Use of designed sequences in protein structure recognition

Background

Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure.

Results

We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation.

Conclusion

The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as ‘linkers’, where natural linkers between distant proteins are unavailable.

Reviewers

This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

Electronic supplementary material

The online version of this article (10.1186/s13062-018-0209-6) contains supplementary material, which is available to authorized users.

Microvesicles in hepatic and peripheral vein can predict nonresponse to corticosteroid therapy in severe alcoholic hepatitis

BACKGROUND

Severe alcoholic hepatitis patients have high mortality and limited response to corticosteroids. Microvesicles reflect cellular stress and disease conditions.

AIMS

To investigate whether microvesicles are associated with severity, response to steroid therapy and inflammation in severe alcoholic hepatitis.

METHODS

Microvesicles originating from different cells were studied pre-therapy in 101 patients; (71 responder to corticosteroid therapy and 30 nonresponders) and 20 healthy controls. Microvesicles and cells were determined in peripheral and hepatic vein samples using flow cytometry and correlated with outcomes. Inflammatory signalling pathways and functional alterations of immune cells after stimulation with microvesicles were also investigated.

RESULTS

Microvesicles mean levels were higher in nonresponders for T cells (CD3⁺ CD4⁺ ; 10.1 MV/μL vs 5.4; P = 0.06), macrophages (CD68⁺ CD11b⁺ ; 136.5 vs 121.9 MV/μL; P = 0.01), haematopoietic stem-cells (CD45⁺ CD34⁺ ; 116.8 vs 13.4 MV/μL; P = 0.0001) and hepatocytes (ASGPR⁺ ; 470 vs 361 MV/μL; P = 0.01); the latter two predicting steroid nonresponse in 94% patients at baseline in peripheral plasma. Microvesicle levels correlated with histological and liver disease severity indices. Whereas, in non-responders hepatic vein CD34+ cells were lower (P = 0.02), the CD34+ microvesicles there from were higher (P = 0.04), thus suggesting impaired regeneration. Also, microvesicles of 0.2-0.4 μm size were higher in nonresponders (P < 0.03) at baseline. Microvesicles from patients trigger more (P = 0.04) ROS generation, TNF-α production (P = 0.04) and up-regulate pro-inflammatory cytokine related genes in neutrophils in vitro.

CONCLUSIONS

Pre-therapy peripheral plasma levels of CD34⁺ and ASGPR⁺ microvesicles are reliable non-invasive markers of steroid nonresponse and mortality in patients with severe alcoholic hepatitis.

Liver failure determines the outcome in patients of acute-on-chronic liver failure (ACLF): comparison of APASL ACLF research consortium (AARC) and CLIF-SOFA models

BACKGROUND AND AIMS

Acute-on-chronic liver failure (ACLF) is a progressive disease associated with rapid clinical worsening and high mortality. Early prediction of mortality and intervention can improve patient outcomes. We aimed to develop a dynamic prognostic model and compare it with the existing models.

METHODS

A total of 1402 ACLF patients, enrolled in the APASL-ACLF Research Consortium (AARC) with 90-day follow-up, were analyzed. An ACLF score was developed in a derivation cohort (n = 480) and was validated (n = 922).

RESULTS

The overall survival of ACLF patients at 28 days was 51.7%, with a median of 26.3 days. Five baseline variables, total bilirubin, creatinine, serum lactate, INR and hepatic encephalopathy, were found to be independent predictors of mortality, with AUROC in derivation and validation cohorts being 0.80 and 0.78, respectively. AARC-ACLF score (range 5-15) was found to be superior to MELD and CLIF SOFA scores in predicting mortality with an AUROC of 0.80. The point scores were categorized into grades of liver failure (Gr I: 5-7; II: 8-10; and III: 11-15 points) with 28-day cumulative mortalities of 12.7, 44.5 and 85.9%, respectively. The mortality risk could be dynamically calculated as, with each unit increase in AARC-ACLF score above 10, the risk increased by 20%. A score of ≥11 at baseline or persisting in the first week was often seen among nonsurvivors (p = 0.001).

CONCLUSIONS

The AARC-ACLF score is easy to use, dynamic and reliable, and superior to the existing prediction models. It can reliably predict the need for interventions, such as liver transplant, within the first week.

Synthesis of platinum nanoparticles using seaweed Padina gymnospora and their catalytic activity as PVP/PtNPs nanocomposite towards biological applications

In the recent years, synthesis of nanomaterials using seaweeds and their diverse applications is escalating research in modern era. Among the noble metals, platinum nanoparticles (PtNPs) are of great importance owing to their catalytic property and less toxicity. The significance of this work is a simple one-step synthesis of PtNPs using aqueous extract of Indian brown seaweed Padina gymnospora and their catalytic activity with a polymer Polyvinylpyrrolidone (PVP) as PVP/PtNPs nanocomposite towards antimicrobial, haemolytic, cytotoxic (Artemia salina) and antioxidant properties. Fourier Transform Infrared (FT-IR) spectrum results showed diversified functional groups (biomoeities such as carbohydrates and proteins) present in the seaweed extract is responsible for the reduction of platinum ions (Pt+) to PtNPs. The seaweed mediated PtNPs was characterized by UV-vis spectrophotometer, X-ray diffraction (XRD) pattern, Field Emission Scanning Electron Microscopy (FESEM) equipped with Energy Dispersive X-ray (EDX) spectroscopy and High Resolution Transmission Electron Microscopy (HRTEM) analysis. The synthesized PtNPs was found to be truncated octahedral in shape with the range of 5-50nm. Crystalline nature of the nanoparticles was evidenced by Selected Area Electron Diffraction (SAED) pattern with bright circular spots corresponding to (111), (200), (220) and (311) Bragg's reflection planes. The size of the PtNPs was further evidenced by Dynamic Light Scattering (DLS) analysis and it is originate to be stable at -22.5mV through Zeta Potential (ZP) analysis. The present study shows that the catalytic behavior of PtNPs as polymer/metal nanocomposite (PVP/PtNPs) preparation for an antibacterial activity against seven disease causing pathogenic bacterial strains with the maximum activity against Escherichia coli (15.6mm) followed by Lactococcus lactis (14.8mm) and Klebsiella pneumoniae (14.4mm). But no haemolytic activity was seen at their effective bactericidal concentration, whereas increase in the haeomyltic activity was seen only in higher concentrations (600, 900 and 1200μgmL-1). On the other hand, PVP/PtNPs nanocomposite has shown cytotoxic activity at 100±4μgmL-1 (LC50) against Artemia salina nauplii. Furthermore, PVP/PtNPs nanocomposite showed an enhanced scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH), superoxide, nitric oxide and hydroxyl radicals.

A Model for the Conservative Management of Mallet Finger

This prospective study assessed the results of a custom-made thermoplastic splint for treatment of mallet finger deformity. From April 1999 to April 2000, 42 patients with mallet finger deformity were recruited. All patients were seen within 1 week and treated with a thermoplastic splint custom made by the hand therapy department. The splint was simple to make, easy to fit and suitable for all finger shapes and sizes. It improved the deformity in 30 out of 34 cases, and caused no skin irritation.

Nomenclature in the Journal of Hand Surgery

Unambiguous description of anatomical structures is essential to communicate information either in the clinical or research context. In view of this and following recommendations by the Nomenclature Committee of the International Societies for Surgery of the Hand (IFSSH), the booklet “Terminology for Hand Surgery” was published in 2001. The aim of this study was to identify whether the nomenclature used in the papers published in the Journal of Hand Surgery (British and European volume) followed its recommendations.

The study showed that we still continue to use traditional terminology. The most common “mistake” is numbering of the metacarpals instead of naming them. Usage of newer terms would improve the clarity of information distributed.

Vascular hepoxilin and trioxilins mediate vasorelaxation through TP receptor inhibition in mouse arteries

AIM

12/15-lipoxygenase (12/15-LO) metabolizes arachidonic acid (AA) into several vasoactive eicosanoids. In mouse arteries, we previously characterized the enzyme's 15-LO metabolites 12(S)-hydroxyeicosatetraenoic acid (HETE), 15-HETE, hydroxyepoxyeicosatrienoic acids (HEETAs) and 11,12,15-trihydroxyeicosatrienoic acids (11,12,15-THETAs) as endothelium-derived relaxing factors. However, the observed 12-LO metabolites remained uncharacterized. The purpose of this study was to determine the structure and biological functions of eicosanoids generated by the enzyme's 12-LO activity.

METHODS

Metabolites extracted from aortas of C57BL/6 male mice were separated using a series of reverse and normal phase chromatographic steps and identified as hepoxilin A₃ , trioxilin A₃ and trioxilin C₃ by mass spectrometry. Activities of these natural compounds were tested on isometric tension and intracellular calcium release. The role of thromboxane (TP) receptor was determined in HEK293 cells overexpressing TPα receptor (TPα -HEK).

RESULTS

All identified vascular 12-LO metabolites were biologically active. In mouse mesenteric arteries, trioxilin A₃ , C₃ and hepoxilin A₃ (3 μm) relaxed arteries constricted with the thromboxane mimetic, U46619-constricted arteries (maximum relaxations of 78.9 ± 3.2, 29.7 ± 4.6, 82.2 ± 5.0 and 88.0 ± 2.4% respectively), but not phenylephrine-constricted arteries. In TPα-HEK cells, trioxilin A₃ , C₃ and hepoxilin A₃ (10 μm) inhibited U46619 (10 nM)-induced increases in intracellular calcium by 53.0 ± 7.2%, 32.8 ± 5.0% and 37.9 ± 13.5% respectively. In contrast, trioxilin B₃ and hepoxilin B₃ were not synthesized in arteries and exhibited little biological activity.

CONCLUSION

Trioxilin A₃ and C₃ and hepoxilin A₃ are endogenous vascular relaxing factors. They are not endothelium-derived hyperpolarizing factors but mediate vascular relaxation by inhibiting TP agonist-induced increases in intracellular calcium. Thus, they regulate vascular homeostasis by acting as endogenous TP antagonists.

Fixed-dose combinations of antimicrobials: A need for special attention

OBJECTIVE

To highlight the issue of freely available fixed-dose combinations (FDCs) of antimicrobials.

METHODS

A critique of two such antimicrobial FDCs was undertaken wherein the following aspects were assessed - rational and regulatory issues and justification for clinical use. Available in vitro, in vivo (animals and humans) evidence from published literature was analysed.

CONCLUSIONS

There are several inadequately addressed aspects of the considered FDCs which are available in Indian market. In view of the growing problem of antimicrobial resistance, this issue must get the required attention.

Systemic chromosome instability in Shugoshin-1 mice resulted in compromised glutathione pathway, activation of Wnt signaling and defects in immune system in the lung

Mitotic error-mediated chromosome instability (CIN) can lead to aneuploidy, chromothripsis, DNA damage and/or whole chromosome gain/loss. CIN may prompt rapid accumulation of mutations and genomic alterations. Thus, CIN can promote carcinogenesis. This CIN process results from a mutation in certain genes or environmental challenge such as smoking, and is highly prevalent in various cancers, including lung cancer. A better understanding of the effects of CIN on carcinogenesis will lead to novel methods for cancer prevention and treatment. Previously Shugoshin-1 (Sgo1(-/+)) mice, a transgenic mouse model of CIN, showed mild proneness to spontaneous lung and liver cancers. In this study, adoptive (T/B-cell based) immunity-deficient RAG1(-/-) Sgo1(-/+) double mutant mice developed lung adenocarcinomas more aggressively than did Sgo1(-/+) or RAG1(-/-) mice, suggesting immune system involvement in CIN-mediated lung carcinogenesis. To identify molecular causes of the lung adenocarcinoma, we used systems biology approach, comparative RNAseq, to RAG1(-/-) and RAG1(-/-) Sgo1(-/+). The comparative RNAseq data and follow-up analyses in the lungs of naive Sgo1(-/+) mice demonstrate that, (i) glutathione is depleted, making the tissue vulnerable to oxidative stress, (ii) spontaneous DNA damage is increased, (iii) oncogenic Wnt signaling is activated, (iv) both major branches of the immune system are weakened through misregulations in signal mediators such as CD80 and calreticulin and (v) the actin cytoskeleton is misregulated. Overall, the results show multi-faceted roles of CIN in lung carcinoma development in Sgo1(-/+) mice. Our model presents various effects of CIN and will help to identify potential targets to prevent CIN-driven carcinogenesis in the lung.

Pneumoperitoneum or Chilaiditi's sign

Chilaiditi's sign describes the incidental radiographic finding of the bowel positioned between the right diaphragm and the liver. This is often misdiagnosed as pneumoperitoneum or free air under the diaphragm, which may lead to unnecessary investigations or surgical procedures. Here, we report two incidental chest radiograph findings of air under the diaphragm in patients who were being screened for pulmonary tuberculosis. This case series highlights the importance of awareness of the diagnosis of Chilaiditi's sign to avoid unnecessary hospital referrals.

Evaluation of virus resistance and agronomic performance of rice cultivar ASD 16 after transfer of transgene against Rice tungro bacilliform virus by backcross breeding

Severe losses of rice yield in south and southeast Asia are caused by Rice tungro disease (RTD) induced by mixed infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to develop transgene-based resistance against RTBV, one of its genes, ORF IV, was used to generate transgenic resistance based on RNA-interference in the easily transformed rice variety Pusa Basmati-1, and the transgene was subsequently introgressed to rice variety ASD 16, a variety popular in southern India, using transgene marker-assisted selection. Here, we report the evaluation of BC3F4 and BC3F5 generation rice plants for resistance to RTBV as well as for agronomic traits under glasshouse conditions. The BC3F4 and BC3F5 generation rice plants tested showed variable levels of resistance, which was manifested by an average of twofold amelioration in height reduction, 1.5-fold decrease in the reduction in chlorophyll content, and 100- to 10,000-fold reduction in the titers of RTBV, but no reduction of RTSV titers, in three backcrossed lines when compared with the ASD 16 parent. Agronomic traits of some of the backcrossed lines recorded substantial improvements when compared with the ASD 16 parental line after inoculation by RTBV and RTSV. This work represents an important step in transferring RTD resistance to a susceptible popular rice variety, hence enhancing its yield in areas threatened by the disease.

INDUCED CYTOMICTIC VARIATIONS AND SYNCYTE FORMATION DURING MICROSPOROGENESIS IN PHASEOLUS VULGARIS L

The intercellular translocation of chromatin material along with other cytoplasmic contents among the proximate meiocytes lying in close contact with each other commonly referred as cytomixis was reported during microsporogenesis in Phaseolus vulgaris L., a member of the family Fabaceae. The phenomenon of cytomixis was observed at three administered doses of gamma rays viz. 100, 200, 300 Gy respectively in the diploid plants of Phaseolus vulgaris L. The gamma rays irradiated plants showed the characteristic feature of inter-meiocyte chromatin/chromosomes transmigration through various means.such as channel formation, beak formation or by direct adhesion between the PMC's (Pollen mother cells). The present study also reports the first instance of syncyte formation induced via cytomictic transmigration in Phaseolus vulgaris L. Though the frequency of syncyteformation was rather low yet these could play a significant role in plant evolution. It is speculated that syncyte enhances the ploidy level of plants by forming 2n gametes and may lead to the production ofpolyploid plants. The phenomenon of cytomixis shows a gradual inclination along with the increasing treatment doses of gamma rays. The preponderance of cytomixis was more frequent during meiosis I as compared to meiosis II. An interesting feature noticed during the present study was the channel formation among the microspores and fusion among the tetrads due to cell wall dissolution. The impact of this phenomenon is also visible on the development of post-meiotic products. The formation of heterosized pollen grains; a deviation from the normal pollen grains has also been reported. The production of gametes with unbalanced chromosomes is of utmost importance and should be given more attention in future studies as they possess the capability of inducing variations at the genomic level and can be further utilized in the improvement of germplasm.

Protein sequence design and its applications

Design of proteins has far-reaching potentials in diverse areas that span repurposing of the protein scaffold for reactions and substrates that they were not naturally meant for, to catching a glimpse of the ephemeral proteins that nature might have sampled during evolution. These non-natural proteins, either in synthesized or virtual form have opened the scope for the design of entities that not only rival their natural counterparts but also offer a chance to visualize the protein space continuum that might help to relate proteins and understand their associations. Here, we review the recent advances in protein engineering and design, in multiple areas, with a view to drawing attention to their future potential.

Endoscopic repair of cerebrospinal fluid rhinorrhoea

GOAL

The purpose of this review was to look at the success rate of transnasal endoscopic repair of CSF rhinorrhoea and the impact of patient factors, repair techniques and adjuvant treatment.

MATERIAL AND METHODS

A literature search was performed on PubMed, Medline and Cochrane Central databases, independently by two of the authors, of all studies reporting the outcomes of CSF rhinorrhoea repair, published until the 1st June 2014, using keywords Cerebrospinal fluid leak, CSF leak, CSF fistula, CSF leak or fistula repair, endoscopic sinus surgery or ESS complications. Sixty-seven papers were included for the review.

RESULT

The repair of CSF rhinorrhoea has rapidly evolved over the past 30 years. Prior to the advent of the endoscopic approach, craniotomy was used for repairs, which carried a variable success rate and morbidity. More recently, there have been several case series and reports that describe various endoscopic methods and materials for repair, with mean success rate of 90% (range: 60-100%). The most common site of CSF leak is the ethmoid roof/cribriform plate region. Traumatic CSF leak, in particular iatrogenic, is still the most common cause. Imaging with CT and MRI remains the gold standard for localisation of CSF leaks. The sphenoid sinus is the most common location for CSF leak repair failure. Lumbar drains and antibiotics are used as adjuvant therapy to endoscopic repair, but their benefits are not clear; intrathecal fluorescein can be used to aid location of CSF leak, but should be reserved for more complex cases. Further work into graft materials used and adjuvant treatment is needed to make any meaningful conclusions about their efficacy.

CONCLUSION

The literature demonstrates that endoscopic repair of CSF rhinorrhoea is safe and effective, with a very low complication rate. It has almost completely replaced the older open techniques.

EFFECT OF WATERLOGGING STRESS ON MEIOTIC COURSE, TETRAD FORMATION AND POLLEN FERTILITY OF SESBANIA PEA

Sesbania cannabina a multipurpose leguminous crop of family Fabaceae, is widely adaptable to adverse climatic conditions such as waterlogging, drought and high salinity. Flooding and water logging are very common phenomena and there may be possibility to become more serious alarms for environment, which is progressively deteriorated by human beings by their anthropogenic activities, polluting the atmosphere. Flooding provides a case of natural selection to the nature which selects the plants which are more adaptable to this condition and renders themselves to survive due to this tolerance or resistance behavior. Present study envisages the effect of waterlogging stress on chromosomal biology of Sesbania pea. To study the effect of waterlogging stress on microsporogensis of Sesbania cannabina, presoaked seeds were sown in experimental pots. Permanent waterlogged condition is created by shifting pots in water filled tanks. Cytological studies showed various types of chromosomal aberrations induced by waterlogging stress and reduction in pollen fertility was also encountered.

Facile and Rapid Synthesis of ZnO Nanoparticles for Photovoltaic Device Application

Well-crystalline ZnO nanoparticles were prepared through simple, facile and rapid solution combustion process and utilized as photoanode material for the fabrication of dye-sensitized solar cell. The detailed characterizations of the ZnO nanoparticles revealed that the crystalline product with wurtzite hexagonal phase was grown in high-density. The chemical composition analyzed through FTIR and EDS confirmed the purity of the ZnO nanoparticles. UV-vis and Raman spectral studies were applied for studying the optical and vibrational properties of as prepared ZnO nanoparticles, respectively. The fabricated dye-sensitized solar cell exhibited overall photo-to-electricity conversion efficiency (η) of 0.94%, open-circuit current (V(oc)) of 0.531 V, short circuit current (J(sc)) of 4.11 mA/cm2 and fill factor (FF) of 0.43.

Brachiocephalic artery haemorrhage during percutaneous tracheostomy

Percutaneous tracheostomy was performed on a 69-year-old woman to facilitate weaning. Insertion of the size 7 tracheostomy tube resulted in profuse bleeding around the tracheostomy site. On inflation of the tracheostomy balloon, the bleeding stopped. Urgent computed tomography demonstrated the brachiocephalic artery was abnormally high and lying in an oblique fashion over the trachea, and the tracheostomy tube was displacing the trachea posteriorly. Surgical repair of the defect in the brachiocephalic artery was undertaken and a surgical tracheostomy was performed in theatre. This case raises important issues about the potential dangers of percutaneous tracheostomy in cases of abnormal anatomy. It also emphasises the importance of direct visualisation of the seeker needle using the endoscope. In cases where there is a suspicion of abnormal anatomy, it is safer to obtain preprocedural imaging or perform a surgical tracheostomy.

Trends of pulmonary embolism before and after kidney transplantation in black versus white patients

BACKGROUND

Pulmonary embolism (PE) is an important cause of in-hospital mortality and is common in renal transplantation and maintenance dialysis patients. PE incidence is higher among patients who are black; however, differences in trends of incidence and outcomes of PE by race among patients on dialysis and after renal transplantation is not well known.

METHODS

In this observational study, the incidences of PE hospitalizations and mortality were studied in those with renal transplant, on maintenance dialysis, and in general population. Incidences were compared across racial groups. Renal transplantation status as a predictor of mortality was also examined.

RESULTS

The incidences of PE in general population, dialysis, and renal transplant groups were 70.5, 518.8, and 158.8 per 100,000 population, respectively. Incidence was higher in blacks across all groups. The age-adjusted incidence of PE admissions increased over time in all groups with greater increase in blacks in non-transplant groups (the slope in dialysis for blacks was 112.1 versus that for whites at 49.4; P = .001; the slope in general population for blacks was 9.3 versus 3.4 for whites; P = .003). The mortality rate in general population was not significantly different than renal transplant group (3.4% versus 1.9%, P = .2); however, was lower than 6.8% seen in dialysis group (P < .001). The mortality rate was not different between whites and blacks. Maintenance dialysis was an independent predictor of mortality (odds ratio [OR] 1.94; 95% confidence interval [CI] 1.62-2.32).

CONCLUSIONS

PE in those with renal transplant is more common than in general population but less common than those on maintenance dialysis. The mortality rate for PE hospitalizations is equivocal between renal transplant and general population but higher for patients on dialysis. The incidence of PE hospitalizations is not only higher among blacks, but is increasing disproportionately in this group among those who are on maintenance dialysis and within general population.

Early infectious acute respiratory distress syndrome is characterized by activation and proliferation of alveolar T-cells

Acute respiratory distress syndrome (ARDS) in humans is characterized by the infiltration of polymorphonuclears in the alveolar spaces. However, the role of T-cells in ARDS is unknown. Our aim was to characterize the T-cell phenotype in bronchoalveolar lavage (BAL) during the early phase of acute lung infection(ALI)/ARDS-infected patients in comparison to a control group (CG). BAL lymphocyte phenotypes of two ALI, 16 ARDS, and eight CG were examined by flow cytometry. ALI/ARDS showed a significant increase in CD4 and CD8 T-cell activation as compared to CG. Moreover, a significant level of proliferation was observed using the Ki67 marker in ARDS patients as compared to controls (median): 37 versus 6 % for CD4 T-cells (p = 0.022) and 34 versus 2 % for CD8 T-cells (p = 0.009). In contrast, the percentage of T-regulatory cells and apoptotic T-cells were similar in both groups. Among costimulatory molecules, we observed an overexpression of CTLA-4/CD152 on CD4 T-cells in ALI/ARDS as compared to CG: 30 versus 7 %, respectively (p = 0.063). In further characterizing T-cell subsets expressing high levels of CD152, we found the presence of IL-17 secreting CD4 T-cells in ALI/ARDS. In humans, ALI/ARDS due to infection is associated with a high level of T-cell activation and proliferation, along with the presence of Th17 cells, which are known to attract polymorphonuclears.

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

NrichD (http://proline.biochem.iisc.ernet.in/NRICHD/) is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural ‘intermediately related sequences’ is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been ‘enriched’ with these artificial intermediary sequences. NrichD database currently contains 3 611 010 artificial sequences that have been generated between 27 882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

Correlation between lead and cadmium concentration and semen quality

There are contrary reports of association of lead and cadmium with the decline in semen quality. This study evaluates whether seminal lead (Pb) and cadmium (Cd) at environmental concentration are associated with altered semen quality. We conducted a study of healthy fertile and infertile men 20-43 years of age attending the Andrology Laboratory of Reproductive Biology Department for semen analysis. The semen analysis was carried out according to the WHO 2010 guidelines. Seminal lead and cadmium were estimated by ICP-AES. The lead and cadmium values were significantly higher in infertile subjects. A negative association between seminal lead or cadmium concentration and sperm concentration, sperm motility and per cent abnormal spermatozoa was found. This study shows that exposure to Pb (5.29-7.25 μg dl(-1) ) and cadmium (4.07-5.92 μg dl(-1) ) might affect semen profile in men. Age, diet, smoking and tobacco chewing habits may have an influence on the increase in exposure to Pb and Cd in the individual subjects.

Development of a novel in vitro method for drug development for fish; application to test efficacy of antimicrosporidian compounds

Few drugs are approved for treating diseases caused by parasites in minor species such as fish. This is due, in part, to the expense of drug development and to the comparatively small market. In vivo effectiveness trials for antiparasitic drugs are costly, time consuming and require ethics approval, therefore an in vitro screening approach is a cost-effective alternative to finding promising drug candidates. We developed an in vitro testing system to test antimicrosporidial compounds against a microsporidian pathogen Heterosporis saurida. Five antiparasitic compounds, albendazole, fumagillin, TNP-70, nitazoxanide and lufenuron, were assayed for antimicrosporidial activity. All compounds reduced the number of H saurida spores in infected cells when applied at a concentration that did not appear to be toxic to the host cells. Albendazole inhibited replication of H saurida by >60 per cent, fumagillin and its analogue TNP-470 inhibited H saurida >80 per cent, nitazoxanide and lufenuron inhibited growth >70 per cent. The data suggest that both fumagillin and its analogous TNP-70 hold the best promise as therapeutic agents against H saurida. The ability to use fish cell cultures to assess drugs against H saurida demonstrates an approach that may be helpful to evaluate other drugs on different microsporidia and host cells.