Genome-Wide Interaction and Pathway-Based Identification of Key Regulators in Multiple Myeloma
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Supplemental Information IRF4 Transcription Factor-Dependent Cd11b+ Dendritic Cells in Human and Mouse Control Mucosal IL-17 C
Immunity, Volume 38 Supplemental Information IRF4 Transcription Factor-Dependent CD11b+ Dendritic Cells in Human and Mouse Control Mucosal IL-17 Cytokine Responses Andreas Schlitzer, Naomi McGovern, Pearline Teo, Teresa Zelante, Koji Atarashi, Donovan Low, Adrian W.S. Ho, Peter See, Amanda Shin, Pavandip Singh Wasan, Guillaume Hoeffel, Benoit Malleret, Alexander Heiseke, Samantha Chew, Laura Jardine, Harriet A. Purvis, Catharien M.U. Hilkens, John Tam, Michael Poidinger, E. Richard Stanley, Anne B. K rug, Laurent Renia, Baalasubramanian Sivasankar, Lai Guan Ng, Matthew Collin, Paola Ricciardi-Castagnoli, Kenya Honda, Muzlifah Haniffa, and Florent Ginhoux Supplemental Inventory 1. Supplemental Figures and Tables Figure S1, Related to Figure 1 Figure S2, Related to Figure 2 and 3 Figure S3, Related to Figure 4 Figure S4, Related to Figure 5 Figure S5, Related to Figure 5 Figure S6, Related to Figure 7 Table S1, Related to Figure 3 Table S2, Related to Figure 6 Table S3, Related to Figure 6 2. Supplemental Experimental Procedures 3. Supplemental References Supplementary figure 1 Sorting strategy for mouse lung and small intestinal DC A Sorting strategy, Lung Singlets Dapi-CD45+ 250K 250K 250K 105 200K 200K 200K 104 A I - 150K 150K 150K C P C C 3 10 S A S S 100K 100K S 100K D S S 102 50K 50K 50K 0 0 0 0 0 50K 100K 150K 200K 250K 0 50K 100K 150K 200K 250K 0 103 104 105 0 103 104 105 FSC FSC-W CD45 GR1 Auto Fluor.- MHCII+ GR1- SSClow CD11c+ CD11b+ 250K 105 105 105 200K 4 104 10 104 150K I 3 I 3 4 3 0 10 3 C 2 H 10 10 100K 1 S D C D S C M 2 C 10 50K 0 0 0 0 0 102 103 104 105 0 103 104 105 0 103 104 105 0 103 104 105 Auto fluor. -
A Human Population-Based Organotypic in Vitro Model for Cardiotoxicity Screening1
ALTEX preprint published July 8, 2018 doi:10.14573/altex.1805301 Research Article A human population-based organotypic in vitro model for cardiotoxicity screening1 Fabian A. Grimm1, Alexander Blanchette1, John S. House2, Kyle Ferguson1, Nan-Hung Hsieh1, Chimeddulam Dalaijamts1, Alec A. Wright1, Blake Anson5, Fred A. Wright3,4, Weihsueh A. Chiu1, Ivan Rusyn1 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; 2Bioinformatics Research Center, 3Department of Biological Sciences, and 4Department of Statistics, North Carolina State University, Raleigh, NC, USA; 5Cellular Dynamics International, Madison, WI, USA Abstract Assessing inter-individual variability in responses to xenobiotics remains a substantial challenge, both in drug development with respect to pharmaceuticals and in public health with respect to environmental chemicals. Although approaches exist to characterize pharmacokinetic variability, there are no methods to routinely address pharmacodynamic variability. In this study, we aimed to demonstrate the feasibility of characterizing inter-individual variability in a human in vitro model. Specifically, we hypothesized that genetic variability across a population of iPSC- derived cardiomyocytes translates into reproducible variability in both baseline phenotypes and drug responses. We measured baseline and drug-related effects in iPSC-derived cardiomyocytes from 27 healthy donors on kinetic Ca2+ flux and high-content live cell imaging. Cells were treated in concentration-response with cardiotoxic drugs: isoproterenol (β- adrenergic receptor agonist/positive inotrope), propranolol (β-adrenergic receptor antagonist/negative inotrope), and cisapride (hERG channel inhibitor/QT prolongation). Cells from four of the 27 donors were further evaluated in terms of baseline and treatment-related gene expression. Reproducibility of phenotypic responses was evaluated across batches and time. -
Gene Expression of Osteosarcoma Cells on Various Coated Titanium Materials
MOLECULAR & CELLULAR TOXICOLOGY, Vol. 3, No. 1, 36-45, March 2007 Gene Expression of Osteosarcoma Cells on Various Coated Titanium Materials Sung-Hwa Sohn1, Jae Bun Lee2, Ki-Nam Kim1, are made with Ti alloys. However, the exact effect of In Kyoung Kim1, Seung Ho Lee1, Hye Won Kim1, Ti on osteoblasts is still unknown2-4. Successful ap- Sang-Hui Seo1, Yu-Ri Kim1, Sang-Wan Shin2, plication of such materials for bone regeneration Jae-Jun Ryu2 & Meyoung-Kon Kim1 often involved mixing with autogenous bone, a sour- ce of osteoblastic cells and precursors2. 1Department of Biochemistry & Molecular Biology Surface topography may affect the formation of a 2Department of Dentistry, College of Medicine, Korea University, fibrous capsule around implants, inflammatory res- Seoul 136-705, Korea ponse at tissue-implant interface, fibroblast attach- Correspondence and requests for materials should be addressed ment, angiogenesis, epithelial down-growth around to M-K. Kim ([email protected]) percutaneous devices, and many cellular processes such as cellular differentiation, transcription, cell Accepted 8 March 2007 metabolism, protein production, and phenotypic ex- pression1,3,5-7. Diverse implant surface may contribute to the regulation of osteoblast differentiation by infl- Abstract uencing the level of gene expression of key osteo- genic factors7,8. Morphometric analyses had shown Several features of the implant surface, such as differences in bone-implant contact percentages with topography, roughness, and composition play a the varying of surface characteristics, as well as a relevant role in implant integration with bone. This sensitivity of cells to surface topography9,10. Gene ex- study was conducted in order to determine the pression in response to the placement of implants effects of different-coatings on Ti surfaces on the with different surface topographies11-16. -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Sex-Dependent Differences in the Secretome of Human Endothelial Cells Maria Grazia Cattaneo1*†, Cristina Banfi2†, Maura Brioschi2, Donatella Lattuada1 and Lucia M
Cattaneo et al. Biology of Sex Differences (2021) 12:7 https://doi.org/10.1186/s13293-020-00350-3 RESEARCH Open Access Sex-dependent differences in the secretome of human endothelial cells Maria Grazia Cattaneo1*†, Cristina Banfi2†, Maura Brioschi2, Donatella Lattuada1 and Lucia M. Vicentini1 Abstract Background: Cellular sex has rarely been considered as a biological variable in preclinical research, even when the pathogenesis of diseases with predictable sex differences is studied. In this perspective, proteomics, and “omics” approaches in general, can provide powerful tools to obtain comprehensive cellular maps, thus favoring the discovery of still unknown sex-biased physio-pathological mechanisms. Methods: We performed proteomic and Gene Ontology (GO) analyses of the secretome from human serum- deprived male and female endothelial cells (ECs) followed by ELISA validation. Apoptosis was detected by FACS and Western blot techniques and efferocytosis through the ability of the macrophage cell line RAW 264.7 to engulf apoptotic ECs. PTX3 mRNA levels were measured by RT-qPCR. Results: Proteomic and GO analyses of the secretome from starved human male and female ECs demonstrated a significant enrichment in proteins related to cellular responses to stress and to the regulation of apoptosis in the secretome of male ECs. Accordingly, a higher percentage of male ECs underwent apoptosis in response to serum deprivation in comparison with female ECs. Among the secreted proteins, we reliably found higher levels of PTX3 in the male EC secretome. The silencing of PTX3 suggested that male ECs were dependent on its expression to properly carry out the efferocytotic process. At variance, female EC efferocytosis seemed to be independent on PTX3 expression. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Unique Concatenate (Description)
Unique Concatenate (Description) Sequence Variable modifications ([position] description) CP-690,550_1CP-690,550_2NVP-BSK805_1NVP-BSK805_2NVP-BBT594 123 ABI1 Isoform 1 of Abl interactor 1 TLEPVKPPTVPNDYMTSPAR [14] Phospho (Y) 5.355704 -0.70208 ABL1 Isoform IA of Proto-oncogene tyrosine-protein kinase ABL1 LMTGDTYTAHAGAK [7] Phospho (Y) -1.08927 -1.09868 -3.96523 ACLY ATP-citrate synthase TTDGVYEGVAIGGDR [6] Phospho (Y) 0.252136 ACSM3 SA hypertension-associated homolog isoform 1 LGIPEYFNFAK [6] Phospho (Y) -0.44989 1.66553 ACTB Actin, cytoplasmic 1 GYSFTTTAER [2] Phospho (Y) 1.066328 -0.37053 -0.0692 ACTB Actin, cytoplasmic 1 KDLYANTVLSGGTTMYPGIADR [4] Phospho (Y) -0.97756 0.141466 1.200179 -1.01433 -1.19347 AGPS Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor IRPVPEYQK [7] Phospho (Y) -0.39593 ALDH1A1 Retinal dehydrogenase 1 ANNTFYGLSAGVFTK [6] Phospho (Y) -0.02661 -1.93143 ALDOA Fructose-bisphosphate aldolase A PYQYPALTPEQK [2] Phospho (Y) 8.071839 -0.26633 ANXA2P2 Putative annexin A2-like protein LSLEGDHSTPPSAYGSVK [14] Phospho (Y) -1.49415 -2.13203 -2.06654 ANXA5 Annexin A5 LYDAYELK [5] Phospho (Y) -0.42726 7.051289 -1.37202 ATP1A1 Isoform Short of Sodium/potassium-transporting ATPase subunit alpha-1 GIVVYTGDR [5] Phospho (Y) -0.32719 BTK Tyrosine-protein kinase BTK HYVVCSTPQSQYYLAEK [12] Phospho (Y) -4.27596 BTK Tyrosine-protein kinase BTK VVALYDYMPMNANDLQLR [6] Phospho (Y)|[9] Oxidation (M)|[11] Oxidation (M) -2.48212 -1.06083 C11orf59 UPF0404 protein C11orf59 ALNGAEPNYHSLPSAR [9] Phospho (Y) -0.52861 -0.97348 C20orf4 -
The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z
REVIEW pubs.acs.org/CR The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z. Long* and Benjamin F. Cravatt* The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States CONTENTS 2.4. Other Phospholipases 6034 1. Introduction 6023 2.4.1. LIPG (Endothelial Lipase) 6034 2. Small-Molecule Hydrolases 6023 2.4.2. PLA1A (Phosphatidylserine-Specific 2.1. Intracellular Neutral Lipases 6023 PLA1) 6035 2.1.1. LIPE (Hormone-Sensitive Lipase) 6024 2.4.3. LIPH and LIPI (Phosphatidic Acid-Specific 2.1.2. PNPLA2 (Adipose Triglyceride Lipase) 6024 PLA1R and β) 6035 2.1.3. MGLL (Monoacylglycerol Lipase) 6025 2.4.4. PLB1 (Phospholipase B) 6035 2.1.4. DAGLA and DAGLB (Diacylglycerol Lipase 2.4.5. DDHD1 and DDHD2 (DDHD Domain R and β) 6026 Containing 1 and 2) 6035 2.1.5. CES3 (Carboxylesterase 3) 6026 2.4.6. ABHD4 (Alpha/Beta Hydrolase Domain 2.1.6. AADACL1 (Arylacetamide Deacetylase-like 1) 6026 Containing 4) 6036 2.1.7. ABHD6 (Alpha/Beta Hydrolase Domain 2.5. Small-Molecule Amidases 6036 Containing 6) 6027 2.5.1. FAAH and FAAH2 (Fatty Acid Amide 2.1.8. ABHD12 (Alpha/Beta Hydrolase Domain Hydrolase and FAAH2) 6036 Containing 12) 6027 2.5.2. AFMID (Arylformamidase) 6037 2.2. Extracellular Neutral Lipases 6027 2.6. Acyl-CoA Hydrolases 6037 2.2.1. PNLIP (Pancreatic Lipase) 6028 2.6.1. FASN (Fatty Acid Synthase) 6037 2.2.2. PNLIPRP1 and PNLIPR2 (Pancreatic 2.6.2. -
Lysine Benzoylation Is a Histone Mark Regulated by SIRT2
ARTICLE DOI: 10.1038/s41467-018-05567-w OPEN Lysine benzoylation is a histone mark regulated by SIRT2 He Huang1, Di Zhang1, Yi Wang2, Mathew Perez-Neut1, Zhen Han3, Y. George Zheng3, Quan Hao2 & Yingming Zhao1 Metabolic regulation of histone marks is associated with diverse biological processes through dynamically modulating chromatin structure and functions. Here we report the identification 1234567890():,; and characterization of a histone mark, lysine benzoylation (Kbz). Our study identifies 22 Kbz sites on histones from HepG2 and RAW cells. This type of histone mark can be stimulated by sodium benzoate (SB), an FDA-approved drug and a widely used chemical food preservative, via generation of benzoyl CoA. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbz marks are associated with gene expression and have physiological relevance distinct from histone acetylation. In addition, we demonstrate that SIRT2, a NAD+-dependent protein deacetylase, removes histone Kbz both in vitro and in vivo. This study therefore reveals a new type of histone marks with potential physiological relevance and identifies possible non-canonical functions of a widely used chemical food preservative. 1 Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA. 2 School of Biomedical Sciences, University of Hong Kong, Hong Kong, China. 3 Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA. Correspondence and requests for materials should be addressed to Y.Z. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:3374 | DOI: 10.1038/s41467-018-05567-w | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-05567-w hromatin structure and transcriptional activity of genes and coelution analysis were performed to compare the synthetic are regulated by diverse protein posttranslational mod- peptide with its in vivo counterpart (Fig. -
New Approach for Untangling the Role of Uncommon Calcium-Binding Proteins in the Central Nervous System
brain sciences Review New Approach for Untangling the Role of Uncommon Calcium-Binding Proteins in the Central Nervous System Krisztina Kelemen * and Tibor Szilágyi Department of Physiology, Doctoral School, Faculty of Medicine, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Târgu Mures, , Romania; [email protected] * Correspondence: [email protected]; Tel.: +40-746-248064 Abstract: Although Ca2+ ion plays an essential role in cellular physiology, calcium-binding proteins (CaBPs) were long used for mainly as immunohistochemical markers of specific cell types in different regions of the central nervous system. They are a heterogeneous and wide-ranging group of proteins. Their function was studied intensively in the last two decades and a tremendous amount of informa- tion was gathered about them. Girard et al. compiled a comprehensive list of the gene-expression profiles of the entire EF-hand gene superfamily in the murine brain. We selected from this database those CaBPs which are related to information processing and/or neuronal signalling, have a Ca2+- buffer activity, Ca2+-sensor activity, modulator of Ca2+-channel activity, or a yet unknown function. In this way we created a gene function-based selection of the CaBPs. We cross-referenced these findings with publicly available, high-quality RNA-sequencing and in situ hybridization databases (Human Protein Atlas (HPA), Brain RNA-seq database and Allen Brain Atlas integrated into the HPA) and created gene expression heat maps of the regional and cell type-specific expression levels of the selected CaBPs. This represents a useful tool to predict and investigate different expression patterns and functions of the less-known CaBPs of the central nervous system. -
Impact of RNA‑Binding Motif 3 Expression on the Whole Transcriptome of Prostate Cancer Cells: an RNA Sequencing Study
ONCOLOGY REPORTS 40: 2307-2315, 2018 Impact of RNA‑binding motif 3 expression on the whole transcriptome of prostate cancer cells: An RNA sequencing study QINGZHUO DONG1, CHENGCHENG LV1, GEJUN ZHANG1,2, ZI YU1,2, CHUIZE KONG2, CHENG FU1 and YU ZENG1 1Department of Urology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042; 2Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China Received March 3, 2018; Accepted July 25, 2018 DOI: 10.3892/or.2018.6618 Abstract. RNA-binding motif 3 (RBM3) is a cold-shock Introduction protein that has been previously shown to attenuate cancer stem cell-like features in prostate cancer (PCa) cells. However, There were 4,292,000 new cases of cancer and 2,814,000 cases the mechanism underlying RBM3 regulation in PCa cells is of cancer-associated mortality reported in 2015 in China (1). largely unknown. The present study investigated the impact Among all types of cancer, prostate cancer (PCa) was diag- of RBM3 expression on the whole transcriptome of PCa nosed in ~603,000 men, and over 26,000 men succumbed to cells using high-throughput RNA sequencing (RNA-seq). this disease (1). Although the incidence and mortality rates of Differentially expressed genes (DEGs) that were identified PCa remain lower in China than in Western countries, they through RNA-seq were applied to Gene Ontology (GO), are increasing rapidly. Thus, PCa has become one of the major pathway analysis, pathway-action networks and protein-protein healthy issues for men in China.