121,426 results match your criteria binding molecules

A Generalized Molecule Approach Capturing the Feshbach-Induced Pairing Physics in the BEC-BCS Crossover.

J Phys Condens Matter 2021 Apr 13. Epub 2021 Apr 13.

Facultad de Matem\'atica, Astronom\'ia, F\'isica y Computaci\'on, Universidad Nacional de Cordoba, Av. Medina Allende s/n, Ciudad Universitaria, X5000HUA C\'ordoba, Argentina, Cordoba, Córdoba, X5000HUA, ARGENTINA.

By including the effect of a trap with characteristic energy given by the Fermi temperature $T_F$ in a two-body two-channel model for Feshbach resonances, we reproduce the measured binding energy of ultracold molecules in a $^{40}$K atomic Fermi gas. We also reproduce the experimental closed-channel fraction $Z$ across the BEC-BCS crossover and into the BCS regime of a $^6$Li atomic Fermi gas. We obtain the expected behavior $Z \propto \sqrt{T_F}$ at unitarity, together with the recently measured proportionality constant. Read More

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An affinity prediction approach for the ligand of E3 ligase Cbl-b and an insight into substrate binding pattern.

Bioorg Med Chem 2021 Apr 2;38:116130. Epub 2021 Apr 2.

State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China. Electronic address:

Protein-protein interactions (PPIs) are essentially fundamental to all cellular processes, so that developing small molecule inhibitors of PPIs have great significance despite representing a huge challenge. Studying PPIs with the help of peptide motifs could obtain the structural information and reference significance to reduce the difficulty in the development of small molecules. Computational methods are powerful tools to characterize peptide-protein interactions, especially molecular dynamics simulation and binding free energy calculation. Read More

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Comparisons of basic Target-Mediated Drug Disposition (TMDD) and Ligand Facilitated Target Removal (LFTR).

Eur J Pharm Sci 2021 Apr 10:105835. Epub 2021 Apr 10.

Firma Biopharmacon, Engelbrektsgatan 5, Gothenburg 41127, Sweden. Electronic address:

In the well-known model for basic Target-Mediated Drug Disposition (TMDD), drug binds to the target and the resulting drug-target complex is removed by a first order process, leading to loss of both drug and target. In the present note we study what happens when, instead, drug is returned to the free drug pool so that it can a new target molecule. What results is a mechanism in which the drug, here referred to as the ligand, facilitates the removal of the target,and then returns to the free ligand pool. Read More

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Chromatin-embedded reporter genes: Quantification of stimulus-induced gene transcription.

Gene 2021 Apr 10:145645. Epub 2021 Apr 10.

Department of Medical Biochemistry and Molecular Biology, Saarland University Medical Faculty, D-66421 Homburg, Germany.

Receptors and ion channels expressed on the cell surface ensure proper communication between the cells and the environment. In multicellular organism, stimulus-regulated gene transcription is the basis for the communication with the environment allowing individual cells to respond to stimuli such as nutrients, chemical stressors and signaling molecules released by other cells of the organism. Hormones, cytokines, and mitogens bind to receptors and ion channels and induce intracellular signaling cascades involving second messengers, kinases, phosphatases, and changes in the concentration of particular ions. Read More

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Identification and functional characterization of AP-2 complex subunit mu-A as a new member of antimicrobial protein.

Dev Comp Immunol 2021 Apr 10:104099. Epub 2021 Apr 10.

Department of Marine Biology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China. Electronic address:

AP-2 complex subunit mu-A (AP2M1A) is a component of the adaptor complexes that link clathrin to receptors in coated vesicles. It has recently been shown to be involved in the resistance to oxidative damage, challenging the conventional role of AP2M1A. Here we demonstrated that AP2M1A was a heparin-binding protein abundantly stored in eggs and embryos of zebrafish, and its gene expression was markedly up-regulated by LPS and LTA treatment. Read More

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Measurements of Real-Time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-Stranded DNA-Binding Proteins.

Methods Mol Biol 2021 ;2281:289-301

Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.

Optical tweezers can monitor and control the activity of individual DNA polymerase molecules in real time, providing in this way unprecedented insight into the complex dynamics and mechanochemical processes that govern their operation. Here, we describe an optical tweezers-based assay to determine at the single-molecule level the effect of single-stranded DNA-binding proteins (SSB) on the real-time replication kinetics of the human mitochondrial DNA polymerase during the synthesis of the lagging strand. Read More

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January 2021

Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio Is a Single-Stranded DNA-Binding Protein.

Methods Mol Biol 2021 ;2281:241-263

Dipartimento di Biologia e Biotecnologie 'C. Darwin', Sapienza, Università di Roma, Rome, Italy.

Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of biological samples with a nanometric resolution. Determination of the physical properties of biological molecules at a single-molecule level is achieved through topographic analysis of the sample adsorbed on a flat and smooth surface. AFM has been widely used for the structural analysis of nucleic acid-protein interactions, providing insights on binding specificity and stoichiometry of proteins forming complexes with DNA substrates. Read More

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January 2021

Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction.

Elife 2021 Apr 13;10. Epub 2021 Apr 13.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

Clamp loaders are AAA+ ATPases that load sliding clamps onto DNA. We mapped the mutational sensitivity of the T4 bacteriophage sliding clamp and clamp loader by deep mutagenesis, and found that residues not involved in catalysis or binding display remarkable tolerance to mutation. An exception is a glutamine residue in the AAA+ module (Gln 118) that is not located at a catalytic or interfacial site. Read More

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Synthesis, α-glucosidase and α-amylase inhibitory activities, acute toxicity and molecular docking studies of thiazolidine-2,4-diones derivatives.

J Biomol Struct Dyn 2021 Apr 13:1-12. Epub 2021 Apr 13.

Laboratory of Pharmacology and Toxicology, Biopharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco.

In the present study, a series of thiazolidine-2,4-diones derivatives () and () were synthesized and characterized by H NMR, C NMR and ESI-MS spectrometry. All compounds were screened for their α-glucosidase and α-amylase inhibitory activities. biological investigations revealed that most of compounds were active against α-glucosidase with IC values in the range of 43. Read More

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Inhibited effect of an RGD peptide hydrogel on the expression of β1-integrin, FAK, and Akt in Tenon's capsule fibroblasts.

J Biomed Mater Res B Appl Biomater 2021 Apr 13. Epub 2021 Apr 13.

Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China.

Tenon's capsule fibroblasts are the main cellular components of filtration tract scar that limit the success rate of glaucoma filtration surgery. Scar formation results from infiltration and proliferation of fibroblasts into damaged areas, meanwhile synthesis of extracellular matrix glycoproteins. Integrins are cell surface receptors for extracellular molecules that mediate cell adhesion, spreading, migration, and invasion. Read More

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Inhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein.

J Biomol Struct Dyn 2021 Apr 13:1-16. Epub 2021 Apr 13.

Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.

Coronavirus disease-2019 (COVID-19) was firstly reported in Wuhan, China, towards the end of 2019, and emerged as a pandemic. The spread and lethality rates of the COVID-19 have ignited studies that focus on the development of therapeutics for either treatment or prophylaxis purposes. In parallel, drug repurposing studies have also come into prominence. Read More

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Modulation of the Protein-Ligand Interaction in the Presence of Graphene Oxide: a Detailed Spectroscopic Study.

Langmuir 2021 Apr 13. Epub 2021 Apr 13.

Department of Chemistry, Indian Institute of Technology Patna, Bihta, Bihar 801103, India.

Several applications of graphene oxide (GO) have been established over the years, and it has the potential to be used as a biomedical material. Studying the effect of GO on protein-ligand (small molecules/drugs) complex systems are vital as the mechanisms involved are not well understood. The interaction of GO on the protein-ligand binding is also vital for the preparation of an effective drug carrier in the bloodstream. Read More

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Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C.

Nat Commun 2021 04 12;12(1):2173. Epub 2021 Apr 12.

Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.

The closely related inhibitory killer-cell immunoglobulin-like receptors (KIR), KIR2DL2 and KIR2DL3, regulate the activation of natural killer cells (NK) by interacting with the human leukocyte antigen-C1 (HLA-C1) group of molecules. KIR2DL2, KIR2DL3 and HLA-C1 are highly polymorphic, with this variation being associated with differences in the onset and progression of some human diseases. However, the molecular bases underlying these associations remain unresolved. Read More

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Design, synthesis, modelling studies and biological evaluation of 1,3,4-oxadiazole derivatives as potent anticancer agents targeting thymidine phosphorylase enzyme.

Bioorg Chem 2021 Mar 29;111:104873. Epub 2021 Mar 29.

Shobhaben Pratapbhai Patel School of Pharmacy Technology Management, SVKM's NMIMS, Mumbai, India. Electronic address:

A series of novel 1,3,4-oxadiazole derivatives with substituted phenyl ring were designed and synthesized with an objective of discovering newer anti-cancer agents targeting thymidine phosphorylase enzyme (TP). The 1,3,4-oxadiazole derivatives were synthesized by simple and convenient methods in the lab. Chemical structure of the all the synthesized compounds were characterized by IR, H NMR and mass spectral methods and evaluated for cytotoxicity by MTT method against two breast cancer cell lines (MCF-7 and MDA-MB-231). Read More

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Structural insight into phospholipid transport by the MlaFEBD complex from P. aeruginosa.

J Mol Biol 2021 Apr 9:166986. Epub 2021 Apr 9.

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China. Electronic address:

The outer membrane (OM) of Gram-negative bacteria, which consists of lipopolysaccharides (LPS) in the outer leaflet and phospholipids (PLs) in the inner leaflet, plays a key role in antibiotic resistance and pathogen virulence. The maintenance of lipid asymmetry (Mla) pathway is known to be involved in PL transport and contributes to the lipid homeostasis of the OM, yet the underlying molecular mechanism and the directionality of PL transport in this pathway remain elusive. Here, we reported the cryo-EM structures of the ATP-binding cassette (ABC) transporter MlaFEBD from P. Read More

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Sieving effect for separation of C2H2/C2H4 in an ultrastable ultramicroporous zinc-organic framework.

Chem Asian J 2021 Apr 12. Epub 2021 Apr 12.

Shandong Normal University, College of Chemistry, CHINA.

The separation of C2H2 from C2H4 is one of the most challenging tasks due to the similarity of their physical properties. In addition, green synthetic protocol and adsorbent's stability are also the major concerns during the separation. Herein, under hydrothermal green synthesis conditions, an ultrastable ultramicroporous Zn-MOF was designed and synthesized with a high yield. Read More

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ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures.

J Chem Inf Model 2021 Apr 12. Epub 2021 Apr 12.

Center for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66041 Saarbrücken, Germany.

Surface pockets, cavities, and tunnels in the 3D structures of proteins play integral functional roles such as enabling enzymatic catalysis, ligand binding, or transport of ions or small molecules across biomembranes. ProPores2 facilitates understanding and analysis of these processes by identifying pores and lining residues, determining their axes, and opening closed connections via side-chain rotation. The fast stand-alone tool introduces a novel mode for pore identification, improved axis determination, and additional features such as parallel batch processing and a graphical user interface. Read More

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Bispecific Estrogen Receptor α Degraders Incorporating Novel Binders Identified Using DNA-Encoded Chemical Library Screening.

J Med Chem 2021 Apr 12. Epub 2021 Apr 12.

X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States.

Bispecific degraders (PROTACs) of ERα are expected to be advantageous over current inhibitors of ERα signaling (aromatase inhibitors/SERMs/SERDs) used to treat ER+ breast cancer. Information from DNA-encoded chemical library (DECL) screening provides a method to identify novel PROTAC binding features as the linker positioning, and binding elements are determined directly from the screen. After screening ∼120 billion DNA-encoded molecules with ERα WT and 3 gain-of-function (GOF) mutants, with and without estradiol to identify features that enrich ERα competitively, the off-DNA synthesized small molecule exemplar exhibited nanomolar ERα binding, antagonism, and degradation. Read More

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On the function and relevance of alternative 3'-UTRs in gene expression regulation.

Wiley Interdiscip Rev RNA 2021 Apr 12:e1653. Epub 2021 Apr 12.

Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.

Messanger RNA (mRNA) isoforms with alternative 3'-untranslated regions (3'-UTRs) are produced by alternative polyadenylation (APA), which occurs during transcription in most eukaryotic genes. APA fine-tunes gene expression in a cell-type- and cellular state-dependent manner. Selection of an APA site entails the binding of core cleavage and polyadenylation factors to a particular polyadenylation site localized in the pre-mRNA and is controlled by multiple regulatory determinants, including transcription, pre-mRNA cis-regulatory sequences, and protein factors. Read More

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Roles and mechanisms of YAP/TAZ in orthodontic tooth movement.

J Cell Physiol 2021 Apr 12. Epub 2021 Apr 12.

State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.

Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) are transcriptional coactivators encoded by paratactic homologous genes, shuttle-crossing between cytoplasm and nucleus to regulate the gene expression and cell behavior and standing at the center place of the sophisticated regulatory networking of mechanotransduction. Orthodontic tooth movement (OTM) is a process in which extracellular mechanical stimuli are transformed into intracellular biochemical signals to regulate cellular responses and tissue remodeling. Literature studies have confirmed that YAP/TAZ plays an important role not only in embryonic development, homeostasis and tumorigenesis, but also in mechanical-biochemical signal transduction of periodontal tissues under the mediation of various signal molecules in its upstream and downstream. Read More

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Boronic Acid Functionalized Nanosilica for Binding Guest Molecules.

ACS Appl Nano Mater 2021 Mar 19;4(3):2866-2875. Epub 2021 Feb 19.

Division of Pure and Applied Biochemistry, Department of Chemistry, Lund University, Box 124, 22100 Lund, Sweden.

Dendritic fibrous nanosilica (DFNS) has very high surface area and well-defined nanochannels; therefore, it is very useful as supporting material for numerous applications including catalysis, sensing, and bioseparation. Due to the highly restricted space, addition of molecular ligands to DFNS is very challenging. This work studies how ligand conjugation in nanoscale pores in DFNS can be achieved through copper-catalyzed click reaction, using an optional, in situ synthesized, temperature-responsive polymer intermediate. Read More

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Binding Sites for Oligosaccharide Repeats from Lactic Acid Bacteria Exopolysaccharides on Bovine β-Lactoglobulin Identified by NMR Spectroscopy.

ACS Omega 2021 Apr 23;6(13):9039-9052. Epub 2021 Mar 23.

Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark.

Lactic acid bacterial exopolysaccharides (EPS) are used in the food industry to improve the stability and rheological properties of fermented dairy products. β-Lactoglobulin (BLG), the dominant whey protein in bovine milk, is well known to bind small molecules such as fatty acids, vitamins, and flavors, and to interact with neutral and anionic polysaccharides used in food and pharmaceuticals. While sparse data are available on the affinity of EPS-milk protein interactions, structural information on BLG-EPS complexes, including the EPS binding sites, is completely lacking. Read More

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Serum Derived Extracellular Vesicles Mediated Delivery of Synthetic miRNAs in Human Endothelial Cells.

Front Mol Biosci 2021 26;8:636587. Epub 2021 Mar 26.

Department of Medical Sciences, Molecular Biotechnology Center, University of Torino, Turin, Italy.

Extracellular vesicles (EVs) have emerged in the last decades as a cell-to-cell communication mechanism. One of their mechanism of action is the direct delivery of their cargo, composed of bioactive molecules to target cells. Different methods (direct electroporation, cell transfection, chemical transfection) were developed to vehicle therapeutic molecules through EVs. Read More

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Macrocycles in Bioinspired Catalysis: From Molecules to Materials.

Front Chem 2021 26;9:635315. Epub 2021 Mar 26.

School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.

Macrocyclic compounds have been studied extensively as the host molecules in supramolecular chemistry. Their structural characteristics make macrocycles desirable in the field of molecular recognition, which is the key to high catalytic efficiencies of natural enzymes. Therefore, macrocycles are ideal building blocks for the design of bioinspired catalysts. Read More

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Demethylated miR-216a Regulates High Mobility Group Box 3 Promoting Growth of Esophageal Cancer Cells Through Wnt/β-Catenin Pathway.

Front Oncol 2021 23;11:622073. Epub 2021 Mar 23.

Department of Thoracic Surgery, Cheeloo College of Medicine, Shandong University, Jinan, China.

Background: Esophageal cancer (EC) is the eighth most common cause of cancer-associated mortality in humans. Recent studies have revealed the important roles of microRNAs (miRs) in mediating tumor initiation and progression. miR-216a has been found to be involved in the progression of EC, but the underlying mechanisms remain largely unknown. Read More

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Computational screening of FDA approved drugs of fungal origin that may interfere with SARS-CoV-2 spike protein activation, viral RNA replication, and post-translational modification: a multiple target approach.

In Silico Pharmacol 2021 4;9(1):27. Epub 2021 Apr 4.

National Institute of Pharmaceutical Education and Research, Kolkata, 700054 India.

Coronavirus spread is an emergency reported globally, and a specific treatment strategy for this significant health issue is not yet identified. COVID-19 is a highly contagious disease and needs to be controlled promptly as millions of deaths have been reported. Due to the absence of proficient restorative alternatives and preliminary clinical restrictions, FDA-approved medications can be a decent alternative to deal with the coronavirus malady (COVID-19). Read More

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Microindoline 581, an Indole Derivative from Sp. RP581 as A Novel Selective Antineoplastic Agent to Combat Hepatic Cancer Cells: Production, Optimization and Structural Elucidation.

Iran J Pharm Res 2020 ;19(4):290-305

Molecular Biotechnology Laboratory, Department of Biology, Faculty of Science, Shiraz University, Iran.

Screening of bioactive compounds with potential binding affinity to DNA as one of the target molecules in fighting against cancer cells has gained the attention of many scientists. Finding such compounds in the cellular content of microorganisms, especially marine bacteria as valuable and rich natural resources, is of great importance. sp. Read More

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January 2020

Identification of PCBP1 as a Novel Modulator of Mammalian Circadian Clock.

Front Genet 2021 26;12:656571. Epub 2021 Mar 26.

Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, Hubei Normal University, Huangshi, China.

The circadian clock governs our daily cycle of behavior and physiology. Previous studies have identified a handful of core clock components and hundreds of circadian modifiers. Here, we report the discovery that poly(C)-binding protein 1 (PCBP1), displaying a circadian expression pattern, was a novel circadian clock regulator. Read More

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Investigating the Underlying Mechanisms of Circular RNAs and Their Application in Clinical Research of Cervical Cancer.

Front Genet 2021 25;12:653051. Epub 2021 Mar 25.

Department of Gynaecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China.

Circular RNAs (circRNAs) are non-coding RNA molecules, and these are differentially expressed in various diseases, including cancer, suggesting that circRNAs can regulate certain diseases. CircRNAs can act as miRNAs sponges, RNA-binding protein (RBP) sponges, and translation regulators, and they can become an important part of the regulation of gene expression. Furthermore, because of their biomedical features in body fluids, such as high abundance, conservation, and stability, circRNAs are seen as potential biomarkers for various cancers. Read More

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Plasma Biomarkers of Risk of Tuberculosis Recurrence in HIV Co-Infected Patients From South Africa.

Front Immunol 2021 25;12:631094. Epub 2021 Mar 25.

Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.

There is an urgent need to identify immunological markers of tuberculosis (TB) risk in HIV co-infected individuals. Previously we have shown that TB recurrence in HIV co-infected individuals on ART was associated with markers of systemic inflammation (IL-6, IL1β and IL-1Rα). Here we examined the effect of additional acute inflammation and microbial translocation marker expression on risk of TB recurrence. Read More

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