Indoxyl Sulfate and P-Cresyl Sulfate Promote Vascular Calcification and Associate with Glucose Intolerance
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Types of Acute Phase Reactants and Their Importance in Vaccination (Review)
BIOMEDICAL REPORTS 12: 143-152, 2020 Types of acute phase reactants and their importance in vaccination (Review) RAFAAT H. KHALIL1 and NABIL AL-HUMADI2 1Department of Biology, College of Science and Technology, Florida Agricultural and Mechanical University, Tallahassee, FL 32307; 2Office of Vaccines, Food and Drug Administration, Center for Biologics Evaluation and Research, Silver Spring, MD 20993, USA Received May 10, 2019; Accepted November 25, 2019 DOI: 10.3892/br.2020.1276 Abstract. Vaccines are considered to be one of the most human and veterinary medicine. Proteins which are expressed cost-effective life-saving interventions in human history. in the acute phase are potential biomarkers for the diagnosis The body's inflammatory response to vaccines has both of inflammatory disease, for example, acute phase proteins desired effects (immune response), undesired effects [(acute (APPs) are indicators of successful organ transplantation phase reactions (APRs)] and trade‑offs. Trade‑offs are and can be used to predict the ameliorative effect of cancer more potent immune responses which may be potentially therapy (1,2). APPs are primarily synthesized in hepatocytes. difficult to separate from potent acute phase reactions. The acute phase response is a spontaneous reaction triggered Thus, studying acute phase proteins (APPs) during vaccina- by disrupted homeostasis resulting from environmental distur- tion may aid our understanding of APRs and homeostatic bances (3). Acute phase reactions (APRs) usually stabilize changes which can result from inflammatory responses. quickly, after recovering from a disruption to homeostasis Depending on the severity of the response in humans, these within a few days to weeks; however, APPs expression levels reactions can be classified as major, moderate or minor. -
Influence of Infection and Inflammation on Biomarkers of Nutritional Status
A2.4 INFLUENCE OF INFECTION AND INFLAMMATION ON BIOMARKERS OF NUTRITIONAL STATUS A2.4 Influence of infection and inflammation on biomarkers of nutritional status with an emphasis on vitamin A and iron David I. Thurnham1 and George P. McCabe2 1 Northern Ireland Centre for Food and Health, University of Ulster, Coleraine, United Kingdom of Great Britain and Northern Ireland 2 Statistics Department, Purdue University, West Lafayette, Indiana, United States of America Corresponding author: David I. Thurnham; [email protected] Suggested citation: Thurnham DI, McCabe GP. Influence of infection and inflammation on biomarkers of nutritional status with an emphasis on vitamin A and iron. In: World Health Organization. Report: Priorities in the assessment of vitamin A and iron status in populations, Panama City, Panama, 15–17 September 2010. Geneva, World Health Organization, 2012. Abstract n Many plasma nutrients are influenced by infection or tissue damage. These effects may be passive and the result of changes in blood volume and capillary permeability. They may also be the direct effect of metabolic alterations that depress or increase the concentration of a nutrient or metabolite in the plasma. Where the nutrient or metabolite is a nutritional biomarker as in the case of plasma retinol, a depression in retinol concentrations will result in an overestimate of vitamin A deficiency. In contrast, where the biomarker is increased due to infection as in the case of plasma ferritin concentrations, inflammation will result in an underestimate of iron deficiency. Infection and tissue damage can be recognized by their clinical effects on the body but, unfortunately, subclinical infection or inflammation can only be recognized by measur- ing inflammation biomarkers in the blood. -
Pathogen Receptor Discovery with a Microfluidic Human Membrane Protein Array
Pathogen receptor discovery with a microfluidic human membrane protein array Yair Glicka,1,Ya’ara Ben-Aria,1, Nir Draymanb, Michal Pellacha, Gregory Neveuc,d, Jim Boonyaratanakornkitc,d, Dorit Avrahamia, Shirit Einavc,d, Ariella Oppenheimb, and Doron Gerbera,2 aMina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Israel; bFaculty of Medicine, Hebrew University, Jerusalem, 9112001, Israel; cDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305; and dDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 Edited by Stephen R. Quake, Stanford University, Stanford, CA, and approved March 1, 2016 (received for review September 20, 2015) The discovery of how a pathogen invades a cell requires one to and translate into proteins in situ (10, 11). This approach has determine which host cell receptors are exploited. This determina- enabled the study of the Pseudomonas aeruginosa outer mem- tion is a challenging problem because the receptor is invariably a brane protein for immunity (12). membrane protein, which represents an Achilles heel in proteomics. Combining integrated microfluidics with microarrays and We have developed a universal platform for high-throughput ex- in vitro transcription and translation (TNT) systems may over- – pression and interaction studies of membrane proteins by creating a come all of the above mentioned difficulties (Fig. 1A) (13 16). microfluidic-based comprehensive human membrane protein array The integrated microfluidic device allows smart liquid manage- (MPA). The MPA is, to our knowledge, the first of its kind and offers ment in very low volumes, partitioning, and process integration a powerful alternative to conventional proteomics by enabling the (i.e., protein expression, immobilization, and interaction exper- simultaneous study of 2,100 membrane proteins. -
Autophagy: from Basic Science to Clinical Application
nature publishing group REVIEW See COMMENTARY page XX Autophagy: from basic science to clinical application J Va n L i m b e r g e n 1 , 2 , 3 , C S t e v e n s 4 , E R N i m m o 1 , D C W i l s o n 2 , 3 a n d J S a t s a n g i 1 Autophagy is a cellular pathway involved in protein and organelle degradation, which is likely to represent an innate adaptation to starvation. In times of nutrient deficiency, the cell can self-digest and recycle some nonessential components through nonselective autophagy, thus sustaining minimal growth requirements until a food source becomes available. Over recent years, autophagy has been implicated in an increasing number of clinical scenarios, notably infectious diseases, cancer, neurodegenerative diseases, and autoimmunity. The recent identification of the importance of autophagy genes in the genetic susceptibility to Crohn ’ s disease suggests that a selective autophagic response may play a crucial role in the pathogenesis of common complex immune-mediated diseases. In this review, we discuss the autophagic mechanisms, their molecular regulation, and summarize their clinical relevance. This progress has led to great interest in the therapeutic potential of manipulation of both selective and nonselective autophagy in established disease. INTRODUCTION The ability to adapt to environmental change is essential for sur- Autophagy encompasses several distinct processes involving vival. This is true for the organism as a whole and for individual the delivery of portions of the cytoplasm to the lysosome for cells alike. -
The Curious Case of Purple Urine
American Journal of Hospital Medicine Promoting research and education in the field of hospital medicine. ISSN 2474-7017 (online) April-June 2016: Volume 8 Issue 2 The Curious Case of Purple Urine April 6, 2016 April-June 2016: Volume 8 Issue 2, Case Reports Keywords Proteus mirabilis The Curious Case of Purple Urine Raj Parikh, M.D., M.P.H. (1); Rajive Tandon, M.D. (2) (1) Department of Internal Medicine, Rush University Medical Center. Chicago, IL (2) Department of Pulmonary and Critical Care Medicine, Rush University Medical Center. Chicago, IL Corresponding Author: Raj Parikh, M.D., 1653 W. Congress Parkway, Chicago, IL 60612, Tel: 860-558-5963, E-mail: [email protected] CASE REPORT A 53-year-old female with a history of spina bifida, complicated by urinary retention requiring a chronic indwelling urinary catheter, presented with altered mental status. The urinalysis was positive for WBCs (28/hpf) and leukocyte esterase. The patient was found to have purple urine (Figure 1). Figure 1: Purple urine noted in the patient’s urine bag at the time of admission. Urine culture grew . Computerized tomography (CT) of the pelvis was concerning for right-sided staghorn calculi as well as dilated calyces in the right kidney and no evidence of underlying renal disease (Figure 2). The patient was started on appropriate antibiotic therapy with Ertapenem (MIC: < 0.5 mcg/ml). Figure 2: CT scan of the abdomen at the time of admission, showing right-sided staghorn calculi (white arrow). Additionally, dilated calyces seen in right kidney without findings of medical renal disease. Multiple renal calculi noted in left kidney. -
Table 1 Gene Name Increased Or Decreased in LTD
Table_1 gene_name increased or decreased in LTD protein_id description keep_supernatant keep_pellet comparison sample hit_annotation_methodpvalue fdr hit hit_annotation 2010300C02RIK increased E9Q3M9 Protein 2010300C02Rik OS=Mus musculus GN=2010300C02Rik PE=1 SV=1 TRUE TRUE NMDA - control pellet fdrtool 0,074667 0,584087 FALSE trend 2310035C23RIK|KIAA1468increased A0A087WSS1|E9QM90|Q148V7|Q148V7-2 Protein 2310035C23Rik OS=Mus musculus GN=2310035C23Rik PE=1 SV=1|Protein 2310035C23Rik OS=Mus musculusTRUE GN=2310035C23Rik PE=1 SV=2|LisH FALSE domain NMDAand HEAT - control repeat-containing protein KIAA1468 supernatant OS=Mus musculus GN=Kiaa1468 fdrtoolPE=1 SV=1|Isoform 0,080056 2 of 0,589077LisH domain FALSEand HEAT trend repeat-containing protein KIAA1468 OS=Mus musculus GN=Kiaa1468 ABR increased E9PUE7|Q5SSL4|Q5SSL4-2|Q5SSL4-3|Q5SSL4-4 Active breakpoint cluster region-related protein OS=Mus musculus GN=Abr PE=1 SV=1|Isoform 2 of Active breakpointTRUE cluster region-related protein TRUE OS=Mus musculus NMDA GN=Abr|Isoform - control 3 of Active breakpoint supernatant cluster region-related protein OS=Mus fdrtool musculus 0,08128 GN=Abr|Isoform 0,592743 4 of Active FALSE breakpoint trend cluster region-related protein OS=Mus musculus GN=Abr ADAM22 increased D3YUP9|Q9R1V6|Q9R1V6-10|Q9R1V6-11|Q9R1V6-12|Q9R1V6-13|Q9R1V6-14|Q9R1V6-15|Q9R1V6-17|Q9R1V6-4|Q9R1V6-5|Q9R1V6-6|Q9R1V6-7|Q9R1V6-8Disintegrin and metalloproteinase domain-containing protein 22 OS=Mus musculus GN=Adam22 PE=1 SV=1|DisintegrinFALSE and metalloproteinase domain-containing TRUE -
Label-Free Proteomic Methodology for the Analysis of Human Kidney Stone Matrix Composition Frank A
Witzmann et al. Proteome Science (2016) 14:4 DOI 10.1186/s12953-016-0093-x METHODOLOGY Open Access Label-free proteomic methodology for the analysis of human kidney stone matrix composition Frank A. Witzmann1*, Andrew P. Evan2, Fredric L. Coe3, Elaine M. Worcester3, James E. Lingeman4 and James C. Williams Jr2 Abstract Background: Kidney stone matrix protein composition is an important yet poorly understood aspect of nephrolithiasis. We hypothesized that this proteome is considerably more complex than previous reports have indicated and that comprehensive proteomic profiling of the kidney stone matrix may demonstrate relevant constitutive differences between stones. We have analyzed the matrices of two unique human calcium oxalate stones (CaOx-Ia and CaOx-Id) using a simple but effective chaotropic reducing solution for extraction/solubilization combined with label-free quantitative mass spectrometry to generate a comprehensive profile of their proteomes, including physicochemical and bioinformatic analysis.` Results: We identified and quantified 1,059 unique protein database entries in the two human kidney stone samples, revealing a more complex proteome than previously reported. Protein composition reflects a common range of proteins related to immune response, inflammation, injury, and tissue repair, along with a more diverse set of proteins unique to each stone. Conclusion: The use of a simple chaotropic reducing solution and moderate sonication for extraction and solubilization of kidney stone powders combined with label-free quantitative mass spectrometry has yielded the most comprehensive list to date of the proteins that constitute the human kidney stone proteome. Keywords: Calcium oxalate, Kidney stone, Label-free quantitative liquid chromatography–tandem mass spectrometry, Matrix protein, Nephrolithiasis, Proteomics Background deposition is the primary event, at least in the formation The organic matrix within urinary stones has long been of CaOx stones over plaque. -
Deficiency in Class III PI3-Kinase Confers Postnatal Lethality with IBD
ARTICLE DOI: 10.1038/s41467-018-05105-8 OPEN Deficiency in class III PI3-kinase confers postnatal lethality with IBD-like features in zebrafish Shaoyang Zhao1,2,3, Jianhong Xia2,3, Xiuhua Wu2,3, Leilei Zhang2,3, Pengtao Wang2,3, Haiyun Wang2,3, Heying Li2, Xiaoshan Wang 2, Yan Chen 2, Jean Agnetti2, Yinxiong Li 2, Duanqing Pei2,3 & Xiaodong Shu2,3 The class III PI3-kinase (PIK3C3) is an enzyme responsible for the generation of phospha- tidylinositol 3-phosphate (PI3P), a critical component of vesicular membrane. Here, we report 1234567890():,; that PIK3C3 deficiency in zebrafish results in intestinal injury and inflammation. In pik3c3 mutants, gut tube forms but fails to be maintained. Gene expression analysis reveals that barrier-function-related inflammatory bowel disease (IBD) susceptibility genes (e-cadherin, hnf4a, ttc7a) are suppressed, while inflammatory response genes are stimulated in the mutants. Histological analysis shows neutrophil infiltration into mutant intestinal epithelium and the clearance of gut microbiota. Yet, gut microorganisms appear dispensable as mutants cultured under germ-free condition have similar intestinal defects. Mechanistically, we show that PIK3C3 deficiency suppresses the formation of PI3P and disrupts the polarized dis- tribution of cell-junction proteins in intestinal epithelial cells. These results not only reveal a role of PIK3C3 in gut homeostasis, but also provide a zebrafish IBD model. 1 School of Life Sciences, University of Science and Technology of China, 230027 Hefei, Anhui, China. 2 CAS Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health-Guangzhou Medical University Joint School of Biological Sciences, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China. -
High-Throughput, Pooled Sequencing Identifies Mutations in NUBPL And
ARTICLES High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency Sarah E Calvo1–3,10, Elena J Tucker4,5,10, Alison G Compton4,10, Denise M Kirby4, Gabriel Crawford3, Noel P Burtt3, Manuel Rivas1,3, Candace Guiducci3, Damien L Bruno4, Olga A Goldberger1,2, Michelle C Redman3, Esko Wiltshire6,7, Callum J Wilson8, David Altshuler1,3,9, Stacey B Gabriel3, Mark J Daly1,3, David R Thorburn4,5 & Vamsi K Mootha1–3 Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases. Complex I of the mitochondrial respiratory chain is a large ~1-MDa assembly factors are probably required, as suggested by the 20 factors macromolecular machine composed of 45 protein subunits encoded necessary for assembly of the smaller complex IV9 and by cohort by both the nuclear and mitochondrial (mtDNA) genomes. -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
An Animal Model with a Cardiomyocyte-Specific Deletion of Estrogen Receptor Alpha: Functional, Metabolic, and Differential Netwo
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2014 An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: Functional, metabolic, and differential network analysis Sriram Devanathan Washington University School of Medicine in St. Louis Timothy Whitehead Washington University School of Medicine in St. Louis George G. Schweitzer Washington University School of Medicine in St. Louis Nicole Fettig Washington University School of Medicine in St. Louis Attila Kovacs Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Devanathan, Sriram; Whitehead, Timothy; Schweitzer, George G.; Fettig, Nicole; Kovacs, Attila; Korach, Kenneth S.; Finck, Brian N.; and Shoghi, Kooresh I., ,"An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: Functional, metabolic, and differential network analysis." PLoS One.9,7. e101900. (2014). https://digitalcommons.wustl.edu/open_access_pubs/3326 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Sriram Devanathan, Timothy Whitehead, George G. Schweitzer, Nicole Fettig, Attila Kovacs, Kenneth S. Korach, Brian N. Finck, and Kooresh I. Shoghi This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/3326 An Animal Model with a Cardiomyocyte-Specific Deletion of Estrogen Receptor Alpha: Functional, Metabolic, and Differential Network Analysis Sriram Devanathan1, Timothy Whitehead1, George G. Schweitzer2, Nicole Fettig1, Attila Kovacs3, Kenneth S. -
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
International Journal of Molecular Sciences Article Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins M. Quadir Siddiqui 1,† , Maulik D. Badmalia 1,† and Trushar R. Patel 1,2,3,* 1 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; [email protected] (M.Q.S.); [email protected] (M.D.B.) 2 Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada 3 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and func- tions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share Citation: Siddiqui, M.Q.; Badmalia, similarities with transcriptional regulators and have positively charged electrostatic patches, which M.D.; Patel, T.R.