Role of heterotrophic nitrifiers and aerobic denitrifiers in simultaneous nitrification and denitrification process: a nonconventional nitrogen removal pathway in wastewater treatment.

Bacterial species capable of performing both nitrification and denitrification in a single vessel under similar conditions have gained significance in the wastewater treatment scenario considering their unique character of performing the above reactions under heterotrophic and aerobic conditions respectively. Such a novel strategy often referred to as simultaneous nitrification and denitrification (SND) has a tremendous potential in dealing with various wastewaters having low C : N content, considering that the process needs very little or no external carbon source and oxygen supply thus adding to its cost-effective and environmentally friendly nature. Though like other micro-organisms, heterotrophic nitrifiers and aerobic denitrifiers convert inorganic or organic nitrogen-containing substances into harmless dinitrogen gas in the wastewater, their ecophysiological role in the global nitrogen cycle is still not fully understood. Attempts to highlight the role played by the heterotrophic nitrifiers and aerobic denitrifiers in dealing with nitrogen pollution under various environmental operating conditions will help in developing a mechanistic understanding of the SND process to address the issues faced by the traditional methods of aerobic autotrophic nitrification-anaerobic heterotrophic denitrification.

Insights in Waste Management Bioprocesses Using Genomic Tools.

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

Identification of an immunodominant epitope in glycoproteins B and G of herpes simplex viruses (HSVs) using synthetic peptides as antigens in assay of antibodies to HSV in herpes simplex encephalitis patients.

Herpes simplex encephalitis (HSE) is a severe viral infection of the central nervous system (CNS). Assay of antibody response is widely used in diagnostics of HSE. The aim of this study was to identify an immunodominant epitope determining the antibody response to herpes simplex viruses (HSVs) in cerebrospinal fluid (CSF) of HSE patients. The synthetic peptides that resembled type-common as well as type-specific domains of glycoproteins B (gB) and G (gG) of these viruses were evaluated for binding with IgM and IgG antibodies in CSF samples from HSE and non-HSE patients in ELISA. The QLHDLRF peptide, derived from gB of HSV was found to be an immunodominant epitope in the IgM and IgG antibody response. The patients with confirmed and suspected HSE showed in ELISA against this peptide 26% and 23% positivities for IgM, 43% and 37% positivities for IgG and 17% and 15% for both IgM and IgG antibodies, respectively. The total positivities of 86% and 75% for both IgM and IgG antibodies were obtained in the patients with confirmed and suspected HSE, respectively. These results demonstrate that a synthetic peptide-based diagnostics of HSE can be an efficient and easily accessible alternative. This is the first report describing the use of synthetic peptides derived from HSVs in diagnostics of HSE using patientsʹ CSF samples.

An overview of post exposure prophylaxis for HIV in health care personals: Gujarat scenario.

Average risk of acquiring HIV infection after a percutaneous exposure to HIV infected blood is 0.3%. Post exposure prophylaxis (PEP) for HIV refers to a set of comprehensive services to prevent HIV infection in exposed individuals where the exposure can be occupational/ non occupational and a provision of short term (28 days) antiretroviral drugs are given depending on the risk assessment. It also includes counselling and relevant laboratory investigations after taking informed consent of the exposed person and source. PEP inhibits the replication of the initial inoculum of virus and thereby prevents establishment of chronic HIV infection, and is best effective when initiated within 2 hours but certainly within 72 hours. Present communication deals with the registry of 278 cases of PEP from Gujarat in terms of various determinants, their status and the outcome in terms of HIV sero positivity.

Evaluation of BioFM liquid medium for culture of cerebrospinal fluid in tuberculous meningitis to identify Mycobacterium tuberculosis.

The present study was designed to evaluate the sensitivity and specificity of liquid culture medium (BioFM broth) for the diagnosis of tuberculous meningitis (TBM) in cerebrospinal fluid (CSF). CSF samples from 200 patients (TBM group = 150 and non-TBM group = 50) were tested for culture of Mycobacterium tuberculosis in BioFM liquid culture medium. Out of 150 TBM cases, 120 were found to be culture positive, indicating a sensitivity of 80% in BioFM broth within 2-3 weeks of inoculation. Positive cultures were also observed for CSF from 32 (64%) out of 50 non-TBM patients in BioFM liquid culture medium within 4 days of sample inoculation. Therefore, according to our study, BioFM broth system yielded 80% sensitivity [95% confidence interval (CI): 67-93%] and 36% specificity (95% CI: 57-98%) for TBM diagnosis. Our results indicate that although BioFM broth allows the detection of positive cultures within a shorter time, it has a high potential for contamination or for the coexistence of M. tuberculosis and non-tuberculous meningitis (NTM). This coexistence may go undetected or potentially lead to erroneous reporting of results.

Determination of polymerase chain reaction efficiency for diagnosis of tuberculous meningitis in Chelex-100 extracted DNA samples.

SETTING: Polymerase chain reaction (PCR) offers great promise for the rapid, sensitive and specific diagnosis of tuberculous meningitis (TBM). However, the isolation of DNA of high quantity and quality from cerebrospinal fluid (CSF) samples is critical for successful PCR assays. OBJECTIVE: To develop and use a single-tube method for the isolation of PCR-compatible DNA from Mycobacterium tuberculosis using Chelex-100 chelating resin, which does not require organic solvents or detergents. DESIGN: The study focused on the standardisation of a suitable Chelex protocol and its evaluation in 32 CSF samples from TBM and non-TBM subjects. A simultaneous comparison was made with the conventional phenol/chloroform extraction method. RESULT: PCR was found to be more sensitive, more rapid and less technically demanding with the Chelex protocol than the conventional phenol/chloroform extraction method (sensitivity 84.2% vs. 73.6%). CONCLUSION: The single-tube method and the simplicity of the procedure permits early and reliable diagnosis of TBM and makes it an attractive method for routine laboratory assays.

Self-organizing maps: a tool to ascertain taxonomic relatedness based on features derived from 16S rDNA sequence.

Exploitation of microbial wealth, of which almost 95% or more is still unexplored, is a growing need. The taxonomic placements of a new isolate based on phenotypic characteristics are now being supported by information preserved in the 16S rRNA gene. However, the analysis of 16S rDNA sequences retrieved from metagenome, by the available bioinformatics tools, is subject to limitations. In this study, the occurrences of nucleotide features in 16S rDNA sequences have been used to ascertain the taxonomic placement of organisms. The tetra- and penta-nucleotide features were extracted from the training data set of the 16S rDNA sequence, and was subjected to an artificial neural network (ANN) based tool known as self-organizing map (SOM), which helped in visualization of unsupervised classification. For selection of significant features, principal component analysis (PCA) or curvilinear component analysis (CCA) was applied. The SOM along with these techniques could discriminate the sample sequences with more than 90% accuracy, highlighting the relevance of features. To ascertain the confidence level in the developed classification approach, the test data set was specifically evaluated for Thiobacillus, with Acidiphilium, Paracocus and Starkeya, which are taxonomically reassigned. The evaluation proved the excellent generalization capability of the developed tool. The topology of genera in SOM supported the conventional chemo-biochemical classification reported in the Bergey manual.

Diagnostic value of early secreted antigenic target-6 for the diagnosis of tuberculous meningitis patients.

BACKGROUND: The early diagnosis of tuberculous meningitis (TBM) is very crucial, since delayed diagnosis can lead to various neurological manifestations. We have previously developed an in-house indirect enzyme-linked immunosorbent assay (ELISA) for TBM diagnosis using the Antigen 85 (Ag 85) complex. It has been suggested that the Ag 85 complex might give false-positive reactions for individuals vaccinated with Bacillus Calmette-Guérin (BCG). OBJECTIVES: In the present study, we describe a prospective evaluation demonstrating that early secreted antigenic target- 6 (ESAT-6), which is absent in Mycobacterium bovis BCG strains, is in the cerebrospinal fluid (CSF) of TBM patients. METHODS: We used an indirect ELISA to detect ESAT-6 antigens in the CSF of TBM patients using polyclonal antibodies against ESAT-6. RESULTS: Using the indirect ELISA method, we demonstrated a sensitivity and specificity of 80% and 94%, respectively, for the diagnosis of TBM. CONCLUSION: The detection of ESAT-6 in the CSF of TBM patients by indirect ELISA is a promising method and can be used to develop an immunodiagnostic assay with increased sensitivity and specificity.

Potential of Bacillus sp. to produce polyhydroxybutyrate from biowaste.

AIM: To test the Bacillus strains for their abilities to produce polyhydroxybutyrate (PHB) from different sugars and biowaste (Pea-shells). METHODS AND RESULTS: Six Bacillus strains were checked for their ability to produce PHB from GM2 medium supplemented with different sugars at the rate of 1% (w/v) and from biowaste and GM2 (BW : M) combinations (3 : 7, 1 : 1, 7 : 3). Glucose supplemented GM2 medium resulted in maximum PHB production of 435 mg l(-1) constituting 31-62% w/w of the total cell dry mass. Substituting GM2 medium to the extent of 50% with biowaste (pea-shell slurry) resulted in 945-1205 mg l(-1) PHB (55-65% w/w). Optimization for additional nitrogen supplementation, inoculum size resulted in a final PHB production of 3010-3370 mg l(-1) equivalent to 300 g kg(-1) biowaste (dry wt). CONCLUSION: The Bacillus strains were able to produce PHB from biowaste (Pea-shells) as cheap source of substrate. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report on usage of pea-shells as feed for PHB production, opening new possibilities for its use for production of PHB and Bacillus as potential candidate for the purpose.

Serodiagnosis of tuberculosis based on the analysis of the 65 kD heat shock protein of Mycobacterium tuberculosis.

OBJECTIVE: To evaluate the 65 kD heat shock protein (hsp) antigen in serum samples of tuberculosis (TB) patients by enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies (mAbs) specific to the 65 kD hsp antigen for the diagnosis of TB. DESIGN: Serum samples were obtained from 188 different groups of patients (confirmed TB [n = 24], clinically suspected TB [n = 48], non-TB disease controls [n = 74] and healthy individuals [n = 42]) and analysed by ELISA using mAbs to the 65 kD hsp antigen. The Kruskal Wallis test (non-parametric analysis of variance) with the Dunnett post test was used for statistical analysis. RESULTS: The method yielded 82% sensitivity and 89% specificity for the diagnosis of TB. The mean (+ or -SD) absorbance value of the 65 kD hsp antigen in TB patients (1.73 + or - 0.27) was significantly higher than in the non-TB disease control group (1.12 + or - 0.42, P < 0.001) and was also higher than among healthy individuals (1.06 + or - 0.42, P < 0.001). CONCLUSION: The detection of the 65 kD hsp antigen in serum samples from confirmed and suspected TB patients by ELISA using mAb against purified 65 kD antigen gives a reliable diagnosis and could be considered as a diagnostic marker for TB. The absence of the 65 kD hsp antigen in healthy control BCG-vaccinated subjects indicates the diagnostic value of this assay in regions of endemicity.

Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste.

Eight aerobic bacterial strains were isolated from pulp paper mill effluent sludge. Out of eight through nutrient enrichment technique three potential aerobic bacterial strains ITRC S(6), ITRC S(7) and ITRC S(8) were found capable to effectively degrade the kraft lignin (KL), a major byproduct of the chemical pulping process and main contributor to the colour and toxicity of effluent. Further, these potential strains (ITRC S(6), ITRC S(7) and ITRC S(8)) were biochemically characterised as Gram variable small rod, Gram negative rod and Gram positive rod respectively. Subsequently, 16S rRNA sequencing showed 95% base sequence homology and it was identified as Paenibacillus sp. (AY952466), Aneurinibacillus aneurinilyticus (AY856831), Bacillus sp. (AY952465) for ITRC S(6), IITRC S(7) and ITRC S(8), respectively. In batch decolourization experiments Bacillus sp. ITRC S(8) reduced the colour of lignin amended mineral salt medium, pH 7.6 by 65% after 6th d, at 30 degrees C, A. aneurinilyticus ITRC S(7) by 56% and Paenibacillus ITRC S(6) 43%. Under these conditions the three strains degraded the KL by 37%, 33% and 30%, respectively while the mixed culture of these three bacteria reduced colour by 69%, lignin by 40% and total substrate by 50% under same conditions. Biodegradation of the KL was not affected by low (<0.2 mg l(-1)) dissolved oxygen content; thus oxygen inhibition is more likely to be a metabolism-dependent event. Initially with 48 h incubation the decolourization was slow with decreased pH. Further incubation there was rapid decolourization with slight increase in pH at 6d compared with initial pH by increasing culture optical density. The lignin analysis from medium with HPLC indicated complete degradation rather than biotransformation with complete loss of absorbance peak at 280 nm.

Demonstration of IgG antibodies to 30 Kd protein antigen in CSF for diagnosis of tuberculous meningitis by antibody-capturing ELISA.

OBJECTIVE: A simple and rapid immunological assay method has been developed to demonstrate the presence of IgG antibodies to 30Kd protein antigen (30Kdpa) and culture filtrate protein (CFP) in the CSF of patients with Tuberculous meningitis (TBM). METHOD: Antibody capturing Enzyme Linked Immunosorbent Assay (ELISA) was standardized with CFP antigen of MTB. The IgG antibodies were assayed in CSF sample from TBM and non-TBM patients against 30 Kdpa. RESULTS: The sensitivity and specificity of IgG antibodies for the diagnosis of suspected patients of TBM using 30 Kdpa was 80% and 91% respectively and the corresponding figures for CFP were 85% and 94% respectively. The sensitivity and specificity in two confirmed cases of TBM was 100%. CONCLUSION: The presence of this 30Kdpa in the CSF of suspected cases of TBM consistently would indicate that the selected protein band carries the candidate protein marker antigen, which is specific to M. tuberculosis and could be considered as a diagnostic marker for TBM.

Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences.

BACKGROUND: Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. Keeping this in view, the aim was to identify a region of 16S rDNA sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns from these stretches that are specific to the genus. RESULTS: Repeating elements that are highly conserved across different species of Pseudomonas were considered as guiding markers to locate a region within the 16S gene. Four repeating patterns showing more than 80% consistency across fifty different species of Pseudomonas were identified. The sub-sequences between the repeating patterns yielded a continuous region of 495 bases. The sub-sequences after alignment and using Shanon's entropy measure yielded a consensus pattern. A stretch of 24 base positions in this region, showing maximum variations across the sampled sequences was focused for possible genus specific patterns. Nine patterns in this stretch showed nearly 70% specificity to the target genus. These patterns were further used to obtain a signature that is highly specific to Pseudomonas. The signature region was used to design PCR primers, which yielded a PCR product of 150 bp whose specificity was validated through a sample experiment. CONCLUSIONS: The developed approach was successfully applied to genus Pseudomonas. It could be tried in other bacterial genera to obtain respective signature patterns and thereby PCR primers, for their rapid tracking in the environmental samples.

Growth phase dependent substrate utilization by Pseudomonas strain PH1.

Pseudomonas strain PH1 can utilize nitro-, chloro-, and aminophenols and has been used in this study. The enzymes of the two-pathway viz., phenol, and meta-aminophenol (MAP) were analyzed under different growth conditions. The enzymes responsible for phenol to catechol conversion followed by the ring cleavage enzyme for catechol; and also the enzymes responsible for MAP oxidation and hydroxylation of resorcinol, were studied. Enzyme and respirometric assays were carried out with cells harvested from log phase and stationary phase from medium with different carbon sources and nitrogen levels. It was observed that the first step for utilization of both the substrates requires the same physiological state of the cells; whereas, the subsequent step follows independent approach to intermediates, based on cellular physiology.

Distinguishing features of 16S rDNA gene for five dominating bacterial genus observed in bioremediation.

Defining a microbial community and identifying bacteria, at least at the genus level, is a first step in predicting the behavior of a microbial community in bioremediation. In biological treatment systems, the most dominating groups observed are Pseudomonas, Moraxella, Acinetobactor, Burkholderia, and Alcaligenes. Our interest lies in identifying the distinguishing features of these bacterial groups based on their 16S rDNA sequence data, which could be used further for generating genus-specific probes. Accordingly, 20 sequences representing different species from each genus above were retrieved, which constituted a training set. A 16-dimensional feature vector comprised of transition probabilities of nucleotides was considered and each sampled sequence was expressed in terms of these features. A stepwise feature selection method was used to identify features that are distinct across the species of these five groups. Wilk's lambda selection criterion was used and resulted in a subset with six distinguishing features. The discriminating efficacy of this subset was tested through multiple group discriminant analysis. Two linear composites, as a function of these features, could discriminate the test set of forty-five sequences from these groups with 95% accuracy, thereby ascertaining the relevance of the identified features. The geometric representation of feature correlation in the reduced discriminant space demonstrated the dominance of identified features in specific groups. These features independently or in combination could be used to generate genus-specific patterns to design probes, so as to develop a tracking tool for the selected group of bacteria.

Synergistic effect of ayurvedic pearl preparation on enhancing effectiveness of antibiotics.

Studies were carried out with ayurvedic preparations derived from pearl, which include preparations bhasma and pishti. The synergistic effect to reduce the dose of antibiotic was tested against E. coli the test bacterium with ampicillin antibiotic by bore well and disks diffusion methods. It was observed that pearl preparations do not show any antibacterial activity but when used at 200 microg/ml concentration with antibiotics, then even at sub-lethal dose, the antibiotic has effectively shown the results with reduced contact time. The protocol was also tested with the other bacteria like, Pseudomonas aeruginosa. Vibrio cholarae, Salmonella typhi, and Staphylococcus aureus and has shown similar results. The pearl bhasma synergistic effect was also tested with other antibiotics such as erythromycin, kanamycin, and ampicillin.

Tracking of phenol degrading genotype.

A simple and rapid protocol has been developed for monitoring of the phenol degrading population in the environmental samples. PCR protocol uses the total DNA prepared from the samples as a template in the amplification reaction. Primers have been designed from the sequence data for Dmp and Phe operon encoding multi-component and single component phenol oxidizing system, respectively. The phenol degrading genotype in various samples have been demonstrated using the developed PCR protocol.

Detection of etiological agent for cholera by PCR protocol.

BACKGROUND: PCR protocol for Vibrio cholerae, the causative agent of the diarrheal disease cholera has been described in this report. We report the detection of Vibrio species in drinking water samples in a duplex PCR reaction. The target loci used in the study were ctxA and tcpA. The sensitivity and efficiency of detection of this protocol can be applied in epidemic conditions, wherein monitoring of target organisms is very crucial. MATERIAL AND METHODS: Single step thermocycling programs have been reported for amplification of specific target loci. We have demonstrated that a gradient multi-step thermocycling program is more efficient in improving the sensitivity of detection by PCR. The method for preparation of template DNA from environmental sample uses filtration of water followed by harvesting the possible bacterial residue. This was further treated with proteinase K and heat to yield DNA compatible for PCR. The protocol was optimized for amplification of target loci from standard strains as well as from environmental water samples. RESULTS: The method can simultaneously detect two different loci of Vibrio cholerae in a single reaction. The sensitivity of detection achieved for the pathogen was 100 cells per reaction. The specificity of the primers was demonstrated by spiking the reaction with non-specific template. The developed protocol was successfully extended to environmental samples. CONCLUSIONS: The developed duplex PCR protocol allows the simultaneous detection of two genetic loci of the target pathogen from water samples. This enhances the efficiency of detection and provides a sensitive tool for the rapid detection of the pathogen that can be useful in epidemic conditions where the time factor involved in the identification of target pathogen is very crucial.

Isolation and characterization of a Pseudomonas sp. strain PH1 utilizing meta-aminophenol.

Pseudomonas sp. strain PH1 was isolated from soil contaminated with pharmaceutical and dye industry waste. The isolate PH1 could use m-aminophenol as a sole source of carbon, nitrogen, and energy to support the growth. PH1 could degrade up to 0.32 mM m-aminophenol in 120 h, when provided as nitrogen source at 0.4 mM concentration with citrate (0.5 mM) as a carbon source in the growth medium. The presence of ammonium chloride as an additional nitrogen source repressed the degradation of m-aminophenol by PH1. To identify strain PH1, the 16S rDNA sequence was amplified by PCR using conserved eubacterial primers. The FASTA program was used to analyze the 16S rDNA sequence and the resulting homology patterns suggested that PH1 is a Pseudomonas.

Cerebellar granule cell membranes and glutamate mediates transactivation of glutamine synthetase promoter.

Potential region of glutamine synthetase promoter driving astrocyte-specific transactivation, mediated by cerebellar granule cell membrane and glutamate has been identified by deletion analysis of promoter and transient transfection. The promoter region from -420 to -765 was found to be potentially important for this transactivation. These results provided further evidence for importance of neuronal-glial and glutamate-glial interactions in regulation of glial gene expression.