CytReD: A database collecting human cytokinome information

The cytokines/related receptors system represents a complex regulatory network that is involved in those chronic inflammatory processes which lead to many diseases as cancers. We developed a Cytokine Receptor Database (CytReD) to collect information on cytokine receptors related to their biological activity, gene data, protein structures and diseases in which these and their ligands are implicated. This large set of information may be used by researchers as well as by physicians or clinicians to identify which cytokines, reported in the literature, are important in a given disease and, therefore, useful for purposes of diagnosis or prognostic. AVAILABILITY: The database is available for free at http://www.cro-m.eu/CytReD/     

Increased Nitric Oxide Production in Patients with Systemic Sclerosis

Nitric oxide (NO, nitrogen monoxide) is a messenger molecule whose synthesis can be induced by proinflammatory cytokines. Increased production of NO has been reported in various inflammatory and autoimmune diseases. We studied serum nitrite and citrulline as surrogate markers for NO production in patients with systemic sclerosis (SSc) and looked for correlation with extent of disease, disease duration, age, and systemic involvement. Thirty-four patients were studied against 20 controls. The nitrite levels were significantly higher in the disease group (1588.4 +/- 998.2 nmol/ml compared to 327.8 +/- 137.7 nmol/ml; P < 0.001). The citrulline levels of the disease group were also significantly higher (5490.1 +/- 2518.3 nmol/ml compared to 3264.5 +/- 2509.7 nmol/ml in the controls; P = 0.005). There was no significant difference among limited and diffuse subgroups. There was no significant difference in patients with or without arthritis or interstitial lung disease or with other systemic involvement. On multivariate analysis there was a trend toward a rising level of nitrite with worsening lung functions (P = 0.07). Hence, there is evidence of increased NO production in patients with SSc. There is no difference between NO levels in disease subgroups or those with systemic involvement.     

Insights into archaeal chaperone machinery: a network-based approach

Molecular chaperones are a diverse group of proteins that ensure proteome integrity by helping the proteins fold correctly and maintain their native state, thus preventing their misfolding and subsequent aggregation. The chaperone machinery of archaeal organisms has been thought to closely resemble that found in humans, at least in terms of constituent players. Very few studies have been ventured into system-level analysis of chaperones and their functioning in archaeal cells. In this study, we attempted such an analysis of chaperone-assisted protein folding in archaeal organisms through network approach using Picrophilus torridus as model system. The study revealed that DnaK protein of Hsp70 system acts as hub in protein-protein interaction network. However, DnaK protein was present only in a subset of archaeal organisms and absent from many archaea, especially members of Crenarchaeota phylum. Therefore, a similar network was created for another archaeal organism, Sulfolobus solfataricus, a member of Crenarchaeota. The chaperone network of S. solfataricus suggested that thermosomes played an integral part of hub proteins in archaeal organisms, where DnaK was absent. We further compared the chaperone network of archaea with that found in eukaryotic systems, by creating a similar network for Homo sapiens. In the human chaperone network, the UBC protein, a part of ubiquitination system, was the most important module, and interestingly, this system is known to be absent in archaeal organisms. Comprehensive comparison of these networks leads to several interesting conclusions regarding similarities and differences within archaeal chaperone machinery in comparison to humans.     

Role of Ca2+/calmodulin-PfPKB signaling pathway in erythrocyte invasion by Plasmodium falciparum

Molecular mechanisms by which signaling pathways operate in the malaria parasite and control its development are promiscuous. Recently, we reported the identification of a signaling pathway in Plasmodium falciparum, which involves activation of protein kinase B-like enzyme (PfPKB) by calcium/calmodulin (Vaid, A., and Sharma, P. (2006) J. Biol. Chem. 281, 27126-27133). Studies carried out to elucidate the function of this pathway suggested that it may be important for erythrocyte invasion. Blocking the function of the upstream activators of this pathway, calmodulin and phospholipase C, resulted in impaired invasion. To evaluate if this signaling cascade controls invasion by regulating PfPKB, inhibitors against this kinase were developed. PfPKB inhibitors dramatically reduced the ability of the parasite to invade erythrocytes. Furthermore, we demonstrate that PfPKB associates with actin-myosin motor and phosphorylates PfGAP45 (glideosome-associated protein 45), one of the important components of the motor complex, which may help explain its role in erythrocyte invasion.     

Low incidence of GJB2, GJB6 and mitochondrial DNA mutations in North Indian patients with non-syndromic hearing impairment

Mutations at the DFNB1 locus which encode connexin 26 (CX26) and connexin 30 (CX30) proteins, respectively, are main cause for sporadic and familial non-syndromic hearing impairment (NSHI) in many populations. 342-kb deletion [del (GJB6-D13S1830)] of Cx30 gene is second most common connexin mutation. Specific mitochondrial DNA (mtDNA) mutations have been found to be associated with NSHI. In this study, we screened 210 NSHI patients for GJB2 mutations, ΔGJB6-D13S1830 deletion and three point mutations in mtDNA (A1555G, A3243G, A7445G) using PCR, DHPLC and sequencing in North Indian cohort. 35delG was found to be the most common mutation (10.9%), followed by W24X (3.8%) and W77X (1.9%) mutations. We did not observe GJB6-D13S1830 deletion and three mitochondrial point mutations in our cohort. Most of patients (50/58) carried monoallelic variations. Our results reveal different spectrum of GJB2 mutations specific to North Indian cohort, with 35delG being most prevalent. These results suggest that different types of GJB2 mutations affect autosomal recessive NSHI according to ethnic background.     

Studies on the mechanism of Salmonella typhimurium enterotoxin-induced diarrhoea

The unidirectional fluxes of Na⁺ and Cl^? were studied in Salmonella typhimurium enterotoxin-treated rats. There was net secretion of Na⁺ and Cl^? in toxin-treated animals, while in control animals there was net absorption of these ions. In the presence of the Ca²⁺-ionophore, there was net secretion of Na²⁺ and Cl^? in the control group, while the ionophore enhanced the secretion of these ions in experimental anaimals. The calcium channel blocker, verapamil, decreased the secretion induced by salmonella toxin, but could not reverse the secretion of absorption. There was no difference in the net absorption of Ca²⁺ in both the control and experimental animals. There was a significant increase in the intracellular free calcium concentrations in enterocytes isolated from toxin-treated rat intestines as compared to that in enterocytes isolated from control animals. In the presence of PMA (phorobol-12-myristated-13-acetate) there was net secretion of Na⁺ and Cl^? in the control group, while in the experimental group there was no change in the fluxes of these ions. The selective, potent inhibitor of protein kinase C, H-7 (1-(5-isoquinolinylsulphonyl)-2-methylpiperazine)_reversed the secretion of Na⁺ and Cl^? in the toxin-treated group to absorption. The addition of indomethacin also inhibited the secretion induced by salmonella toxin, but failed to reverse it to absorption. However, the addition both H-7 and indomethacin to the experimental group had a partial additive effect. These studies demonstrate that the Salmonella enterotoxin-mediated fluid secretion involved protein kinase C and the arachidonic acid metabolites and perhaps does not involve the extracellular calcium pools.     

Correction to: ACE2, CALM3 and TNNI3K polymorphisms as potential disease modifiers in hypertrophic and dilated cardiomyopathies

Molecular and Cellular Biochemistry - In the original publication of the article, the location and rs number of TNNI3K mouse SNP (3784 C&gt;T) (rs49812611) has been mentioned inadvertently in...     

Evidence for the Involvement of Loosely Bound Plastosemiquinones in Superoxide Anion Radical Production in Photosystem II

Recent evidence has indicated the presence of novel plastoquinone-binding sites, Q_C and Q_D, in photosystem II (PSII). Here, we investigated the potential involvement of loosely bound plastosemiquinones in superoxide anion radical (O₂^•−) formation in spinach PSII membranes using electron paramagnetic resonance (EPR) spin-trapping spectroscopy. Illumination of PSII membranes in the presence of the spin trap EMPO (5-(ethoxycarbonyl)-5-methyl-1-pyrroline N-oxide) resulted in the formation of O₂^•−, which was monitored by the appearance of EMPO-OOH adduct EPR signal. Addition of exogenous short-chain plastoquinone to PSII membranes markedly enhanced the EMPO-OOH adduct EPR signal. Both in the unsupplemented and plastoquinone-supplemented PSII membranes, the EMPO-OOH adduct EPR signal was suppressed by 50% when the urea-type herbicide DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) was bound at the Q_B site. However, the EMPO-OOH adduct EPR signal was enhanced by binding of the phenolic-type herbicide dinoseb (2,4-dinitro-6-sec-butylphenol) at the Q_D site. Both in the unsupplemented and plastoquinone-supplemented PSII membranes, DCMU and dinoseb inhibited photoreduction of the high-potential form of cytochrome b₅₅₉ (cyt b₅₅₉). Based on these results, we propose that O₂^•− is formed via the reduction of molecular oxygen by plastosemiquinones formed through one-electron reduction of plastoquinone at the Q_B site and one-electron oxidation of plastoquinol by cyt b₅₅₉ at the Q_C site. On the contrary, the involvement of a plastosemiquinone formed via the one-electron oxidation of plastoquinol by cyt b₅₅₉ at the Q_D site seems to be ambiguous. In spite of the fact that the existence of Q_C and Q_D sites is not generally accepted yet, the present study provided more spectroscopic data on the potential functional role of these new plastoquinone-binding sites.     

Protein structure and fold prediction using Tree-Augmented naïve Bayesian classifier

Due to the large volume of protein sequence data, computational methods to determine the structure class and the fold class of a protein sequence have become essential. Several techniques based on sequence similarity, Neural Networks, Support Vector Machines (SVMs), etc. have been applied. Since most of these classifiers use binary classifiers for multi-classification, there may be (N) c2 classifiers required. This paper presents a framework using the Tree-Augmented Bayesian Networks (TAN) which performs multi-classification based on the theory of learning Bayesian Networks and using improved feature vector representation of (Ding et al., 2001). In order to enhance TAN's performance, pre-processing of data is done by feature discretization and post-processing is done by using Mean Probability Voting (MPV) scheme. The advantage of using Bayesian approach over other learning methods is that the network structure is intuitive. In addition, one can read off the TAN structure probabilities to determine the significance of each feature (say, hydrophobicity) for each class, which helps to further understand the complexity in protein structure. The experiments on the datasets used in three prominent recent works show that our approach is more accurate than other discriminative methods. The framework is implemented on the BAYESPROT web server and it is available at http://www-appn.comp.nus.edu.sg/~bioinfo/bayesprot/Default.htm. More detailed results are also available on the above website.