Major sources of sinking particulate organic matter in the western Bay of Bengal

Impacts of river discharge on coastal ocean processes are multi-dimensional. Studies on sinking particle fluxes, composition and their seasonal variability in coastal oceans are very limited. In this study, we investigated the impact of river discharge on seasonal variability in sinking fluxes of total mass, biogenic and lithogenic material in a river-dominated continental margin, western coastal Bay of Bengal. Higher POC, lithogenic and total mass fluxes were found during early southwest monsoon, and are decoupled with peak river discharge and elevated primary production. It is attributed to cross-shelf transport of re-suspended surface sediments from shelf region. Peak river discharge followed by elevated chlorophyll-a suggest nutrients supply though river discharge support primary production. Elemental C:N ratios, δ13C and δ15N results likely suggest that both marine and terrestrial sources contributed to sinking POM, . Overall, higher sinking fluxes during southwest monsoon than rest of the year suggest that seasonal river discharge exerts considerable impact on sinking fluxes in the western coastal Bay of Bengal.

Helicobacter pylori enhances HLA-C expression in the human gastric adenocarcinoma cells AGS and can protect them from the cytotoxicity of natural killer cells

Helicobacter pylori (H. pylori) seems to play causative roles in gastric cancers. H. pylori has also been detected in established gastric cancers. How the presence of H. pylori modulates immune response to the cancer is unclear. The cytotoxicity of natural killer (NK) cells, toward infected or malignant cells, is controlled by the repertoire of activating and inhibitory receptors expressed on their surface. Here, we studied H. pylori-induced changes in the expression of ligands, of activating and inhibitory receptors of NK cells, in the gastric adenocarcinoma AGS cells, and their impacts on NK cell responses. AGS cells lacked or had low surface expression of the class I major histocompatibility complex (MHC-I) molecules HLA-E and HLA-C-ligands of the major NK cell inhibitory receptors NKG2A and killer-cell Ig-like receptor (KIR), respectively. However, AGS cells had high surface expression of ligands of activating receptors DNAM-1 and CD2, and of the adhesion molecules LFA-1. Consistently, AGS cells were sensitive to killing by NK cells despite the expression of inhibitory KIR on NK cells. Furthermore, H. pylori enhanced HLA-C surface expression on AGS cells. H. pylori infection enhanced HLA-C protein synthesis, which could explain H. pylori-induced HLA-C surface expression. H. pylori infection enhanced HLA-C surface expression also in the hepatoma Huh7 and HepG2 cells. Furthermore, H. pylori-induced HLA-C surface expression on AGS cells promoted inhibition of NK cells by KIR, and thereby protected AGS cells from NK cell cytotoxicity. These results suggest that H. pylori enhances HLA-C expression in host cells and protects them from the cytotoxic attack of NK cells expressing HLA-C-specific inhibitory receptors.

Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase

S-adenosylmethionine (SAM) is a ubiquitous co-factor that serves as a donor for methylation reactions and additionally serves as a donor of other functional groups such as amino and ribosyl moieties in a variety of other biochemical reactions. Such versatility in function is enabled by the ability of SAM to be recognized by a wide variety of protein molecules that vary in their sequences and structural folds. To understand what gives rise to specific SAM binding in diverse proteins, we set out to study if there are any structural patterns at their binding sites. A comprehensive analysis of structures of the binding sites of SAM by all-pair comparison and clustering, indicated the presence of 4 different site-types, only one among them being well studied. For each site-type we decipher the common minimum principle involved in SAM recognition by diverse proteins and derive structural motifs that are characteristic of SAM binding. The presence of the structural motifs with precise three-dimensional arrangement of amino acids in SAM sites that appear to have evolved independently, indicates that these are winning arrangements of residues to bring about SAM recognition. Further, we find high similarity between one of the SAM site types and a well known ATP binding site type. We demonstrate using in vitro experiments that a known SAM binding protein, HpyAII.M1, a type 2 methyltransferase can bind and hydrolyse ATP. We find common structural motifs that explain this, further supported through site-directed mutagenesis. Observation of similar motifs for binding two of the most ubiquitous ligands in multiple protein families with diverse sequences and structural folds presents compelling evidence at the molecular level in favour of convergent evolution.

CRISPR Correction of the GBA Mutation in Human-Induced Pluripotent Stem Cells Restores Normal Function to Gaucher Macrophages and Increases Their Susceptibility to Mycobacterium tuberculosis

Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder caused by mutations in the β-glucocerebrosidase (GCase) GBA gene, which result in macrophage dysfunction. CRISPR (clustered regularly interspaced short palindromic repeats) editing of the homozygous L444P (1448T→C) GBA mutation in type 2 GD (GBA-/-) human-induced pluripotent stem cells (hiPSCs) yielded both heterozygous (GBA+/-) and homozygous (GBA+/+) isogenic lines. Macrophages derived from GBA-/-, GBA+/- and GBA+/+ hiPSCs showed that GBA mutation correction restores normal macrophage functions: GCase activity, motility, and phagocytosis. Furthermore, infection of GBA-/-, GBA+/- and GBA+/+ macrophages with the Mycobacterium tuberculosis H37Rv strain showed that impaired mobility and phagocytic activity were correlated with reduced levels of bacterial engulfment and replication suggesting that GD may be protective against tuberculosis.

Impact of atmospheric dry deposition of nutrients on phytoplankton pigment composition and primary production in the coastal Bay of Bengal

Atmospheric deposition of pollutants decreases pH and increases the nutrient concentration in the surface water. To examine its impact on coastal phytoplankton composition and primary production, monthly atmospheric aerosol samples were mixed with coastal waters in the microcosm experiments. These experiments suggested that the biomass of Bacillariophyceae, Dinophyceae and Chlorophyceae were increased and primary production of the coastal waters increased by 3 to 19% due to the addition of aeolian nutrients. The increase in primary production displayed significant relation with a concentration of sulphate and nitrate in the atmospheric aerosols suggesting that both decreases in pH and fertilization enhanced primary production. The impact of acidification on primary production was found to be 22%, whereas 78% was contributed by the nutrient increase. The atmospheric pollution is increasing rapidly over the northern Indian Ocean since past two decades due to rapid industrialization. Hence, it is suggested that the impact of atmospheric pollution on the coastal ecosystem must be included in the numerical models to predict possible changes in the coastal ecosystem due to climate change.

Genome Editing Revolution in Life Sciences

Programmable nucleases—ZFNs, TALENs and CRISPR-Cas9—have equipped scientists with an unprecedented ability to modify cells and organisms almost at will, with great implications across life sciences: biology, agriculture, ecology and medicine. Nucleases-based genome editing (aka gene editing) depends on cellular responses to a targeted double-strand break (DSB). The first truly targetable reagents were zinc finger nucleases (ZFNs) showing that arbitrary DNA sequences within a mammalian genome, could be addressed by protein engineering, ushering in the era of genome editing. ZFNs that are fusions of zinc finger proteins (ZFPs) and FokI cleavage domain, resulted from the basic research on Type IIs FokI restriction enzyme, which showed a bipartite structure with a separable DNA-binding domain and a non-specific cleavage domain. Studies on 3-finger ZFNs established that the preferred substrates were paired binding sites, which doubled the size of the target recognition sequence from 9 to 18 bp that is large enough to specify a unique genomic locus in plant and mammalian cells, including human cells. Subsequently, a ZFN-induced DSB was shown to stimulate homologous recombination in frog eggs. Transcription activator-like effector nucleases (TALENs) that are based on bacterial TALEs fused to FokI cleavage domain expanded the capability. ZFNs and TALENs have been successfully used to modify a multitude of recalcitrant organisms and cell types that were unapproachable previously attesting to the success of protein engineering, long before the arrival of CRISPR. The recent technique to deliver a targeted DSB to cellular genomes are RNA-guided nucleases as exemplified by the Type II prokaryotic CRISPR-Cas9 system. Unlike ZFNs and TALENs that use protein motifs for DNA sequence recognition, CRISPR-Cas9 depends on RNA-DNA recognition. The advantages of the CRISPR-Cas9 system, which include ease of RNA design for new targets and dependence on a single constant Cas9 protein, have led to its wide adoption by research labs around the world. The 2020 Nobel Prize for Chemistry was awarded to Jennifer Doudna and Emmanualle Charpentier for harnessing CRISPR-Cas9 system to provide a simplified technique for genome editing. The programmable nucleases have also been shown to cut at off-target sites with mutagenic consequences, which is a serious concern for human therapeutic applications. Therefore, applications of genome editing technologies to human therapeutics will ultimately depend on risk versus benefit analysis and informed consent

Changes in the behaviour of monocyte subsets in acute post-traumatic sepsis patients

Trauma remains a major public health problem worldwide, marked as the fourth leading cause of death among all diseases. Trauma patients who survived at initial stages in the Emergency Department (ED), have significantly higher chances of mortality due to sepsis associated complications in the ICU at the later stage. There is paucity of literature regarding the role of circulating monocytes subsets and development of sepsis complications following trauma haemorrhagic shock (THS). The study was conducted to investigate the circulating level of monocyte subsets (Classical, Inflammatory, and Patrolling) and its functions in patients with acute post-traumatic sepsis. A total 72, THS patients and 30 age matched healthy controls were recruited. Blood samples were collected at different time points on days 1, 7, and 14 to measure the serum levels of cytokines by Cytometric bead assay (CBA), for the immunophenotyping of monocytes subsets, and also for the cell sorting of monocytes subsets for the functional studies. The circulating levels of monocytes subsets were found to be significantly differs among THS patients, who developed sepsis when compared with others who did not. The levels of patrolling monocytes were elevated in THS patients who developed sepsis and showed negative correlation with Sequential organ failure assessment (SOFA) score on days 7 and 14. Classical monocytes responded strongly to bacterial TLR-agonist (LPS) and produced anti-inflammatory cytokines, whereas patrolling monocytes responded with viral TLR agonist TLR-7/8 (R848) and produced inflammatory cytokines in post-traumatic sepsis patients. In conclusion, this study shows disparity in the behaviour of monocytes subsets in patients with acute post-traumatic sepsis.

[MutL Protein from the Neisseria gonorrhoeae Mismatch Repair System: Interaction with ATP and DNA]

The mismatch repair system (MMR) ensures the stability of genetic information during DNA replication in almost all organisms. Mismatch repair is initiated after recognition of a non-canonical nucleotide pair by the MutS protein and the formation of a complex between MutS and MutL. Eukaryotic and most bacterial MutL homologs function as endonucleases that introduce a single-strand break in the daughter strand of the DNA, thus activating the repair process. However, many aspects of the functioning of this protein remain unknown. We studied the ATPase and DNA binding functions of the MutL protein from the pathogenic bacterium Neisseria gonorrhoeae (NgoMutL), which exhibits endonuclease activity. For the first time, the kinetic parameters of ATP hydrolysis by the full-length NgoMutL protein were determined. Its interactions with single- and double-stranded DNA fragments of various lengths were studied. NgoMutL was shown to be able to efficiently form complexes with DNA fragments that are longer than 40 nucleotides. Using modified DNA duplexes harboring a 2-pyridyldisulfide group on linkers of various lengths, we obtained NgoMutL conjugates with DNA for the first time. According to these results, the Cys residues of the wild-type protein are located at a distance of approximately 18-50 Å from the duplex. The efficiency of the affinity modification of Cys residues in NgoMutL with reactive DNAs was shown to decrease in the presence of ATP or its non-hydrolyzable analog, as well as ZnCl2, in the reaction mixture. We hypothesize that the conserved Cys residues of the C-terminal domain of NgoMutL, which are responsible for the coordination of metal ions in the active center of the protein, are involved in its interaction with DNA. This information may be useful in reconstruction of the main stages of MMR in prokaryotes that are different from γ-proteobacteria, as well as in the search for new targets for drugs against N. gonorrhoeae.

Molecular dissection of Helicobacter pylori Topoisomerase I reveals an additional active site in the carboxyl terminus of the enzyme

DNA topoisomerases play a crucial role in maintaining DNA superhelicity, thereby regulating various cellular processes. Unlike most other species, the human pathogen Helicobacter pylori has only two topoisomerases, Topoisomerase I and DNA gyrase, the physiological roles of which remain to be explored. Interestingly, there is enormous variability among the C-terminal domains (CTDs) of Topoisomerase I across bacteria. H. pylori Topoisomerase I (HpTopoI) CTD harbors four zinc finger motifs (ZFs). We show here that sequential deletion of the third and/or fourth ZFs had only a marginal effect on the HpTopoI activity, while deletion of the second, third and fourth ZFs severely reduced DNA relaxation activity. Deletion of all ZFs drastically hampered DNA binding and thus abolished DNA relaxation. Surprisingly, mutagenesis of the annotated active site tyrosine residue (Y297 F) did not abrogate the enzyme activity and HpTopoI CTD alone (spanning the four ZFs) showed DNA relaxation activity. Additionally, a covalent linkage between the DNA and HpTopoI CTD was identified. The capacity of HpTopoI CTD to complement Escherichia coli topA mutant strains further supported the in vitro observations. Collectively these results imply that not all ZFs are dispensable for HpTopoI activity and unveil the presence of additional non-canonical catalytic site(s) within the enzyme.

Tumor microenvironment: Challenges and opportunities in targeting metastasis of triple negative breast cancer

Triple negative breast cancer (TNBC) is most aggressive subtype of breast cancers with high probability of metastasis as well as lack of specific targets and targeted therapeutics. TNBC is characterized with unique tumor microenvironment (TME), which differs from other subtypes. TME is associated with induction of proliferation, angiogenesis, inhibition of apoptosis and immune system suppression, and drug resistance. Exosomes are promising nanovesicles, which orchestrate the TME by communicating with different cells within TME. The components of TME including transformed ECM, soluble factors, immune suppressive cells, epigenetic modifications and re-programmed fibroblasts together hamper antitumor response and helps progression and metastasis of TNBCs. Therefore, TME could be a therapeutic target of TNBC. The current review presents latest updates on the role of exosomes in modulation of TME, approaches for targeting TME and combination of immune checkpoint inhibitors and target chemotherapeutics. Finally, we also discussed various phytochemicals that alter genetic, transcriptomic and proteomic profiles of TME along with current challenges and future implications. Thus, as TME is associated with the hallmarks of TNBC, the understanding of the impact of different components can improve the clinical benefits of TNBC patients.

Association of dietary intake below recommendations and micronutrient deficiencies during pregnancy and low birthweight

Background Pregnancy is associated with biochemical changes leading to increased nutritional demands for the developing fetus that result in altered micronutrient status. The Indian dietary pattern is highly diversified and the data about dietary intake patterns, blood micronutrient profiles and their relation to low birthweight (LBW) is scarce. Methods Healthy pregnant women (HPW) were enrolled and followed-up to their assess dietary intake of nutrients, micronutrient profiles and birthweight using a dietary recall method, serum analysis and infant weight measurements, respectively. Results At enrolment, more than 90% of HPW had a dietary intake below the recommended dietary allowance (RDA). A significant change in the dietary intake pattern of energy, protein, fat, vitamin A and vitamin C (P < 0.001) was seen except for iron (Fe) [chi-squared (χ2) = 3.16, P = 0.177]. Zinc (Zn) deficiency, magnesium deficiency (MgDef) and anemia ranged between 54-67%, 18-43% and 33-93% which was aggravated at each follow-up visit (P ≤ 0.05). MgDef was significantly associated with LBW [odds ratio (OR): 4.21; P = 0.01] and the risk exacerbate with the persistence of deficiency along with gestation (OR: 7.34; P = 0.04). Pre-delivery (OR: 0.57; P = 0.04) and postpartum (OR: 0.37; P = 0.05) anemia, and a vitamin A-deficient diet (OR: 3.78; P = 0.04) were significantly associated with LBW. LBW risk was much higher in women consuming a vitamin A-deficient diet throughout gestation compared to vitamin A-sufficient dietary intake (OR: 10.00; P = 0.05). Conclusion The studied population had a dietary intake well below the RDA. MgDef, anemia and a vitamin A-deficient diet were found to be associated with an increased likelihood of LBW. Nutrient enrichment strategies should be used to combat prevalent micronutrient deficiencies and LBW.

N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori

Many bacterial genomes exclusively display an N⁴-methyl cytosine base (m4C), whose physiological significance is not yet clear. Helicobacter pylori is a carcinogenic bacterium and the leading cause of gastric cancer in humans. Helicobacter pylori strain 26695 harbors a single m4C cytosine methyltransferase, M2.HpyAII which recognizes 5′ TCTTC 3′ sequence and methylates the first cytosine residue. To understand the role of m4C modification, M2.hpyAII deletion strain was constructed. Deletion strain displayed lower adherence to host AGS cells and reduced potential to induce inflammation and apoptosis. M2.hpyAII gene deletion strain exhibited reduced capacity for natural transformation, which was rescued in the complemented strain carrying an active copy of M2.hpyAII gene in the genome. Genome-wide gene expression and proteomic analysis were carried out to discern the possible reasons behind the altered phenotype of the M2.hpyAII gene deletion strain. Upon the loss of m4C modification a total of 102 genes belonging to virulence, ribosome assembly and cellular components were differentially expressed. The present study adds a functional role for the presence of m4C modification in H. pylori and provides the first evidence that m4C signal acts as a global epigenetic regulator in H. pylori.

Mechanism of formation of a toroid around DNA by the mismatch sensor protein

The DNA mismatch repair (MMR) pathway removes errors that appear during genome replication. MutS is the primary mismatch sensor and forms an asymmetric dimer that encircles DNA to bend it to scan for mismatches. The mechanism utilized to load DNA into the central tunnel was unknown and the origin of the force required to bend DNA was unclear. We show that, in absence of DNA, MutS forms a symmetric dimer wherein a gap exists between the monomers through which DNA can enter the central tunnel. The comparison with structures of MutS-DNA complexes suggests that the mismatch scanning monomer (Bm) will move by nearly 50 Å to associate with the other monomer (Am). Consequently, the N-terminal domains of both monomers will press onto DNA to bend it. The proposed mechanism of toroid formation evinces that the force required to bend DNA arises primarily due to the movement of Bm and hence, the MutS dimer acts like a pair of pliers to bend DNA. We also shed light on the allosteric mechanism that influences the expulsion of adenosine triphosphate from Am on DNA binding. Overall, this study provides mechanistic insight regarding the primary event in MMR i.e. the assembly of the MutS-DNA complex.

Kinetic and catalytic properties of M.HpyAXVII, a phase-variable DNA methyltransferase from Helicobacter pylori

The bacterium Helicobacter pylori is one of the most common infectious agents found in the human stomach. H. pylori has an unusually large number of DNA methyltransferases (MTases), prompting speculation that they may be involved in the cancerization of epithelial cells. The mod-4a/4b locus, consisting of the hp1369 and hp1370 ORFs, encodes for a truncated and inactive MTase in H. pylori strain 26695. However, slipped-strand synthesis within the phase-variable polyguanine tract in hp1369 results in expression of an active HP1369-1370 fusion N ⁶-adenine methyltransferase, designated M.HpyAXVII. Sequence analysis of the mod-4a/4b locus across 74 H. pylori strain genomes has provided insights into the regulation of M.HpyAXVII expression. To better understand the role of M.HpyAXVII in the H. pylori biology, here we cloned and overexpressed the hp1369-70 fusion construct in Escherichia coli BL21(DE3) cells. Results from size-exclusion chromatography and multi-angle light scattering (MALS) analyses suggested that M.HpyAXVII exists as a dimer in solution. Kinetic studies, including product and substrate inhibition analyses, initial velocity dependence between substrates, and isotope partitioning, suggested that M.HpyAXVII catalyzes DNA methylation in an ordered Bi Bi mechanism in which the AdoMet binding precedes DNA binding and AdoMet's methyl group is then transferred to an adenine within the DNA recognition sequence. Altering the highly conserved catalytic motif (DPP(Y/F)) as well as the AdoMet-binding motif (FXGXG) by site-directed mutagenesis abolished the catalytic activity of M.HpyAXVII. These results provide insights into the enzyme kinetic mechanism of M.HpyAXVII. We propose that AdoMet binding conformationally "primes" the enzyme for DNA binding.

Role of Trace Elements, Oxidative Stress and Immune System: a Triad in Premature Ovarian Failure

The risk of premature ovarian failure (POF) increases in association with alteration in immunological parameters and oxidative stress (OS). Adequate intake of trace elements is required for antioxidant property and immune defense mechanism. The aim of this study was to explore the involvement of trace elements, OS, and immunological parameters in POF. This was a cross-sectional, case-control study, involving 65 participants divided into the POF (n = 35) and control (n = 30) groups. Serum levels of Se, Zn, and Cu were determined along with hormonal, OS, and immunological markers. POF group had significantly lower levels of Zn, Cu, Se, and Zn:Cu ratio. However, Se:Cu ratio was not significant between the groups. FSH and LH levels were negatively correlated with Zn and Cu levels and positively correlated with Se levels. Estrogen levels were negatively correlated with all the studied trace elements. Inter-element association between Zn and Se was significant in POF (r = - 0.39, p = 0.02) compared to control group (r = - 0.078, p = 0.65). In all the POF patients, SOD and GPx activities were significantly (p < 0.05) lower and MDA level was higher (p > 0.05) than control group. B cell marker CD19 was significantly (p < 0.0001) high in POF group. There are involvement of trace elements in hormonal regulation and antioxidant defense mechanism, which once gets altered leads to high ROS generation and affect functions of the immune system. Exaggereative immune system causing higher expression of B cell associated markers (CD19) leading to autoimmune condition in POF.

Indocyanine green clearance test to evaluate liver function in rat model of extrahepatic biliary atresia

BACKGROUND

Indocyanine green clearance test (ICG-K) has been shown as a sensitive marker of liver function in patients with cirrhosis. However, its role in the assessment of liver function in children with biliary atresia is not well established. The present study was undertaken to evaluate the ICG-K in an experimental model of cholangitis and partial biliary obstruction.

MATERIALS AND METHODS

Thirty albino rats were divided into 3 groups of 10 each. After exploration under anesthesia, a vial of OK-432 diluted in 0.2 ml of normal saline was injected into the common bile duct (CBD) in rats of Groups B and C. In the control Group A, only saline was injected. Re-exploration was done at 3 weeks in Groups A and B and at 6 weeks in Group C, and freshly prepared ICG was injected into the inferior vena cava. Blood samples were collected at periodic intervals, optical density of the serum was measured, and half-life of ICG and fractional clearance (K) were calculated. Blood and tissue samples were obtained for biochemical tests and histological examination.

RESULTS

The histological changes in CBD and liver were maximum in Group B; this correlated well with the K-value in this group, which was significantly delayed. In Group C, clearance was delayed than the control group with histological changes ranged from mild to moderate inflammation. The control group had normal histology of liver and CBD, and only four rats showed mild portal inflammation.

CONCLUSION

ICG clearance rate is a reliable marker of liver function and can be utilized for evaluation of liver function in postoperative extrahepatic biliary atresia patients.

IL-12 and IL-23 modulate plasticity of FoxP3+ regulatory T cells in human Leprosy

Leprosy is a bacterial disease caused by M. leprae. Its clinical spectrum reflects the host's immune response to the M. leprae and provide an ideal model to investigate the host pathogen interaction and immunological dysregulation. Tregs are high in leprosy patients and responsible for immune suppression of the host by producing IL-10 and TGF-β cytokines. In leprosy, plasticity of Tregs remain unstudied. This is the first study describing the conversion of Tregs into Th1-like and Th17-like cells using in vitro cytokine therapy in leprosy patients. Peripheral blood mononuclear cells from leprosy patients were isolated and stimulated with M. leprae antigen (MLCwA), rIL-12 and rIL-23 for 48h. Expression of FoxP3 in CD4⁺CD25⁺ Tregs, intracellular cytokines IFN-γ, TGF-β, IL-10 and IL-17 in Tregs cells were evaluated by flow cytometry (FACS) after stimulation. rIL-12 treatment increases the levels of pStat4 in Tregs and IFN-γ production. In the presence of rIL-23, pStat3⁺ and IL-17A⁺ cells increase. rIL-12 and r-IL-23 treatment downregulated the FoxP3 expression, IL-10 and TGF-β production by Tregs and enhances the expression of co-stimulatory molecules (CD80, CD86). In conclusion rIL-12 converts Tregs into IFN-γ producing cells through STAT-4 signaling while rIL-23 converts Tregs into IL-17 producing cells through STAT-3 signaling in leprosy patients. This study may helpful to provide a new avenue to overcome the immunosuprression in leprosy patients using in vitro cytokine.

Micronutrients Drift During Daily and Weekly Iron Supplementation in Non-anaemic and Anaemic Pregnancy

AIMS

Pregnancy is a phenomenon associated with dynamic changes in physical, mental and biochemical status of body and demands increased nutritional intake for developing foetus. The level of various micronutrients which act as co-factors for antioxidant enzymes or it-self as antioxidants gets altered with the progression of pregnancy. The present longitudinal study summarized the trend of selected micronutrients level in anaemic (AP) and non-anaemic primigravida (NAP) supplemented with daily and weekly oral iron folic acid (IFA) tablet during pregnancy and postpartum.

METHODS

A total of 200 primigravida {N = 100; NAP (Hb > 11 g/dl) and N = 100 AP (Hb = 8-11 g/dl) assigned daily (N = 50) and weekly (N = 50) supplementation} were recruited and overnight fasting blood samples were withdrawn at 13-16 weeks, after 3 months and 6 weeks postpartum. The serum iron, copper, zinc, magnesium and manganese were estimated by inductively coupled plasma-atomic emission spectrophotometer.

RESULTS

Serum manganese (p < 0.05) at baseline and magnesium (p < 0.01) at postpartum was significantly different between NAP and AP supplemented with daily IFA tablets. The trend of copper found to be increased during pregnancy and later declined at postpartum in both the groups. Daily supplementation resulted in significantly high iron (p < 0.05) in NAP during third trimester.

CONCLUSIONS

Hypozincemia and hypomagnesemia was observed in anaemic pregnancy supplemented with weekly and daily IFA respectively. Clear evidence of altered micronutrients levels during healthy and anaemic pregnancy was seen. The reference values may be drawn from this study for the nutritional assessment during pregnancy for healthy pregnancy outcomes.

TRIAL REGISTRATION

Clinical Trial Registry-India, http://ctri.nic.in, CTRI/2014/10/005135.

Coexistence of Th1/Th2 and Th17/Treg imbalances in patients with post traumatic sepsis

INTRODUCTION

Multiple organ dysfunction syndrome (MODS) developed due to the insult of trauma is a leading cause of death. The high mortality rate in these patients with and without sepsis has been reported up to 50%, throughout the world and thus required an urgent insight to overcome this problem.

OBJECTIVE

The aim of this study is to examine the differential changes in subsets of T cells, imbalance in cytokine profile, immune-paralysis (T cell anergy) in Trauma hemorrhagic shock (THS) and post traumatic sepsis patients.

METHODOLOGY

114, THS patients and 50 healthy controls were recruited in the present study. We have measured the T cell proliferation assay using dominant antigens of both gram positive (LTA, 100ng/ml) and gram negative (LPS-100ng/ml) bacteria and PHA (4μg/ml) using radioactive thymidine (1H³) assay. Simultaneously, we have measured the culture supernatant level of cytokines using Cytokine bead assay (CBA). The other parts of this study include the analysis of different subsets of T cells.

RESULTS AND CONCLUSION

We observed significantly (P<0.05) reduced T cell proliferation in THS patients as compared to control. Our study also showed patients died due to sepsis/septic shock, had significantly (p<0.05) lower T cell response and had significantly elevated levels of IL-4, IL-10andTGF-β, but low level of IL-2andIFN-γ in culture supernatant. THS patients who developed sepsis complication had significantly higher T regulatory cells and lower Th17 cells in comparison to non-sepsis. In conclusion, our study showed an imbalance in cell mediated immune response and disturbance in Th1/Th2/Th17 and T reg population of T helper cells and also the shifts towards Th2 and T17 in THS patients who had developed sepsis and showed poor outcomes.

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

EcoP15I DNA methyltransferase (M.EcoP15I) recognizes short asymmetric sequence, 5'-CAGCAG-3', and methylates the second adenine only on one strand of the double-stranded DNA (dsDNA). In vivo, this methylation is sufficient to protect the host DNA from cleavage by the cognate restriction endonuclease, R.EcoP15I, because of the stringent cleavage specificity requirements. Biochemical and structural characterization support the notion that purified M.EcoP15I exists and functions as dimer. However, the exact role of dimerization in M.EcoP15I reaction mechanism remains elusive. Here we engineered M.EcoP15I to a stable monomeric form and studied the role of dimerization in enzyme catalyzed methylation reaction. While the monomeric form binds single-stranded DNA (ssDNA) containing the recognition sequence it is unable to methylate it. Further we show that, while the monomeric form has AdoMet binding and Mg(2+) binding motifs intact, optimal dsDNA binding required for methylation is dependent on dimerization. Together, our biochemical data supports a unique subunit organization for M.EcoP15I to catalyze the methylation reaction.

Evaluation of circulating haematopoietic progenitor cells in patients with Trauma Haemorrhagic shock and its correlation with outcomes

Background:

Haemorrhagic shock accounts up to 50% of early trauma deaths. Hematopoietic failure has been observed in experimental animals and human following shock and injury. One of the facets of bone marrow failure is multiple organ dysfunction syndrome and is commonly seen in patients recovering from severe trauma and hemorrhagic shock. Bone Marrow (BM) dysfunction is associated with mobilization of hematopoietic progenitor cells (HPCs) into peripheral blood. Present study explored the association of peripheral blood hematopoietic progenitor cells (HPCs) with mortality in trauma haemorrhagic shock patients (T/HS).

Materials and Methods:

Prospective cohort studies of patients presenting within 8 hrs of injury with T/HS to the Department of Emergency Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences were recruited. Peripheral blood samples were collected in each patient for measurement of peripheral blood HPCs. Peripheral blood progenitor cell (PBPC) quantification was performed by measuring HPCs counts using the haematology analyzer (Sysmex XE-2100). Clinical and laboratory data were prospectively collected after consent. Ethical approval was taken and data was analysed by Stata 11.2.

Results:

39 patients with trauma hemorrhagic shock and 30 normal healthy controls were recruited. HPCs were significantly higher (P < 0.001) in the T/HS as compared to control. Among study group, 14 patients died within 24 h. at the hospital admission, and found HPCs concentrations were highly significant (<0.001) in non-survivors (n = 14) when compared with survivors (n = 25) among T/HS patients.

Conclusions:

Our studies suggest the peripheral blood HPCs may be early prognostic marker for mortality among patients who presented with trauma hemorrhagic shock on admission. But the exact molecular mechanism and signalling pathway involved in the change of the behaviour of bone marrow microenvironment is still unclear.

Generation of Catalytic Antibodies Is an Intrinsic Property of an Individual's Immune System: A Study on a Large Cohort of Renal Transplant Patients

Renal transplant is the treatment of choice for patients with terminal end-stage renal disease. We have previously identified low levels of catalytic IgG as a potential prognosis marker for chronic allograft rejection. The origin and physiopathological relevance of catalytic Abs is not well understood, owing to the fact that catalytic Abs have been studied in relatively small cohorts of patients with rare diseases and/or without systematic follow-up. In the current study, we have followed the evolution of the levels of catalytic IgG in a large cohort of renal transplant patients over a 2-y period. Our results demonstrate that, prior to transplant, patients with renal failure present with heterogeneous levels of IgG hydrolyzing the generic proline-phenylalanine-arginine-methylcoumarinamide (PFR-MCA) substrate. PFR-MCA hydrolysis was greater for patients' IgG than for a therapeutic preparation of pooled IgG from healthy donors. Renal transplant was marked by a drastic decrease in levels of catalytic IgG over 3 mo followed by a steady increase during the next 21 mo. Patients who displayed high levels of catalytic IgG pretransplant recovered high levels of catalytic Abs 2 y posttransplant. Interestingly, IgG-mediated hydrolysis of a model protein substrate, procoagulant factor VIII, did not correlate with that of PFR-MCA prior transplantation, whereas it did 12 mo posttransplant. Taken together, our results suggest that the level of circulating catalytic IgG under pathological conditions is an intrinsic property of each individual's immune system and that recovery of pretransplant levels of catalytic IgG is accompanied by changes in the repertoire of target Ags.

Generation of catalytic antibodies is an intrinsic property of an individual’s immune system: a study on a large cohort of renal transplant patients

The origin and physiopathological relevance of catalytic antibodies is not well understood owing to the fact that catalytic antibodies have been studied in relatively small cohorts of patients with rare diseases and/or without systematic follow-up. In the present study, we have followed the evolution of the levels of catalytic IgG in a large cohort of 100 renal transplant patients over a 2-year period. Prior to transplant, hydrolysis of the generic substrate PFR-MCA was greater for patients’ IgG than for a therapeutic preparation of pooled IgG from healthy donors (6.6±0.9 vs 0.65±0.03 fmol/min per pmol). Renal transplant was marked by a drastic decrease in levels of catalytic IgG over 3 months (6.6±0.9 vs 2.4±0.2 fmol/min/pmol; P&lt;0.0001) followed by a steady increase at 12 months (3.2±0.3 fmol/min/pmol; P=0.015) and further at 24 months (5.1±0.6 fmol/min/pmol; P=0.004). When divided into quartiles based on the rates of IgG-mediated PFR-MCA hydrolysis measured in pre-transplant samples, the IgG catalytic activity in the upper quartile of patients was significantly high both pre-transplant (12.03±1.6 vs 2.7±0.2 fmol/min/pmol, P&lt;0.0001) and 24 months post-transplant (6.8±1.2 vs 4.6±0.7, fmol/min/pmol, P=0.0004). Interestingly, IgG-mediated hydrolysis of a model protein substrate, pro-coagulant factor VIII, did not correlate with that of PFR-MCA prior transplantation, while it did 12 months post-transplant (P&lt;0.0001, R2=0.4). Taken together, our results suggest that the level of circulating catalytic IgG under pathological conditions is an intrinsic property of each individual’s immune system, and that recovery of pre-transplant levels of catalytic IgG is accompanied by changes in the repertoire of target antigens.

Mutations in the nucleotide binding and hydrolysis domains of Helicobacter pylori MutS2 lead to altered biochemical activities and inactivation of its in vivo function

Background

Helicobacter pylori MutS2 (HpMutS2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. Although HpMutS2 belongs to a highly conserved family of ABC transporter ATPases, the role of its ATP binding and hydrolysis activities remains elusive.

Results

To explore the putative role of ATP binding and hydrolysis activities of HpMutS2 we specifically generated point mutations in the nucleotide-binding Walker-A (HpMutS2-G338R) and hydrolysis Walker-B (HpMutS2-E413A) domains of the protein. Compared to wild-type protein, HpMutS2-G338R exhibited ~2.5-fold lower affinity for both ATP and ADP while ATP hydrolysis was reduced by ~3-fold. Nucleotide binding efficiencies of HpMutS2-E413A were not significantly altered; however the ATP hydrolysis was reduced by ~10-fold. Although mutations in the Walker-A and Walker-B motifs of HpMutS2 only partially reduced its ability to bind and hydrolyze ATP, we demonstrate that these mutants not only exhibited alterations in the conformation, DNA binding and nuclease activities of the protein but failed to complement the hyper-recombinant phenotype displayed by mutS2-disrupted strain of H. pylori. In addition, we show that the nucleotide cofactor modulates the conformation, DNA binding and nuclease activities of HpMutS2.

Conclusions

These data describe a strong crosstalk between the ATPase, DNA binding, and nuclease activities of HpMutS2. Furthermore these data show that both, ATP binding and hydrolysis activities of HpMutS2 are essential for the in vivo anti-recombinase function of the protein.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0629-3) contains supplementary material, which is available to authorized users.

Bone marrow hematopoietic stem cells behavior with or without growth factors in trauma hemorrhagic shock

Background:

Hemorrhagic shock (HS) is the major leading cause of death after trauma. Up to 50% of early deaths are due to massive hemorrhage. Excessive release of pro-inflammatory cytokine and hypercatecholamine induces hematopoietic progenitor cells (HPCs) apoptosis, leading to multiorgan failure and death. However, still, result remains elusive for hematopoietic stem cells (HSCs) behavior in trauma HS (T/HS).

Objectives:

Therefore, our aim was to evaluate the in vitro HSCs behavior with or without recombinant human erythropoietin (rhEPO), recombinant human granulocyte macrophage-colony-stimulating factor (rhGM-CSF), recombinant human interleukin-3 (rhIL-3) alone, and combination with rhEPO + rhGM-CSF + rhIL-3 (EG3) in T/HS patients.

Methodology:

Bone marrow (BM) aspirates (n = 14) were collected from T/HS patients, those survived on day 3. BM cells were cultured for HPCs: Colony-forming unit-erythroid (CFU-E), burst-forming unit-erythroid (BFU-E), and colony-forming unit-granulocyte, monocyte/macrophage colonies growth. HPCs were counted with or without rhEPO, rhGM-CSF, rhIL-3 alone, and combination with EG3 in T/HS patients.

Results:

BM HSCs growth significantly suppressed in T/HS when compared with control group (P < 0.05). In addition, CFU-E and BFU-E colony growth were increased with additional growth factor (AGF) (rhEPO, rhGM-CSF, and rhIL-3) as compared to baseline (without AGF) (P < 0.05).

Conclusion:

Suppressed HPCs may be reactivated by addition of erythropoietin, GM-CSF, IL-3 alone and with combination in T/HS.

Insights into the Functional Roles of N-Terminal and C-Terminal Domains of Helicobacter pylori DprA

DNA processing protein A (DprA) plays a crucial role in the process of natural transformation. This is accomplished through binding and subsequent protection of incoming foreign DNA during the process of internalization. DprA along with Single stranded DNA binding protein A (SsbA) acts as an accessory factor for RecA mediated DNA strand exchange. H. pylori DprA (HpDprA) is divided into an N-terminal domain and a C- terminal domain. In the present study, individual domains of HpDprA have been characterized for their ability to bind single stranded (ssDNA) and double stranded DNA (dsDNA). Oligomeric studies revealed that HpDprA possesses two sites for dimerization which enables HpDprA to form large and tightly packed complexes with ss and dsDNA. While the N-terminal domain was found to be sufficient for binding with ss or ds DNA, C-terminal domain has an important role in the assembly of poly-nucleoprotein complex. Using site directed mutagenesis approach, we show that a pocket comprising positively charged amino acids in the N-terminal domain has an important role in the binding of ss and dsDNA. Together, a functional cross talk between the two domains of HpDprA facilitating the binding and formation of higher order complex with DNA is discussed.

Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N(6)-adenine DNA methyltransferases of Neisseria meningitidis

Phase variation (random ON/OFF switching) of gene expression is a common feature of host-adapted pathogenic bacteria. Phase variably expressed N(6)-adenine DNA methyltransferases (Mod) alter global methylation patterns resulting in changes in gene expression. These systems constitute phase variable regulons called phasevarions. Neisseria meningitidis phasevarions regulate genes including virulence factors and vaccine candidates, and alter phenotypes including antibiotic resistance. The target site recognized by these Type III N(6)-adenine DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome analysis was used to identify the recognition site for three key N. meningitidis methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY M6A: G-3'), ModA12 (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC M6A: CC-3') and ModD1 (exemplified by M.Nme579I) (5'-CC M6A: GC-3'). Restriction inhibition assays and mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and atypical and is dependent on the type of pyrimidine at the central position, in combination with the bases flanking the core recognition sequence 5'-CGY M6A: G-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome ranged from 4.6% at 5'-GCGC M6A: GG-3' sites, to 100% at 5'-ACGT M6A: GG-3' sites. Analysis of the distribution of modified sites in the respective genomes shows many cases of association with intergenic regions of genes with altered expression due to phasevarion switching.

The nuclease activities of both the Smr domain and an additional LDLK motif are required for an efficient anti-recombination function of Helicobacter pylori MutS2

Helicobacter pylori, a human pathogen, is a naturally and constitutively competent bacteria, displaying a high rate of intergenomic recombination. While recombination events are essential for evolution and adaptation of H. pylori to dynamic gastric niches and new hosts, such events should be regulated tightly to maintain genomic integrity. Here, we analyze the role of the nuclease activity of MutS2, a protein that limits recombination during transformation in H. pylori. In previously studied MutS2 proteins, the C-terminal Smr domain was mapped as the region responsible for its nuclease activity. We report here that deletion of Smr domain does not completely abolish the nuclease activity of HpMutS2. Using bioinformatics analysis and mutagenesis, we identified an additional and novel nuclease motif (LDLK) at the N-terminus of HpMutS2 unique to Helicobacter and related ε-proteobacterial species. A single point mutation (D30A) in the LDLK motif and the deletion of Smr domain resulted in ∼ 5-10-fold loss of DNA cleavage ability of HpMutS2. Interestingly, the mutant forms of HpMutS2 wherein the LDLK motif was mutated or the Smr domain was deleted were unable to complement the hyper-recombination phenotype of a mutS2(-) strain, suggesting that both nuclease sites are indispensable for an efficient anti-recombinase activity of HpMutS2.

Nasal delivery of PLG microparticle encapsulated defensin peptides adjuvanted gp41 antigen confers strong and long-lasting immunoprotective response against HIV-1

Defensins display immunostimulatory activities including a chemotactic effect for T lymphocytes/immature dendritic cells and secretion of pro-inflammatory cytokines suggest their role in bridging innate and adaptive immunity. We hypothesized whether defensins with separately emulsified HIV-1 immunogen would elicit peptide-specific systemic and mucosal antibody response in mice. The HIV-1 peptide alone in microsphere showed low peptide-specific antibody response in sera and different washes, while the presence of defensins markedly increased the antibody peak titre both in sera (102,400-409,600) (p < 0.05) and in washes (800-25,600) (p < 0.001). Defensins with HIV-1 peptide were showing 43.0-83.2% and 38.7-72.3% in vitro neutralization against laboratory isolates in serum and lavage samples, respectively, higher than HIV-1 peptide alone. Our findings may have implications in the development of new mucosal adjuvant for AIDS vaccination.

Comparison of haematological and biochemical changes between non-anaemic and anaemic primigravid women in a north Indian population to establish normative values

Pregnancy is accompanied by several haemodynamic, biochemical and haematological changes, which may lead to severe problems, if they are not suitably addressed. The current study highlights the haematological and biochemical differences observed in anaemic (AP) and non-anaemic primigravida (NAP), in the 2nd trimester, in a north Indian population. There were significant differences (p < 0.05) in the body weight and body temperature of NAP compared with AP. A significant decrease (p < 0.001) in haematological parameters including haemoglobin, haematocrit, erythrocyte count, MCH and MCHC, was observed in AP; however, MCV was found to be significantly higher (p = 0.038). Many biochemical parameters viz. potassium, albumin, total protein and calcium levels were significantly reduced (p < 0.01) in AP, except alkaline phosphatase whose level was found significantly increased (p < 0.01). The findings of the study suggest that haematological and biochemical changes take place in anaemia during pregnancy. Further, the results obtained should be used for establishing normative values for similar populations.

Mycobacterium tuberculosis DinG is a structure-specific helicase that unwinds G4 DNA: implications for targeting G4 DNA as a novel therapeutic approach

The significance of G-quadruplexes and the helicases that resolve G4 structures in prokaryotes is poorly understood. The Mycobacterium tuberculosis genome is GC-rich and contains >10,000 sequences that have the potential to form G4 structures. In Escherichia coli, RecQ helicase unwinds G4 structures. However, RecQ is absent in M. tuberculosis, and the helicase that participates in G4 resolution in M. tuberculosis is obscure. Here, we show that M. tuberculosis DinG (MtDinG) exhibits high affinity for ssDNA and ssDNA translocation with a 5' → 3' polarity. Interestingly, MtDinG unwinds overhangs, flap structures, and forked duplexes but fails to unwind linear duplex DNA. Our data with DNase I footprinting provide mechanistic insights and suggest that MtDinG is a 5' → 3' polarity helicase. Notably, in contrast to E. coli DinG, MtDinG catalyzes unwinding of replication fork and Holliday junction structures. Strikingly, we find that MtDinG resolves intermolecular G4 structures. These data suggest that MtDinG is a multifunctional structure-specific helicase that unwinds model structures of DNA replication, repair, and recombination as well as G4 structures. We finally demonstrate that promoter sequences of M. tuberculosis PE_PGRS2, mce1R, and moeB1 genes contain G4 structures, implying that G4 structures may regulate gene expression in M. tuberculosis. We discuss these data and implicate targeting G4 structures and DinG helicase in M. tuberculosis could be a novel therapeutic strategy for culminating the infection with this pathogen.

Current understanding of HIV-1 and T-cell adaptive immunity: progress to date

The cellular immune response to human immunodeficiency virus (HIV) has different components originating from both the adaptive and innate immune systems. HIV cleverly utilizes the host machinery to survive by its intricate nature of interaction with the host immune system. HIV evades the host immune system at innate ad adaptive, allows the pathogen to replicate and transmit from one host to another. Researchers have shown that HIV has multipronged effects especially on the adaptive immunity, with CD4(+) cells being the worst effect T-cell populations. Various analyses have revealed that, the exposure to HIV results in clonal expansion and excessive activation of the immune system. Also, an abnormal process of differentiation has been observed suggestive of an alteration and blocks in the maturation of various T-cell subsets. Additionally, HIV has shown to accelerate immunosenescence and exhaustion of the overtly activated T-cells. Apart from causing phenotypic changes, HIV has adverse effects on the functional aspect of the immune system, with evidences implicating it in the loss of the capacity of T-cells to secrete various antiviral cytokines and chemokines. However, there continues to be many aspects of the immune- pathogenesis of HIV that are still unknown and thus required further research in order to convert the malaise of HIV into a manageable epidemic.

Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

Preparation of peptide microspheres using tumor antigen-derived peptides

Due to its distinct biological attributes, poly(D,L lactide-co glycolide) (PLGA) is one of the most preferred methods for DNA/protein/peptide encapsulation for therapeutics. Importantly, PLGA acts as an adjuvant for weakly immunogenic antigens and mimics booster responses after a single dose of administration, thereby serving as a single-shot vaccine delivery vehicle. Efficient delivery of antigens to antigen-presenting cells (APC) has been made possible by the use of a PLGA particle-based vaccine delivery system. Also, the plasma half-life of the PLGA-encapsulated vaccine increases as it is protected from degradation, prior to its further release. PLGAs are reported to be catabolized into individual nontoxic units once inside the host and further degraded via normal metabolic pathways. In this chapter, we have described the preparation and characterization of tumor peptide encapsulated PLGA microparticles as a model for controlled-release peptide delivery system.

Multiple antigen peptide containing B and T cell epitopes of F1 antigen of Yersinia pestis showed enhanced Th1 immune response in murine model

Yersinia pestis is a facultative bacterium that can survive and proliferate inside host macrophages and cause bubonic, pneumonic and systemic infection. Apart from humoral response, cell-mediated protection plays a major role in combating the disease. Fraction 1 capsular antigen (F1-Ag) of Y. pestis has long been exploited as a vaccine candidate. In this study, F1-multiple antigenic peptide (F1-MAP or MAP)-specific cell-mediated and cytokine responses were studied in murine model. MAP consisting of three B and one T cell epitopes of F1-antigen with one palmitoyl residue was synthesized using Fmoc chemistry. Mice were immunized with different formulations of MAP in poly DL-lactide-co-glycolide (PLGA) microspheres. F1-MAP with CpG oligodeoxynucleotide (CpG-ODN) as an adjuvant showed enhanced in vitro T cell proliferation and Th1 (IL-2, IFN-γ and TNF-α) and Th17 (IL-17A) cytokine secretion. Similar formulation also showed significantly higher numbers of cytokine (IL-2, IFN-γ)-secreting cells. Moreover, F1-MAP with CpG formulation showed significantly high (P < 0.001) percentage of CD4(+) IFN-γ(+) cells as compared to CD8(+) IFN-γ(+) cells, and also more (CD4- IFN-γ)(+) cells secrete perforin and granzyme as compared to (CD8- IFN-γ)(+) showing Th1 response. Thus, the study highlights the importance of Th1 cytokine and existence of CD4(+) and CD8(+) immune response. This study proposes a new perspective for the development of vaccination strategies for Y. pestis that trigger T cell immune response.

Modulation of HIV peptide antigen specific cellular immune response by synthetic α- and β-defensin peptides

Defensin peptides have their direct role in host defense against microbial infection as innate molecules and also thought to contribute to adaptive immunity by recruiting naïve T-cells and immature dendritic cells at the site of infection through CCR6 receptor. The main aim of the present study is to investigate the efficacy of defensins for the induction of cell mediated immune response against the peptide antigen of HIV-1 encapsulated in PLG microparticles through intranasal (IN) route in mice model. To characterized, we have analyzed T-cell proliferation, Th1/Th2 cytokines, β-chemokines production and IFN-γ/perforin secretion from CD4(+)/CD8(+) T-cells in response to HIV immunogen alone and with defensins at different mucosal site i.e. lamina propria (LP), spleen (SP) and peyer's patches (PP). The cellular immunogenicity of HIV peptide with defensin formulations showed a significantly higher (p<0.001) proliferation response as compared to individual HIV peptide. The enhanced cytokines measurement profile showed mixed Th1 and Th2 type of peptide specific immune response by the incorporation of defensins. In the continuation, enhancement in MIP-1α and RANTES level was also observed in HIV peptide-defensin formulations. The FACS data had revealed that CD4(+)/CD8(+) T-cells showed significantly (p<0.001) higher IFN-γ and perforin secretion in HIV with defensin peptide formulations than HIV antigen alone group. Thus, the study emphasized here that defensin peptides have a potential role as mucosal adjuvant, might be responsible for the induction of cell mediated immunity when administered in mice through IN route with HIV peptide antigen.

Helicobacter pylori DprA alleviates restriction barrier for incoming DNA

Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformation by foreign DNA. Yet, mechanisms that protect incoming double-stranded DNA (dsDNA) from restriction enzymes are not well understood. A DNA-binding protein, DNA Processing Protein A (DprA) has been shown to facilitate natural transformation of several Gram-positive and Gram-negative bacteria by protecting incoming single-stranded DNA (ssDNA) and promoting RecA loading on it. However, in this study, we report that H. pylori DprA (HpDprA) binds not only ssDNA but also dsDNA thereby conferring protection to both from various exonucleases and Type II restriction enzymes. Here, we observed a stimulatory role of HpDprA in DNA methylation through physical interaction with methyltransferases. Thus, HpDprA displayed dual functional interaction with H. pylori R-M systems by not only inhibiting the restriction enzymes but also stimulating methyltransferases. These results indicate that HpDprA could be one of the factors that modulate the R-M barrier during inter-strain natural transformation in H. pylori.

Role of DNA methyltransferases in epigenetic regulation in bacteria

In prokaryotes, alteration in gene expression was observed with the modification of DNA, especially DNA methylation. Such changes are inherited from generation to generation with no alterations in the DNA sequence and represent the epigenetic signal in prokaryotes. DNA methyltransferases are enzymes involved in DNA modification and thus in epigenetic regulation of gene expression. DNA methylation not only affects the thermodynamic stability of DNA, but also changes its curvature. Methylation of specific residues on DNA can affect the protein-DNA interactions. DNA methylation in prokaryotes regulates a number of physiological processes in the bacterial cell including transcription, DNA mismatch repair and replication initiation. Significantly, many reports have suggested a role of DNA methylation in regulating the expression of a number of genes in virulence and pathogenesis thus, making DNA methlytransferases novel targets for the designing of therapeutics. Here, we summarize the current knowledge about the influence of DNA methylation on gene regulation in different bacteria, and on bacterial virulence.

Multiple antigen peptide consisting of B- and T-cell epitopes of F1 antigen of Y. pestis showed enhanced humoral and mucosal immune response in different strains of mice

Yersinia pestis is a causative agent of plague. F1 and V antigen based vaccines have shown remarkable protection in experimental animals. In order to develop epitope based immunogen, three B and one T-cell epitopes of F1 antigen with palmitate residue at amino terminal were assembled on a lysine backbone as multiple antigen peptide (MAP or F1-MAP). MAP was characterized by SDS-PAGE, immunoblot and immunoreactivity with anti F1 sera. MAP was entrapped in PLGA (polylactide-co-glycolide) microparticles and humoral, mucosal immune responses were studied after intranasal immunization with/without CpG ODN 1826 (CpG)/murabutide in different strains of mice. Serum and mucosal washes were measured for MAP specific IgG, IgA, sIgA and IgG subclasses in three strains of mice. F1-MAP showed high serum antibody and mucosal IgG and IgA peak antibody titers. MAP with CpG showed significantly high (p<0.001) peak antibody titer ranging from 102,400 to 204,800 for IgG and 6400 to 12,800 for IgA. High mucosal sIgA and its secretary component detection confirmed generation of mucosal response in intestinal and lung washes. MAP antisera also showed significant immunoreactivity with individual peptides. Moreover, antibody specific activity (IgG, IgA and sIgA) positively correlates with peak antibody titers. Predominantly IgG2a/IgG2b subclass was observed with CpG formulation but in other formulation a mixed IgG1 and IgG2a response was observed. The present study highlights the importance of multiple antigen peptide approach of F1-antigen with CpG as an alternative approach for subunit vaccine.

Immunomodulation of ovalbumin-specific IgG and other classes of antibody response by honey in mice

It was reported earlier that intraperitoneal administration of honey had immunosuppressive activity on elicitation of allergen-specific murine antibody response as evaluated by passive cutaneous anaphylaxis and double immunodiffusion methods. In this study, the immunomudulatory effect of honey is evaluated by enzyme linked immunosorbent assay (ELISA) using ovalbumin as model allergen. It was found that ovalbumin (OVA)-specific IgG antibody responses elicited with various doses of OVA were significantly suppressed by rock bee honey (p<0.01). Honey was also found to have inhibited the production of OVA-specific IgM, IgA, IgG(1), and IgG(2b) whereas that of IgG(2a) and IgG(3) were not affected. Furthermore, honey also suppressed the OVA-specific total IgG antibody response in various inbred mice with different genetic background. In addition, the suppressive activity of honey was examined in different groups of mice by injecting honey at different time intervals, before and after immunization with OVA. The anti-OVA IgG antibody response was suppressed significantly when honey was injected 12 hours prior/latter to OVA injection. These results confirm the suppressive activity of honey on antibody response and suggest possible clinical application.

Observations on some chemical and physical characteristics of buffalo meat

Proximate composition, sarcoplasmic and myofibrillar protein fractions of buffalo meat were similar to those of beef. Buffalo meat was also rich in lysine. Meat from young animals had a lower collagen content than that from old ones. As the temperature of holding the carcasses was increased, the rate of pH fall was faster. Meat from stressed animals showed a higher ultimate pH. Percentage of cooking loss and thermal shrinkage was higher in muscles of old animals than in young ones, which probably reflected the poor condition of the older animals. Meat cooked by pressure cooking showed lower Warner-Bratzler shear values as compared with meat cooked in boiling water.

Comparative transcriptomics of H. pylori strains AM5, SS1 and their hpyAVIBM deletion mutants: possible roles of cytosine methylation

Helicobacter pylori is an important human pathogen and one of the most successful chronic colonizers of the human body. H. pylori uses diverse mechanisms to modulate its interaction with the host in order to promote chronic infection and overcome host immune response. Restriction-modification genes are a major part of strain-specific genes present in H. pylori. The role of N⁶ - adenine methylation in bacterial gene regulation and virulence is well established but not much is known about the effect of C⁵ -cytosine methylation on gene expression in prokaryotes. In this study, it was observed by microarray analysis and RT-PCR, that deletion of an orphan C⁵ -cytosine methyltransferase, hpyAVIBM in H. pylori strains AM5and SS1 has a significant effect on the expression of number of genes belonging to motility, adhesion and virulence. AM5ΔhpyAVIBM mutant strain has a different LPS profile and is able to induce high IL-8 production compared to wild-type. hpyAVIBM from strain 26695 is able to complement mutant SS1 and AM5 strains. This study highlights a possible significance of cytosine methylation in the physiology of H. pylori.

Cell-mediated immune response to epitopic MAP (multiple antigen peptide) construct of LcrV antigen of Yersinia pestis in murine model

Yersinia pestis is the causative agent of plague. Cellular immunity seems to play an important role in defense against this disease. The subunit vaccine based on V (Lcr V) antigen has been proved to be immunogenic in animals and in humans. The multiple antigen peptide (MAP), incorporating all the relevant B and T cell epitopes is highly immunogenic in mice through intranasal route of immunization in PLGA particles containing CpG-ODN as an immunoadjuvant inducing humoral and mucosal immune response. In the present study, cell-mediated immune response using same MAP was studied in murine model. Primary and memory T cell responses were studied in outbred and inbred mice immunized intranasally with MAP in the presence of two immunoadjuvants (Murabutide and CpG-ODN). All the three compartments (Spleen, Lamina propria and Peyer's patches) of the lymphoid system showed increased lymphoproliferative response. Highest lymphoproliferative response was observed especially with CpG-ODN. Cytokine profile in the culture supernatant showed highest Th(1) and Th(17) levels. FACS analysis showed expansion of both CD4(+) and CD8(+) T cells producing gamma-interferon, perforin and granzyme-B with major contribution from CD4(+) T cells.

Functional characterization of UvrD helicases from Haemophilus influenzae and Helicobacter pylori

Haemophilus influenzae and Helicobacter pylori are major bacterial pathogens that face high levels of genotoxic stress within their host. UvrD, a ubiquitous bacterial helicase that plays important roles in multiple DNA metabolic pathways, is essential for genome stability and might, therefore, be crucial in bacterial physiology and pathogenesis. In this study, the functional characterization of UvrD helicase from Haemophilus influenzae and Helicobacter pylori is reported. UvrD from Haemophilus influenzae (HiUvrD) and Helicobacter pylori (HpUvrD) exhibit strong single-stranded DNA-specific ATPase and 3'-5' helicase activities. Mutation of highly conserved arginine (R288) in HiUvrD and glutamate (E206) in HpUvrD abrogated their activities. Both the proteins were able to bind and unwind a variety of DNA structures including duplexes with strand discontinuities and branches, three- and four-way junctions that underpin their role in DNA replication, repair and recombination. HiUvrD required a minimum of 12 nucleotides, whereas HpUvrD preferred 20 or more nucleotides of 3'-single-stranded DNA tail for efficient unwinding of duplex DNA. Interestingly, HpUvrD was able to hydrolyze and utilize GTP for its helicase activity although not as effectively as ATP, which has not been reported to date for UvrD characterized from other organisms. HiUvrD and HpUvrD were found to exist predominantly as monomers in solution together with multimeric forms. Noticeably, deletion of distal C-terminal 48 amino acid residues disrupted the oligomerization of HiUvrD, whereas deletion of 63 amino acids from C-terminus of HpUvrD had no effect on its oligomerization. This study presents the characteristic features and comparative analysis of Haemophilus influenzae and Helicobacter pylori UvrD, and constitutes the basis for understanding the role of UvrD in the biology and virulence of these pathogens.