，若未得到有效治疗，可能发展为肝癌、肝硬化等终末期肝病并导致死亡。夏宁邵教授团队研究发展了一种新型的B细胞表位嵌合型类病毒颗粒乙肝治疗性疫苗（治疗性蛋白），在多种模型中证实了其对慢性乙肝感染的治疗潜力，为研发治疗慢性乙肝的原创药物提供了新思路。 我校博士后张天英、博士生郭雪染和博士生巫洋涛为该论文共同第一作者，夏宁邵教授、袁权副教授、张军教授为该论文的共同通讯作者。【Abstract】Objective: This study aimed to develop a novel therapeutic vaccine based on a unique B cell epitope and investigate its therapeutic potential against chronic hepatitis B (CHB) in animal models. Methods: A series of peptides and carrier proteins were evaluated in HBV-tolerant mice to obtain an optimized therapeutic molecule. The immunogenicity,therapeutic efficacy and mechanism of the candidate were investigated systematically. Results: Among the HBsAg-aa119-125-containing peptides evaluated in this study, HBsAg-aa113-135 (SEQ13) exhibited the most striking therapeutic effects. A novel immuno-enhanced virus-like particle carrier (CR-T3) derived from the roundleaf bat HBV core antigen (RBHBcAg) was created and used to display SEQ13, forming candidate molecule CR-T3-SEQ13. Multiple copies of SEQ13 displayed on the surface of this particulate antigen promote the induction of a potent anti-HBs antibody response in mice, rabbits and cynomolgus monkeys. Sera and purified polyclonal IgG from the immunized animals neutralized HBV infection in vitro and mediated efficient HBV/HBsAg clearance in the mice. CR-T3-SEQ13-based vaccination induced long-term suppression of HBsAg and HBV DNA in HBV transgenic mice and eradicated the virus completely in hydrodynamic-based HBV carrier mice. The suppressive effects on HBsAg were strongly correlated with the anti-HBs level after vaccination, suggesting that the main mechanism of CR-T3-SEQ13 vaccination therapy was the induction of a SEQ13-specific antibody response that mediated HBV/HBsAg clearance. Conclusions: The novel particulate protein CR-T3-SEQ13 suppressed HBsAg effectively through induction of a humoral immune response in HBV-tolerant mice. This B cell epitope-based therapeutic vaccine may provide a novel immunotherapeutic agent against chronic HBV infection in humans.This work was supported by the National Scientific and Technological Major project (2017ZX10202203-001), the National Natural Science Foundation of China (31730029, 81672023, 81871316 and 81702006) and the Xiamen University President Fund Project (20720160063). 该研究获得了“艾滋病和病毒性肝炎等重大传染病防治”科技重大专项、国家自然科学基金等资助