Structure-Based Virtual Screening and Discovery of New Bi-functional DAPK1 Inhibitors

Recently, a new signaling complex Death-Associated Protein Kinase 1 (DAPK1)-N-methyl D-aspartate receptor subtype 2B (NR2B) engaged in the neuronal death cascade was identified where it was found that after stroke injury, N-methyl-D-aspartate glutamate (NMDA) receptors interact with DAPK1 through NR2B subunit and lead to excitotoxicity via overactivation of NMDA receptors. In this study, we used ZINC-12 database to find out potential inhibitor of DAPK1 and found some natural compounds showing good binding affinity towards DAPK1. These natural compounds showed interactions with ATP-binding site residues as well as substrate-recognition motifs. Thus, it has been concluded that the ligands those are showing interactions with both the sites could be considered as potential inhibitors for DAPK1.

Idiopathic pulmonary fibrosis (IPF): disease pathophysiology, targets, and potential therapeutic interventions

Idiopathic pulmonary fibrosis (IPF) is a progressive, degenerative pulmonary condition. Transforming growth factor (TGF)-β, platelet-derived growth factor (PDGF), and tumor necrosis factor-α (TNF-α) are the major modulators of IPF that mediate myofibroblast differentiation and promote fibrotic remodeling of the lung. Cigarette smoke, asbestos fiber, drugs, and radiation are known to favor fibrotic remodeling of the lungs. Oxidative stress in the endoplasmic reticulum (ER) also leads to protein misfolding and promotes ER stress, which is predominant in IPF. This phenomenon further results in excess reactive oxygen species (ROS) aggregation, increasing oxidative stress. During protein folding in the ER, thiol groups on the cysteine residue are oxidized and disulfide bonds are formed, which leads to the production of hydrogen peroxide (H2O2) as a by-product. With the accumulation of misfolded proteins in the ER, multiple signaling cascades are initiated by the cell, collectively termed as the unfolded protein response (UPR). UPR also induces ROS production within the ER and mitochondria and promotes both pro-apoptotic and pro-survival pathways. The prevalence of post-COVID-19 pulmonary fibrosis (PCPF) is 44.9%, along with an alarming increase in "Coronavirus Disease 2019" (COVID-19) comorbidities. Fibrotic airway remodeling and declined lung function are the common endpoints of SARS-CoV-2 infection and IPF. Flavonoids are available in our dietary supplements and exhibit medicinal properties. Apigenin is a flavonoid found in plants, including chamomile, thyme, parsley, garlic, guava, and broccoli, and regulates several cellular functions, such as oxidative stress, ER stress, and fibrotic responses. In this study, we focus on the IPF and COVID-19 pathogenesis and the potential role of Apigenin in addressing disease progression.

Role of death-associated protein kinase 1 (DAPK1) in retinal degenerative diseases: an in-silico approach towards therapeutic intervention

The Death-associated protein kinase 1 (DAPK1) has emerged as a crucial player in the pathogenesis of degenerative diseases. As a serine/threonine kinase family member, DAPK1 regulates critical signaling pathways, such as apoptosis and autophagy. In this study, we comprehensively analyzed DAPK1 interactors and enriched molecular functions, biological processes, phenotypic expression, disease associations, and aging signatures to elucidate the molecular networks of DAPK1. Furthermore, we employed a structure-based virtual screening approach using the PubChem database, which enabled the identification of potential bioactive compounds capable of inhibiting DAPK1, including caspase inhibitors and synthetic analogs. Three selected compounds, CID24602687, CID8843795, and CID110869998, exhibited high docking affinity and selectivity towards DAPK1, which were further investigated using molecular dynamics simulations to understand their binding patterns. Our findings establish a connection between DAPK1 and retinal degenerative diseases and highlight the potential of these selected compounds for the development of novel therapeutic strategies. This study provides valuable insights into the molecular mechanisms underlying DAPK1-related diseases, and offers new opportunities for the discovery of effective treatments for retinal degeneration.Communicated by Ramaswamy H. Sarma.

Genome-wide screening and identification of potential kinases involved in endoplasmic reticulum stress responses

AIM

This study aims to identify endoplasmic reticulum stress response elements (ERSE) in the human genome to explore potentially regulated genes, including kinases and transcription factors, involved in the endoplasmic reticulum (ER) stress and its related diseases.

MATERIALS AND METHODS

Python-based whole genome screening of ERSE was performed using the Amazon Web Services elastic computing system. The Kinome database was used to filter out the kinases from the extracted list of ERSE-related genes. Additionally, network analysis and genome enrichment were achieved using NDEx, the Network and Data Exchange software, and web-based computational tools. To validate the gene expression, quantitative RT-PCR was performed for selected kinases from the list by exposing the HeLa cells to tunicamycin and brefeldin, ER stress inducers, for various time points.

KEY FINDINGS

The overall number of ERSE-associated genes follows a similar pattern in humans, mice, and rats, demonstrating the ERSE's conservation in mammals. A total of 2705 ERSE sequences were discovered in the human genome (GRCh38.p14), from which we identified 36 kinases encoding genes. Gene expression analysis has shown a significant change in the expression of selected genes under ER stress conditions in HeLa cells, supporting our finding.

SIGNIFICANCE

In this study, we have introduced a rapid method using Amazon cloud-based services for genome-wide screening of ERSE sequences from both positive and negative strands, which covers the entire genome reference sequences. Approximately 10 % of human protein-protein interactomes were found to be associated with ERSE-related genes. Our study also provides a rich resource of human ER stress-response-based protein networks and transcription factor interactions and a reference point for future research aiming at targeted therapeutics.

COVID-19 and Retinal Degenerative Diseases: Promising link “Kaempferol”

Coronavirus disease (COVID-19) outbreak has caused unprecedented global disruption since 2020. Approximately 238 million people are affected worldwide where the elderly succumb to mortality. Post-COVID syndrome and its side effects have popped up with several health hazards, such as macular degeneration and vision loss. It thus necessitates better medical care and management of our dietary practices. Natural flavonoids have been included in traditional medicine and have also been used safely against COVID-19 and several other diseases. Kaempferol is an essential flavonoid that has been demonstrated to influence several vital cellular signaling pathways involved in apoptosis, angiogenesis, inflammation, and autophagy. In this review, we emphasize the plausible regulatory effects of Kaempferol on hallmarks of COVID-19 and macular degeneration.

IRE1α is critical for Kaempferol-induced neuroblastoma differentiation

Neuroblastoma is an embryonic malignancy that arises out of the neural crest cells of the sympathetic nervous system. It is the most common childhood tumor known for its spontaneous regression via the process of differentiation. The induction of differentiation using small molecules such as retinoic acid is one of the therapeutic strategies to treat the residual disease. In this study, we have reported the effect of kaempferol (KFL) in inducing differentiation of neuroblastoma cells in vitro. Treatment of neuroblastoma cells with KFL reduced the proliferation and enhanced apoptosis along with the induction of neuritogenesis. Analysis of the expression of neuron-specific markers such as β-III tubulin, neuron-specific enolase, and N-myc downregulated gene 1 revealed the process of differentiation accompanying KFL-induced apoptosis. Further analysis to understand the molecular mechanism of action showed that the effect of KFL is mediated by the activation of the endoribonuclease activity of inositol-requiring enzyme 1 alpha (IRE1α), an endoplasmic reticulum-resident transmembrane protein. In silico docking analysis and biochemical assays using recombinant human IRE1α confirm the binding of KFL to the ATP-binding site of IRE1α, which thereby activates IRE1α ribonuclease activity. Treatment of cells with the small molecule STF083010, which specifically targets and inhibits the endoribonuclease activity of IRE1α, showed reduced expression of neuron-specific markers and curtailed neuritogenesis. The knockdown of IRE1α using plasmid-based shRNA lentiviral particles also showed diminished changes in the morphology of the cells upon KFL treatment. Thus, our study suggests that KFL induces differentiation of neuroblastoma cells via the IRE1α -XBP1 pathway.

Identification of FDA-approved drugs as novel allosteric inhibitors of human executioner caspases

The regulation of apoptosis is a tightly coordinated process and caspases are its chief regulators. Of special importance are the executioner caspases, caspase-3/7, the activation of which irreversibly sets the cell on the path of death. Dysregulation of apoptosis, particularly an increased rate of cell death lies at the root of numerous human diseases. Although several peptide-based inhibitors targeting the homologous active site region of caspases have been developed, owing to their non-specific activity and poor pharmacological properties their use has largely been restricted. Thus, we sought to identify FDA-approved drugs that could be repurposed as novel allosteric inhibitors of caspase-3/7. In this study, we virtually screened a catalog of FDA-approved drugs targeting an allosteric pocket located at the dimerization interface of caspase-3/7. From among the top-scoring hits we short-listed 5 compounds for experimental validation. Our enzymatic assays using recombinant caspase-3 suggested that 4 out of the 5 drugs effectively inhibited caspase-3 enzymatic activity in vitro with IC₅₀ values ranging ~10-55 μM. Structural analysis of the docking poses show the 4 compounds forming specific non-covalent interactions at the allosteric pocket suggesting that these molecules could disrupt the adjacently-located active site. In summary, we report the identification of 4 novel non-peptide allosteric inhibitors of caspase-3/7 from among FDA-approved drugs.

CDDO and ATRA Instigate Differentiation of IMR32 Human Neuroblastoma Cells

Neuroblastoma is the most common solid extra cranial tumor in infants. Improving the clinical outcome of children with aggressive tumors undergoing one of the multiple treatment options has been a major concern. Differentiating neuroblastoma cells holds promise in inducing tumor growth arrest and treating minimal residual disease. In this study, we investigated the effect of partial PPARγ agonist 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO) on human neuroblastoma IMR32 cells. Our results demonstrate that treatment with low concentration of CDDO and particularly in combination with all trans retinoic acid (ATRA) induced neurite outgrowth, increased the percentage of more than two neurites bearing cells, and decreased viability in IMR32 cells. These morphological changes were associated with an increase in expression of bonafide differentiation markers like β3-tubulin and Neuron Specific Enolase (NSE). The differentiation was accompanied by a decrease in the expression of MYCN whose amplification is known to contribute to the pathogenesis of neuroblastoma. MYCN is known to negatively regulate NMYC downstream-regulated gene 1 (NDRG1) in neuroblastomas. MYCN down-regulation induced by CDDO correlated with increased expression of NDRG1. CDDO decreased Anaplastic Lymphoma Kinase (ALK) mRNA expression without affecting its protein level, while ATRA significantly down-regulated ALK. Antagonism of PPARγ receptor by T0070907 meddled with differentiation inducing effects of CDDO as observed by stunted neurite growth, increased viability and decreased expression of differentiation markers. Our findings indicate that IMR32 differentiation induced by CDDO in combination with ATRA enhances, differentiation followed by cell death via cAMP-response-element binding protein (CREB) independent and PPARγ dependent signaling mechanisms.

Autophagy: The spotlight for cellular stress responses

Autophagy is an essential cellular mechanism which plays "housekeeping" role in normal physiological processes including removing of long lived, aggregated and misfolded proteins, clearing damaged organelles, growth regulation and aging. Autophagy is also involved in a variety of biological functions like development, cellular differentiation, defense against pathogens and nutritional starvation. The integration of autophagy into these biological functions and other stress responses is determined by the transcriptional factors that undertake the regulatory mechanism. This review discusses the machinery of autophagy, the molecular web that connects autophagy to various stress responses like inflammation, hypoxia, ER stress, and various other pathologic conditions. Defects in autophagy regulation play a central role in number of diseases, including neurodegenerative diseases, cancer, pathogen infection and metabolic diseases. Similarly, inhibiting autophagy would contribute in the treatment of cancer. However, understanding the biology of autophagy regulation requires pharmacologically active compounds which modulate the autophagy process. Inducers of autophagy are currently receiving considerable attention as autophagy upregulation may be a therapeutic benefit for certain neurodegenerative diseases (via removal of protein aggregates) while the inhibitors are being investigated for the treatment of cancers. Both induction and inhibition of autophagy have been proven to be beneficial in the treatment of cancer. This dual role of autophagy in cancers is now getting uncovered by the advancement in the research findings and development of effective autophagy modulators.

Exploring putative inhibitors of Death Associated Protein Kinase 1 (DAPK1) via targeting Gly-Glu-Leu (GEL) and Pro-Glu-Asn (PEN) substrate recognition motifs

Recently, a new signaling complex Death Associated Protein Kinase 1 (DAPK1) ̶ N-methyl-D-aspartate receptor subtype 2B (NMDAR2B or NR2B) engaged in the neuronal death cascade was identified and it was found that after stroke injury, N-methyl-D-aspartate glutamate (NMDA) receptors interact with DAPK1 through NR2B subunit and lead to excitotoxicity via over-activation of NMDA receptors. An acute brain injury, such as stroke, is a serious life-threatening medical condition which occurs due to poor blood supply to the brain and further leads to neuronal cell death. During a stroke, activated DAPK1 migrates towards the extra-synaptic site and binds to NR2B subunit of NMDA receptor. It is this DAPK1-NR2B interaction that arbitrates the pathological processes like apoptosis, necrosis, and autophagy of neuronal cells observed in stroke injury, hence we aimed to inhibit this vital interaction to prevent neuronal damage. In the present study, using PubChem database, we applied an integrative approach of virtual screening and molecular dynamic simulations and identified a potential lead compound 11 that interrupts DAPK1-NR2B interaction by competing with both ATP and substrate for their binding sites on DAPK1. This inhibitor was found potent and considerably selective to DAPK1 as it made direct contact with the ATP binding sites as well as substrate recognition motifs: Gly-Glu-Leu (GEL) and Pro-Glu-Asn (PEN). Further in vitro and in vivo experiments are demanded to validate the efficacy of compound 11 nevertheless, it can be considered as suitable starting point for designing DAPK1 inhibitors.

Death Associated Protein Kinase 1 (DAPK1): A Regulator of Apoptosis and Autophagy

Death-Associated Protein Kinase 1 (DAPK1) belongs to a family of five serine/threonine (Ser/Thr) kinases that possess tumor suppressive function and also mediate a wide range of cellular processes, including apoptosis and autophagy. The loss and gain-of–function of DAPK1 is associated with various cancer and neurodegenerative diseases respectively. In recent years, mechanistic studies have broadened our knowledge of the molecular mechanisms involved in DAPK1-mediated autophagy/apoptosis. In the present review, we have discussed the structural information and various cellular functions of DAPK1 in a comprehensive manner.

A molecular web: endoplasmic reticulum stress, inflammation, and oxidative stress

Execution of fundamental cellular functions demands regulated protein folding homeostasis. Endoplasmic reticulum (ER) is an active organelle existing to implement this function by folding and modifying secretory and membrane proteins. Loss of protein folding homeostasis is central to various diseases and budding evidences suggest ER stress as being a major contributor in the development or pathology of a diseased state besides other cellular stresses. The trigger for diseases may be diverse but, inflammation and/or ER stress may be basic mechanisms increasing the severity or complicating the condition of the disease. Chronic ER stress and activation of the unfolded-protein response (UPR) through endogenous or exogenous insults may result in impaired calcium and redox homeostasis, oxidative stress via protein overload thereby also influencing vital mitochondrial functions. Calcium released from the ER augments the production of mitochondrial Reactive Oxygen Species (ROS). Toxic accumulation of ROS within ER and mitochondria disturbs fundamental organelle functions. Sustained ER stress is known to potentially elicit inflammatory responses via UPR pathways. Additionally, ROS generated through inflammation or mitochondrial dysfunction could accelerate ER malfunction. Dysfunctional UPR pathways have been associated with a wide range of diseases including several neurodegenerative diseases, stroke, metabolic disorders, cancer, inflammatory disease, diabetes mellitus, cardiovascular disease, and others. In this review, we have discussed the UPR signaling pathways, and networking between ER stress-induced inflammatory pathways, oxidative stress, and mitochondrial signaling events, which further induce or exacerbate ER stress.

In silico identification of genetic variants in glucocerebrosidase (GBA) gene involved in Gaucher's disease using multiple software tools

Gaucher's disease (GD) is an autosomal recessive disorder caused by the deficiency of glucocerebrosidase, a lysosomal enzyme that catalyses the hydrolysis of the glycolipid glucocerebroside to ceramide and glucose. Polymorphisms in GBA gene have been associated with the development of Gaucher disease. We hypothesize that prediction of SNPs using multiple state of the art software tools will help in increasing the confidence in identification of SNPs involved in GD. Enzyme replacement therapy is the only option for GD. Our goal is to use several state of art SNP algorithms to predict/address harmful SNPs using comparative studies. In this study seven different algorithms (SIFT, MutPred, nsSNP Analyzer, PANTHER, PMUT, PROVEAN, and SNPs&GO) were used to predict the harmful polymorphisms. Among the seven programs, SIFT found 47 nsSNPs as deleterious, MutPred found 46 nsSNPs as harmful. nsSNP Analyzer program found 43 out of 47 nsSNPs are disease causing SNPs whereas PANTHER found 32 out of 47 as highly deleterious, 22 out of 47 are classified as pathological mutations by PMUT, 44 out of 47 were predicted to be deleterious by PROVEAN server, all 47 shows the disease related mutations by SNPs&GO. Twenty two nsSNPs were commonly predicted by all the seven different algorithms. The common 22 targeted mutations are F251L, C342G, W312C, P415R, R463C, D127V, A309V, G46E, G202E, P391L, Y363C, Y205C, W378C, I402T, S366R, F397S, Y418C, P401L, G195E, W184R, R48W, and T43R.

Cytogenetic, Y chromosome microdeletion, sperm chromatin and oxidative stress analysis in male partners of couples experiencing recurrent spontaneous abortions

PURPOSE

Etiology in majority of couples experiencing recurrent spontaneous abortions (RSA) is still unknown. The aim of the study was to find the role of cytogenetic abnormalities, Y chromosome microdeletion, oxidative stress (OS) and sperm DNA fragmentation in male partners of couples experiencing RSA.

METHODS

Forty-eight couples with history of RSA and 20 fertile controls were included in the study. The study subjects were divided into male partners of RSA couples with abnormal sperm parameters (SA) (N = 16), male partners of RSA couples with normal sperm parameters (NS) (N = 32) and age-matched fertile controls with normal sperm parameters (FC) (N = 20).

RESULTS

One of 48 men (2%) showed 46, XY (1qh-) chromosomal complement. None of the cases including FC showed deletion in any of the 3 AZF loci on Y chromosome long arm. Sperm count was found be significantly lower in SA cases as compared to group NS cases (P < 0.0001) and FC (P < 0.005). Sperm forward motility was found to be significantly (P < 0.05) lower in SA cases as compared to NS and FC. Male partners of RSA couples with abnormal sperm parameters had higher reactive oxygen species (ROS) levels (P < 0.005) and sperm DNA damage (P < 0.0001), however, in male partners of RSA couples with normal sperm parameters had only increased (P < 0.0001) sperm DNA damage.

CONCLUSION

Other than chromosomal anomalies, sperm DNA fragmentation and seminal OS may be the underlying pathology in RSA, thus screening for seminal ROS levels and DNA fragmentation has diagnostic and prognostic capabilities.

Profile of Live-born Infants of In-vitro Fertilisation

INTRODUCTION

The Army Hospital (R&R) is the only service hospital providing in-vitro fertilisation (IVF) facility. Neonatal characteristics of live-born infants at this centre over a two-year period are analyzed in this study.

METHODS

Data on 504 consecutive live-born IVF infants over a two-year period (01 Feb 2007 to 31 Jan 2009) were analysed.

RESULT

Of the 504 neonates, 190 (37.7%) were born by vaginal delivery, 156 (30.9%) by elective lower segment cesarean section (LSCS) and 127 (25.19%) following emergency LSCS. Maternal illness posing specific risk to the neonate was present in 165 out of 504 (32.7%). There were 239 (47.4%) preterm neonates. Males formed 51.8% of the cohort. Singletons accounted for 51.2%, while the rest (48.8%) were products of twin pregnancies. Small for gestational age neonates formed 22.6% (n = 114). A total of 20 (3.9%) infants had congenital malformations. There were 242 (48.1%) low birth weight neonates. A total of 128 (25.4%) neonates needed neonatal intensive care. Of the 504, there were 474 (94.1%) survivors while 30 (5.9%) did not survive. Twenty-nine (6.1%) neonates required readmission during the neonatal period.

CONCLUSION

In our setting, neonates born following IVF appeared to be at increased risk of prematurity, multiple births and low birth weight. Proper obstetric and neonatal management can result in good neonatal outcomes.

Synthetic triterpenoid cyano enone of methyl boswellate activates intrinsic, extrinsic, and endoplasmic reticulum stress cell death pathways in tumor cell lines

We explored the effect of a novel synthetic triterpenoid compound cyano enone of methyl boswellates (CEMB) on various prostate cancer and glioma cancer cell lines. CEMB displayed concentration-dependent cytotoxic activity with submicromolar lethal dose 50% (LD(50)) values in 10 of 10 tumor cell lines tested. CEMB-induced cytotoxicity is accompanied by activation of downstream effector caspases (caspases 3 and 7) and by upstream initiator caspases involved in both the extrinsic (caspase 8) and intrinsic (caspase 9) apoptotic pathways. By using short interfering RNAs (siRNA), we show evidence that knockdown of caspase 8, DR4, Apaf-1, and Bid impairs CEMB-induced cell death. Similar to other proapoptotic synthetic triterpenoid compounds, CEMB-induced apoptosis involved endoplasmic reticulum stress, as shown by partial rescue of tumor cells by siRNA-mediated knockdown of expression of genes involved in the unfolded protein response such as IRE1α, PERK, and ATF6. Altogether, our results suggest that CEMB stimulates several apoptotic pathways in cancer cells, suggesting that this compound should be evaluated further as a potential agent for cancer therapy.

Antioxidant levels in blood and seminal plasma and their impact on sperm parameters in infertile men

Excess reactive oxygen species (ROS) beyond the scavenging capacity of antioxidants leads to DNA damage and oxidation of lipoprotein components at the cellular and subcellular level. The oxidative stress (OS) adversely affects sperm function by altering membrane fluidity, permeability and impairs sperm functional competence. In the present study, the OS status in seminal plasma and blood serum in infertile men and its relationship with spermatozoa parameters have been investigated. Four groups of infertile men viz., oligozoospermic (n = 15), asthenozoospermic (n = 17), teratozoospermic (n = 19), and oligoasthenoteratozoospermic (n = 9), and healthy fertile controls (n = 40) have been analyzed for superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and malondialdehyde (MDA) in seminal plasma and blood serum. Significant correlation between blood serum SOD and sperm count has been observed in patients (p = 0.018) and controls (p = 0.021). Similarly, significant correlation between blood serum GSH and sperm progressive motility in patients (p = 0.036) and controls (p = 0.029) is observed. The low seminal MDA is associated with increase in sperm progressive motility in patients (p = 0.039) and controls (p = 0.028). Positive correlation is found between increased seminal MDA levels and abnormal sperm morphology in both patients and controls (r = 0.523, p = 0.029; r = 0.612, p = 0.034 respectively). Correlations between blood SOD and sperm count and between blood GSH levels and progressive motility suggest that these can be important biochemical markers in assaying the sperm count and motility. A negative correlation of motility with seminal MDA indicates that sperm membrane lipid peroxidation affects the fluidity and thus mobility of sperm axoneme. This affects functional competence of the sperm and acts like a biological safeguard. The results of the present study suggest the prospects of using the blood serum and seminal plasma antioxidants as a valuable tool to evaluate the sperm reproductive capacity and functional competence.

Novel systems biology insights using antifibrotic approaches for diabetic kidney disease

Although several interventions slow the progression of diabetic nephropathy, current therapies do not halt progression completely. Recent preclinical studies suggested that pirfenidone (PFD) prevents fibrosis in various diseases, but the mechanisms underlying its antifibrotic action are incompletely understood. To explore the therapeutic potential of PFD, we studied the PFD-treated db/db diabetic mouse kidney by liquid chromatography-tandem mass spectrometry proteomics. A total of 21 proteins unique to PFD-treated diabetic kidneys were identified. Analysis of gene ontology and protein-protein interactions of these proteins suggested that PFD may regulate RNA translation. Two key proteins involved in mRNA translation initiation and elongation were further evaluated and found to be regulated by PFD at the level of phosphorylation. In conclusion, insights from combining proteomics and bioinformatics improve the likelihood of rapid advancement of novel clinical therapies focused on reducing inflammation and fibrosis for diabetic complications.

Oxidative stress and sperm mitochondrial DNA mutation in idiopathic oligoasthenozoospermic men

Physiological function of reactive oxygen species (ROS) has been known since a long, but recently toxic effects of ROS on spermatozoa have gained much importance in male infertility. Mitochondrial DNA (mtDNA) is believed to be both source and target of ROS. mtDNA unlike nuclear DNA is not compactly packed and hence more susceptible to oxidative stress (OS) than nuclear DNA. In the present study, the role of OS in mitochondrial genome changes was studied in men with idiopathic infertility. The study included 33 infertile oligo-asthenozoospermic (OA) men and 30 fertile controls. Semen analyses were performed and OS was measured by estimating the level of malondialdehye (MDA) in the seminal plasma and ROS in the sperm. Sperm mtDNA was sequenced by standard PCR-DNA sequencing protocol for ATPase and nicotinamide adenine dinucleotide dehydrogenase (ND) groups of genes. Sperm count and progressive motility were found to be significantly lower in infertile group than the fertile controls. Semen MDA and ROS levels of infertile group were significantly higher (p<0.0001), when compared to the control group. However, catalase and glutathione peroxidase (GPx) levels were significantly lower in infertile group, compared to controls, but no significant difference in superoxide dismutase (SOD) activity was observed between control and cases. This might be due to higher expression of SOD alone in order to overcome OS in the semen. mtDNA analysis showed significant and high frequency of nucleotide changes in the ATPase (6 and 8), ND (2, 3, 4 and 5) genes of infertile cases compared to the controls. Hence excess ROS and low antioxidant levels in the semen might cause mtDNA mutations and vice versa in OA men that might impair the fertilizing capacity of spermatozoa. Thus, it is important to understand the etiology of mitochondrial genome mutations in idiopathic OA cases for better diagnostic and prognostic value in infertility treatment/assisted reproductive technique.

DNA integrity and semen quality in men with low seminal antioxidant levels

Accurate transmission of information coded in the sperm genome is vital to the pre- and post-natal development of the offspring. Recent advances in reproductive biology have proposed evaluation of sperm DNA integrity as an important assessment tool to infer the presence of DNA strand breaks, numerical abnormalities in sperm chromosome complement, and alterations in the epigenetic regulation of the paternal genome. Oxidative stress (OS), characterized by increased free radicals, may lead to the production of apurine sites, apyrimidine sites, oxidation of nucleotides of sperm genome. This study was performed to assess the impact of OS on DNA integrity in sperms. 52 infertile men [oligozoospermic-13, asthenozoospermic-15, teratozoospermic-19, oligoasthenoteratozoospermic-5] and 20 fertile controls were investigated for products of lipidperoxides as malondialdehyde; antioxidants such as superoxide dismutase, catalase and glutathione in seminal plasma by biochemical methods. DNA integrity of the sperms was analyzed by visual scoring method in which the comets were graded into 4 categories (A-D) on the basis of their tail length indicative of increasing levels of DNA damage. Significant increase in DNA damage (higher number of sperms in group D) in cases (oligozoospermic (O)-20%, asthenozoospermic (A)-24%, teratozoospermic (T)-28%, OAT-43%) as compared to controls (8%) was found. Increased malondialdehyde levels, abnormal sperm morphology and higher DNA damage were observed in the cases. The antioxidants superoxide dismutase, catalase and glutathione had a positive association with sperm count and motility while a negative association with the percentage of dead sperms and abnormal morphology was observed. This study highlights the influence of low antioxidants on sperm genome integrity and indicates sperm DNA integrity as a better and more reliable prognostic tool for infertility evaluation than simple quantitative and morphologic evaluation of spermatozoa.

PMAP: databases for analyzing proteolytic events and pathways

The Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic ‘Molecule Pages’, rich in molecular information. PMAP also contains two community annotated databases focused on function; CutDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition specificity of proteases. Together, the content within these four databases will ultimately feed PathwayDB, which will be comprised of known pathways whose function can be dynamically modeled in a rule-based manner, and hypothetical pathways suggested by semi-automated culling of the literature. A Protease Toolkit is also available for the analysis of proteases and proteolysis. Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis.

Confirmation of human protein interaction data by human expression data

BACKGROUND

With microarray technology the expression of thousands of genes can be measured simultaneously. It is well known that the expression levels of genes of interacting proteins are correlated significantly more strongly in Saccharomyces cerevisiae than those of proteins that are not interacting. The objective of this work is to investigate whether this observation extends to the human genome.

RESULTS

We investigated the quantitative relationship between expression levels of genes encoding interacting proteins and genes encoding random protein pairs. Therefore we studied 1369 interacting human protein pairs and human gene expression levels of 155 arrays. We were able to establish a statistically significantly higher correlation between the expression levels of genes whose proteins interact compared to random protein pairs. Additionally we were able to provide evidence that genes encoding proteins belonging to the same GO-class show correlated expression levels.

CONCLUSION

This finding is concurrent with the naive hypothesis that the scales of production of interacting proteins are linked because an efficient interaction demands that involved proteins are available to some degree. The goal of further research in this field will be to understand the biological mechanisms behind this observation.

The family and peer group influences in aggression

This study attempts to find a relationship between factors in the family, peer group, and levels of adolescent aggression. 148 adolescents and their mothers were studied. It was found that negative parenting and exposure to deviant peers influenced aggression among the adolescents.

Laboratory techniques for diagnosis of chlamydial infections of the eye

Giemsa and fluorescence antibody (FA) staining were used to diagnose patients clinically suspected to be suffering from trachoma. A total of 52 controls i.e. individuals with refractive errors and no clinical trachoma and 173 cases suffering from different stages of trachoma were studied. FA was found to be 2.52 times more sensitive in confirming the presence of Chlamydia trachomatis compared to Giemsa staining. 28/52 (53.8%) and 4/52 (7.,69%) controls were also positive by FA and Giemsa staining, respectively, indicating sub-clinical infection without symptoms. Post treatment staining with both methods revealed that clinical cure of trachoma did not necessarily mean the absence of Chlamydia trachomatis in the conjunctival smears. As a corollary it can be deduced that mere presence of Chlamydia trachomatis in conjunctival epithelial cells may not cause clinical trachoma, certain host factors (local immunity etc.) may play an important role in clinical disease.

Secondary fungal infections in chronic suppurative otitis media

A clinical, bacteriological and mycological study of 103 cases of 'safe' chronic suppurative otitis media with intractable otorrhoea was conducted to observe the role of fungi in the pathogenesis and perpetuation of the disease process. Mycotic otitis media was found in 42 cases (40.77%).45 patients with draining ears which grew pure bacterial growth were treated with ear drops. Fifteen of these patients were treated with topical antibiotics (polymyxin, Neomycin & Gramicidin). Other 15 patients were put on antibiotic steroid (Polymxin, Neomycin and Hydrocortisone) ear drops. The remaining 15 patients acted as controls with dry mopping treatment only.It was noted that prolonged exposure to antibiotic ear drops and antibiotic-steroid ear drops led to the growth of pathogenic fungi in 5 patients (33.33%) each from two study subgroups while the third control subgroup of 15 patients grew fungi of low virulence in 3 cases (20%).It was concluded that the routine and prolonged use of topical antibiotics or antibiotics-steroids in cases of wet 'safe' chronic suppurative otitis media, from the onset is not justified.

Candida overgrowth after treatment of duodenal ulcer. A comparison of cimetidine, famotidine, and omeprazole

Acid-reducing drugs can cause increased growth of microbes, including fungus, because of high gastric pH. Our purpose was to evaluate the occurrence of mycotic infection in patients with duodenal ulcer on anti-ulcer therapy and to compare the effects of cimetidine, famotidine, and omeprazole. Eighty patients with duodenal ulcer (62 males and 18 female patients, 16-65 years old) were evaluated for mycotic infection before and after 6 weeks of therapy (cimetidine, 20 patients; famotidine, 40 patients; omeprazole, 20 patients). Mycotic infection was diagnosed by endoscopic biopsy from the ulcer edge subjected to smear, culture, and histopathology and by endoscopic brush samples and gastric aspirate. On the basis of these studies, patients were categorized as having no fungal growth, saprophytic growth, or significant fungal growth. Thirty-five (43.8%) patients had evidence of fungus before ulcer therapy, and 16 of the 35 (20%) had significant fungal growth. The fungal isolation rate was higher in older patients (> and = 45 years of age) and in those with an ulcer size > and = 2 cm. While there was no significant increase in the total number of patients with evidence of fungus after therapy (n = 36), there was a significant increase in those with significant growth (n = 27, p < 0.05) compared with pretreatment status. We found that posttreatment gastric pH of > and = 4 was associated with a higher fungal positivity rate (59.4%) than pH values < 4 (32.4%, p < 0.05). However, neither the type of drug used nor the response in terms of ulcer healing correlated with the presence of fungus. Regardless of the type of drug used, acid-reducing therapy is associated with increased significant fungal growth.

Fungal colonization of untreated peptic ulcer

AIM

To evaluate the relationship between Candida and peptic ulcer.

METHODS

One hundred consecutive patients with untreated peptic ulcer (81 with duodenal ulcer and 19 with gastric ulcer) were studied using histopathology, culture and fungal serology. Twenty subjects with non-ulcer dyspepsia were taken as controls.

RESULTS

Forty seven patients (47%) with peptic ulcer were colonized by Candida as compared to 3 patients (15%) with non ulcer dyspepsia (p < 0.05). Confluent growth of Candida on culture of gastric aspirate or biopsy from ulcer edge was a more sensitive method for diagnosis of peptic ulcer-associated candidiasis than histological examination. There was no significant difference in the prevalence of Candida isolation in relation to age or sex of the patients, smoking habit and alcoholism. Large ulcers (> 2 cm) were, however, more often colonized by Candida (75%) than smaller ones (43%) (p < 0.05). Candida albicans was the commonest species isolated (60%). Invasive candidiasis was associated with Candida agglutinin titer of 1:128 in 81% of cases.

CONCLUSION

Candida colonization rate in peptic ulcer is significantly higher than in non-ulcer dyspepsia.

Incidence of cryptococcosis in and around Chandigarh, India, during the period 1982-91

The incidence of cryptococcosis was evaluated in and around Chandigarh, India over a period of 10 years (1982-91). Different species of Cryptococcus were isolated from 38 patients. Cryptococcus neoformans was the predominant isolate (26 = 68%) followed by Cr. albidus (2), Cr. laurentii (1) and not precisely identified Cryptococcus species (9 = 24%). Serotyping of the 18 isolates of Cr. neoformans revealed that 13 (72%) were serotype A, two (11%) were serotype AD and three (17%) were serotype B (Cr. neoformans var. gattii). Cryptococcus species were found to produce infection in 24 patients and were possibly transient colonizers in another 14 patients. In addition, in 11 patients no Cryptococcus species was isolated from any site but the latex agglutination test for antigen (Crypto-LA) was positive in serum and/or cerebrospinal fluid. Response to various antifungal drugs was also studied in these patients.

Isolation of dermatophytes from clinically normal sites in patients with tinea cruris

Sixty patients clinically suspected of tinea cruris were studied by collecting skin scrapings from the site of their lesions and six clinically normal sites including the thighs, scrotum, crural clefts, natal cleft and the web between their 4th and 5th toes. Dermatophytes were detected in scrapings in 46 (77%) and by culture in 36 (60%) patients from lesions. Trichophyton rubrum was isolated from 32 and Epidermophyton floccosum from 4 patients. Dermatophytes were also isolated with maximum isolation from the scrotum, crural clefts and the natal cleft in that order. Thus, when tinea cruris is treated with topical antifungal agents they should be applied also to the potential carriage sites to prevent recurrence.

Fatal pulmonary sporotrichosis caused by Sporothrix schenckii var. luriei in India

The first case of fatal pulmonary sporotrichosis caused by Sporothrix schenckii var. luriei in a patient from the northwestern region of India is described. In the absence of cultures, the diagnosis was suspected by notation, in lung tissue, of large, thick-walled, hyaline fungal cells that divided internally by septation or a budding process. The thick-walled, internally septated cells often became muriform. The presence of an "eyeglass" configuration of incompletely separated cells characteristic of S. schenckii var. luriei in large numbers aided the diagnosis. The identity of the etiologic agent was confirmed by application of a fluorescent-antibody reagent specific for S. schenckii.

Surveillance of nosocomial fungal infections in a burn care unit

A survey was conducted to trace the source of nosocomial fungal infections in the burn care unit of Nehru Hospital, Chandigarh, India, by collection of samples from wounds of 25 severely burnt patients and their surroundings. The environmental sampling revealed predominant fungal contamination by dematiceous hyphomycetes, aspergilli, Penicillium, Fusarium and yeasts (Candida albicans, Candida tropicalis, Candida krusei, Candida parapsilosis), whereas the colonising or invading fungi from the patients were Aspergillus flavus and yeasts of the genus Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, Torulopsis glabrata). This study thus corroborates the more pathogenic potential of some of the environmental fungal isolates located in the vicinity of the immunocompromised patients and stresses the need for decontamination of the environment of the burn care unit.

Cimetidine therapy and duodenal candidiasis: role in healing process

Patients with Candida colonization and invasion were studied in 20 duodenal ulcer (DU) patients, 10 non-ulcer dyspepsia (NUD) cases and 10 controls with non-gastroenterological disorders. Of 20 DU patients, Candida albicans was cultured from duodenal aspirates of 6 (30%) DU patients and pseudohyphae, indicating invasive form, were present in two (10%) prior to treatment. NUD patients and controls had positive Candida culture in 3 (30%) and 1 (10%) cases respectively; pseudohyphae were found in none. Six DU patients (30%) failed to heal with 4 weeks of cimetidine therapy; all six showed invasion of duodenal ulcer mucosa with Candida on histology. The pseudohyphae form of Candida was always found to be associated with non-healing of DU. Candidal invasion is associated with failure to respond to, H2-receptor antagonist therapy.

Comparative bioavailability and in-vitro antimicrobial activity of two different brands of rifampicin

A comparative bioavailability study was undertaken between a new formulation of rifampicin 'Famcin' and a standard formulation of rifampicin 'R-cin' in eight healthy male volunteers at two dose levels: 300 mg and 450 mg given orally under both single dose and steady state conditions. Plasma rifampicin was assayed spectrophotometrically. The study documented comparable rate and extent of bioavailability. (Cmax, Tmax and AUC0-infinity) and elimination half-lives (t1/2) of the two brands of rifampicin when compared at similar dose levels. The study establishes the bioequivalence of Famcin to that of the standard brand R-cin. Further, a comparative in vitro microbiological sensitivity of the two brands of rifampicin was undertaken against several strains of two test micro-organism viz. Staphylococcus aureus and Mycobacterium tuberculosis. For both the micro-organisms the minimal inhibitory concentration of Famcin was lower than that of R-cin, suggesting a somewhat greater potency of Famcin in suppressing the growth of test micro-organisms.

In vitro proteinase production by Candida species

A total of 290 Candida isolates from patients were investigated for in vitro proteinase production. Overall, sixty percent of these strains were found to be proteinase producers. Of the C. albicans strains, 81.4% of the significant isolates in contrast to 19.7% of nonsignificant isolates were proteinase producers, the difference being statistically significant (P less than 0.001). Amongst the different Candida species, the proteinase production was found not only in Candida albicans, but also in C. tropicalis, C. parapsilosis and C. glabrata. Thus this in vitro method of demonstration of proteinase may be a good adjunct to smear and culture examination in identifying pathogenic Candida species from anatomical sites where they can also be present as commensals.

Retinitis following disseminated cryptococcosis in a renal allograft recipient. Efficacy of oral fluconazole

A case of retinitis following disseminated cryptococcus neoformans infection in a renal allograft recipient is reported. Therapy with oral fluconazole showed a remarkable improvement at the end of 8 weeks. This is the first report of the use of fluconazole in the treatment of cryptococcal retinitis.

Subacute cutaneous lupus erythematosus-immunogenetic associations

Thirty-two patients who fulfilled criteria for subacute cutaneous lupus erythematosus (SCLE) were examined for their immunogenetic associations. Our results confirm the previously reported association of HLA-DR3 (15/31 48% P less than 0.01) and also demonstrate an increase in HLA-DR2 (14/31, 45%, P = less than 0.05). These findings indicate there are two distinct immunogenetic (HLA) populations of Ro(SS-A) antibody-positive SCLE patients. The increased frequency of HLA-DR2 and DR3 appears to be associated with expression of the Ro(SS-A) antibody, since no HLA associations were seen in Ro(SS-A)-negative SCLE patients when compared with normal population controls. Furthermore, these data indicate that the distinctive cutaneous lesions of SCLE are not associated with one specific HLA allele, as previously suspected. These findings contrast with the relatively homogeneous immunogenetic background seen in other lupus erythematosus subsets with a high frequency of Ro(SS-A) antibody, i.e., neonatal lupus erythematosus and Sjögren's syndrome/lupus erythematosus overlap (increased frequency of HLA-DR3, DQw2 and DRW52).

Fungal diarrhoea: association of different fungi and seasonal variation in their incidence

A total of 854 patients (640 children and 214 adults) admitted with acute or chronic diarrhoea suspected of non-invasive overgrowth of fungi in intestine were screened during a period of 3 years. Fungal proliferation was noted in 54.8% of these patients (53.6% in children, 58.4% in adults). The predominant fungal species isolated were Candida albicans (64.5%), followed by C. tropicalis (23.3%) C. krusei (6.9%). Torulopsis glabrata (1.6%). Trichosporon sp. and Geotrichum sp. were found to be responsible in 2.3% of adults. As seen in bacterial diarrhoea, higher incidence was noted in children from April to August. No such seasonal variation was noted in adults.

Brain abscess due to Nocardia

Cerebral Nocardiosis is a rare disease, usually occurring in immunocompromised hosts. We report here two cases of brain abscess due to Nocardia species-one due to usual N. asteroides and other by uncommon N. caviae. N. asteroides affected the brain in a post renal transplant patient, whereas N. caviae caused infection of brain in an apparently healthy individual. To the best of our knowledge, all the previous cases of brain abscess due to Nocardia caviae have been reported in compromised hosts. Agar dilution antimicrobial testing showed relatively higher resistant pattern in N. asteroides. In spite of antimicrobial therapy, both the patients succumbed, one within 4 days and other after an initial improvement for four weeks due to drainage of abscess.