Genome-based in silico identification of new Mycobacterium tuberculosis antigens activating polyfunctional CD8+ T cells in human tuberculosis

Although CD8(+) T cells help control Mycobacterium tuberculosis infection, their M. tuberculosis Ag repertoire, in vivo frequency, and functionality in human tuberculosis (TB) remains largely undefined. We have performed genome-based bioinformatics searches to identify new M. tuberculosis epitopes presented by major HLA class I supertypes A2, A3, and B7 (covering 80% of the human population). A total of 432 M. tuberculosis peptides predicted to bind to HLA-A*0201, HLA-A*0301, and HLA-B*0702 (representing the above supertypes) were synthesized and HLA-binding affinities determined. Peptide-specific CD8(+) T cell proliferation assays (CFSE dilution) in 41 M. tuberculosis-responsive donors identified 70 new M. tuberculosis epitopes. Using HLA/peptide tetramers for the 18 most prominently recognized HLA-A*0201-binding M. tuberculosis peptides, recognition by cured TB patients' CD8(+) T cells was validated for all 18 epitopes. Intracellular cytokine staining for IFN-γ, IL-2, and TNF-α revealed mono-, dual-, as well as triple-positive CD8(+) T cells, indicating these M. tuberculosis peptide-specific CD8(+) T cells were (poly)functional. Moreover, these T cells were primed during natural infection, because they were absent from M. tuberculosis-noninfected individuals. Control CMV peptide/HLA-A*0201 tetramers stained CD8(+) T cells in M. tuberculosis-infected and noninfected individuals equally, whereas Ebola peptide/HLA-A*0201 tetramers were negative. In conclusion, the M. tuberculosis-epitope/Ag repertoire for human CD8(+) T cells is much broader than hitherto suspected, and the newly identified M. tuberculosis Ags are recognized by (poly)functional CD8(+) T cells during control of infection. These results impact on TB-vaccine design and biomarker identification.     

The Conserved Lid Tryptophan,W211, Potentiates Thermostability and Thermoactivity in Bacterial Thermoalkalophilic Lipases

We hypothesize that aggregation of thermoalkalophilic lipases could be a thermostability mechanism. The conserved tryptophans (W211, W234) in the lid are of particular interest owing to their previous involvements in aggregation and thermostability mechanisms in many other proteins. The thermoalkalophilic lipase from Bacillus thermocatenulatus (BTL2) and its mutants (W211A, W234A) were expressed and purified to homogeneity. We found that, when aggregated, BTL2 is more thermostable than its non-aggregating form, showing that aggregation potentiates thermostability in the thermoalkalophilic lipase. Among the two lid mutants, the W211A lowered aggregation tendency drastically and resulted in a much less thermostable variant of BTL2, which indicated that W211 stabilizes the intermolecular interactions in BTL2 aggregates. Further thermoactivity and CD spectroscopy analyses showed that W211A also led to a strong decrease in the optimal and the melting temperature of BTL2, implying stabilization by W211 also to the intramolecular interactions. The other lid mutant W234A had no effects on these properties. Finally, we analyzed the molecular basis of these experimental findings in-silico using the dimer (PDB ID: 1KU0) and the monomer (PDB ID: 2W22) lipase structures. The computational analyses confirmed that W211 stabilized the intermolecular interactions in the dimer lipase and it is critical to the stability of the monomer lipase. Explicitly W211 confers stability to the dimer and the monomer lipase through distinct aromatic interactions with Y273-Y282 and H87-P232 respectively. The insights revealed by this work shed light not only on the mechanism of thermostability and its relation to aggregation but also on the particular role of the conserved lid tryptophan in the thermoalkalophilic lipases.     

A new methodology to associate SNPs with human diseases according to their pathway related context

Genome-wide association studies (GWAS) with hundreds of żthousands of single nucleotide polymorphisms (SNPs) are popular strategies to reveal the genetic basis of human complex diseases. Despite many successes of GWAS, it is well recognized that new analytical approaches have to be integrated to achieve their full potential. Starting with a list of SNPs, found to be associated with disease in GWAS, here we propose a novel methodology to devise functionally important KEGG pathways through the identification of genes within these pathways, where these genes are obtained from SNP analysis. Our methodology is based on functionalization of important SNPs to identify effected genes and disease related pathways. We have tested our methodology on WTCCC Rheumatoid Arthritis (RA) dataset and identified: i) previously known RA related KEGG pathways (e.g., Toll-like receptor signaling, Jak-STAT signaling, Antigen processing, Leukocyte transendothelial migration and MAPK signaling pathways); ii) additional KEGG pathways (e.g., Pathways in cancer, Neurotrophin signaling, Chemokine signaling pathways) as associated with RA. Furthermore, these newly found pathways included genes which are targets of RA-specific drugs. Even though GWAS analysis identifies 14 out of 83 of those drug target genes; newly found functionally important KEGG pathways led to the discovery of 25 out of 83 genes, known to be used as drug targets for the treatment of RA. Among the previously known pathways, we identified additional genes associated with RA (e.g. Antigen processing and presentation, Tight junction). Importantly, within these pathways, the associations between some of these additionally found genes, such as HLA-C, HLA-G, PRKCQ, PRKCZ, TAP1, TAP2 and RA were verified by either OMIM database or by literature retrieved from the NCBI PubMed module. With the whole-genome sequencing on the horizon, we show that the full potential of GWAS can be achieved by integrating pathway and network-oriented analysis and prior knowledge from functional properties of a SNP.     

Changes in brain size during the menstrual cycle

Background

There is increasing evidence for hormone-dependent modification of function and behavior during the menstrual cycle, but little is known about associated short-term structural alterations of the brain. Preliminary studies suggest that a hormone-dependent decline in brain volume occurs in postmenopausal, or women receiving antiestrogens, long term. Advances in serial MR-volumetry have allowed for the accurate detection of small volume changes of the brain. Recently, activity-induced short-term structural plasticity of the brain was demonstrated, challenging the view that the brain is as rigid as formerly believed.

Methodology/Principal Findings

We used MR-volumetry to investigate short-term brain volume changes across the menstrual cycle in women or a parallel 4 week period in men, respectively. We found a significant grey matter volume peak and CSF loss at the time of ovulation in females. This volume peak did not correlate with estradiol or progesterone hormone levels. Men did not show any significant brain volume alterations.

Conclusions/Significance

These data give evidence of short-term hormone-dependent structural brain changes during the menstrual cycle, which need to be correlated with functional states and have to be considered in structure-associated functional brain research.     

Protein profiling of anastomosed facial nerve treated with mesenchymal stromal cells

Background aimsThe types of proteins released from mesenchymal stromal cells (MSC) are still unclear. Our aim was to compare apoptosis scores and the expression of myelin-associated glycoprotein (MAG), myelin basic protein (MBP), neural cell adhesion molecule (NCAM)-1,matrix metalloproteinase (MMP)-1A, tissue inhibitor of metalloproteinase (TIMP)-1, TIMP-1/MMP-1A ratio, nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), ciliary neurotrophic factor (CNTF), neurotrophin (NT)-3, NT-4, glial cell-derived neurotropic factor (GDNF), leukemia inhibitory factor (LIF), basic fibroblast growth factor (FGF)-2, insulin-like growth factor (IGF)-1, platelet-derived growth factor (PDGF)-α and transforming growth factor (TGF)-β1 in anastomosed facial nerves that had been treated with or without MSC.MethodsIn seven rats, the buccal branch of the right facial nerve was transected, anastomosed and treated with MSC (anastomosed + MSC group). The left buccal branch was anastomosed only (anastomosed-only group). The left mandibular branch served as an intact nerve group. On days 18–20, the distal segments of the branches were examined in terms of expression of the mentioned proteins and apoptosis scores using polymerase chain reaction (PCR) and terminal deoxynucleotidyl transferase-mediated digoxigenin-UTP nick end labeling (TUNEL) assays.ResultsMSC application significantly increased CNTF, PDGF-α, LIF, TGF-β1, BDNF and NT-3 expression (P < 0.05). MAG expression slightly decreased whereas NCAM-1, MMP-1A and FGF-2 slightly increased(P > 0.05). Changes in other proteins and apoptosis scores were not significant.ConclusionsThese results suggest that MSC increases expression of CNTF, PDGF-α, LIF,TGF-β1, BDNF and NT-3. MAG, NCAM-1, MMP-1A and FGF-2 expressions were slightly changed in this stage of nerve regeneration. The comparison of apoptotic activity was not conclusive. Overall, it appears that MSC might have differential effects on the mentioned tissue-related proteins and trophic/growth factors.     

Post-testicular protection of male gametes from oxidative damage. The role of the epididymis

Spermatozoa leave the testis in an immature functional state and are devoid of self defense mechanisms. They will become motile and ready to fertilize only after their descent and their progressive maturation within the epididymal tubule. The epididymis also ensures the survival and the protection of male gametes while they go through the epididymis and during their storage in between two ejaculations. Amongst common stresses that concern spermatozoa, oxidative stress occupies a peculiar and dual position. While the events of epididymal sperm maturation necessitate a given level of oxidation, spermatozoa are particularly sensitive to oxidative damage. A fine balance between beneficial oxidation versus detrimental oxidative damage has to be maintained in the epididymal environment. Antioxidant enzymes of the glutathione peroxidase family play a key role in controling such a situation in the epididymis.     

Diversity of killer cell immunoglobulin-like receptor genes in Southern Turkey

Killer cell immunoglobulin-like receptors (KIRs) are a family of inhibitory and activating receptors expressed by natural killer (NK) cells and regulate NK cells’ activity. KIR genes are highly polymorphic markers, characterized by a wide diversity, and can therefore be considered as good population genetic markers. The aim of this study was to determine KIR gene frequencies, ratios of haplotypes and genotypes in Southern Turkey and also to compare the data with other worldwide populations studied previously. The study group consisted of 200 non-related individuals from Southern Turkey. The percentage of each KIR gene in the population group was determined by direct counting. Differences between populations in the distribution of each KIR gene and genotype profile were estimated by two-tailed Fisher Exact test. The most frequent non-framework KIR genes detected in Southern Turkey population were: KIR 2DL1 (97%), KIR 3DL1 (91%), KIR 2DS4 (92%) and the pseudogene 2DP1 (96%). Fourty different genotypes were found in 200 subjects and AA1 genotype was the most frequent (27%). Among 40 different genotypes, ten of these were described for the first time in this study and were added to the database () numerized as genotype ID from 400 to 409. Gene frequencies and found genotypes demonstrated similarity of Southern Turkey’s KIR repertoire with the KIR repertoires of Middle East and European population. High variability seen in KIR genome in this region is thought to be formed as a result of migration and settlement of different civilizations in this region and heterogenity formed in time.     

HingeProt: automated prediction of hinges in protein structures

Proteins are highly flexible molecules. Prediction of molecular flexibility aids in the comprehension and prediction of protein function and in providing details of functional mechanisms. The ability to predict the locations, directions, and extent of molecular movements can assist in fitting atomic resolution structures to low-resolution EM density maps and in predicting the complex structures of interacting molecules (docking). There are several types of molecular movements. In this work, we focus on the prediction of hinge movements. Given a single protein structure, the method automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein-protein and protein-ligand docking, flexible docking of protein structures into cryo-EM maps, and refinement of low-resolution EM structures. The web server of HingeProt provides convenient visualization of the results and is available with two mirror sites at http://www.prc.boun.edu.tr/appserv/prc/HingeProt3 and http://bioinfo3d.cs.tau.ac.il/HingeProt/.     

Antibiotic susceptibility patterns of respiratory isolates of Staphylococcus aureus in a Turkish university hospital

A total of 391 respiratory isolates of Staphylococcus aureus in Sivas (Turkey) were studied between January 1999-2002. The organisms were cultured from the following specimens: throat (43%), sputum (28%), transtracheal/endotracheal aspirates (27%), and bronchial lavage (2%). The isolates were tested against 11 different antibiotics by a disk diffusion method or standardized microdilution technique. Methicillin-resistant isolates constituted 76.9% of all isolates. Most of the methicillin-resistant isolates (95.1%) were isolated from inpatients. The rate of methicillin-resistant isolates in throat, sputum, and tracheal aspirates was 17.2%, 60.1%, and 68.9%, respectively. The resistance of methicillin-resistant isolates in throat to teicoplanin was 3.4%. The methicillin-sensitive isolates were susceptible to most agents tested, while most methicillin-resistant isolates were resistant to these agents. Overall resistance to erythromycin was 61.9%, tetracycline 56.6%, gentamicin 50.7%, ofloxacin 42.0%, rifampin 40.8%, clindamycin 38.9%, chloramphenicol 19.0%, co-trimoxazole 10.2%, and vancomycin 0%.