Virulence profile and clonal relationship among the Vibrio cholerae isolates from ground and surface water in a cholera endemic area during rainy season

All the V. cholerae non-O1, non-O139 isolates from ground and surface water samples collected during the rainy season (rainfall contributes significantly in the spread of cholera) contained ompW and a regulatory toxR gene, while many others possessed accessory cholera toxin (ace), hemolysin (hlyA) and outer membrane protein (ompU) genes. All the isolates lacked ctxAB, tcp, zot, rfbO1 and rfbO139 genes. The strains could be grouped into two main clusters colligating the isolates from ground water and surface water samples. The results suggest that surface water harbors various virulent V. cholerae strains that contaminate the ground water due to rain or poor hygienic practices, and result in the emergence of new toxigenic strains for cholera.

Are clinical parameters and biomarkers predictive of severity of acute pulmonary emboli on CTPA?

BACKGROUND

Previous studies have shown that findings of computed tomography pulmonary angiography (CTPA) relate to outcome in pulmonary embolus (PE). These include clot burden as quantified using an obstruction index and markers of pressure overload such as right ventricle to left ventricle size ratio (RV/LV ratio). Little data exists correlating these findings with clinical presentation and biomarkers.

AIM

To explore the link between clinical presentation and biomarkers with CTPA findings.

METHODS

Retrospective case note analysis of consecutive cases presenting to a large teaching hospital. An independent radiologist reviewed CTPAs and clot burden quantified using an obstruction index.

RESULTS

One hundred and seventy cases were identified and notes retrieved in 137 cases. (i)

CLINICAL PRESENTATION

correlation was seen between clot burden and systolic blood pressure (BP) (r = -0.299, P = 0.0006) and heart rate (r = 0.240, P = 0.0056). Median obstruction index was significantly higher in those with a presenting BP <90 mmHg [41.25% (95% CI 30-50) vs. 15% (95% CI 12.5-25), (P = 0.0004)]. Clot burden was significantly higher in patients with temperature of >37.5 degrees C [30% (95% CI 25.0-42.5) vs. 15% (95% CI 12.5-28.3), P = 0.02)] and (ii)Biomarkers: significant correlation between clot burden and D-dimer was seen (r = 0.36, P = 0.0001). Location of thrombus was associated with significant differences in D-dimer level. A subgroup of patients had cardiac biomarkers measured (n = 24). There was a statistically significant correlation between troponin I and clot burden (r = 0.412, P = 0.048) and RV/LV ratio (r = 0.699, P = 0.0013).

DISCUSSION

These findings suggest that clinical parameters and biomarkers have a role in predicting the radiological severity of PE. These data support the need for further studies of risk stratification in patients presenting with acute PE.

Estrogen receptor beta gene mutations in Indian infertile men

Recent studies suggest that estrogens play an important role in male fertility. Estrogen signaling is mediated by Estrogen Receptors (ERalpha and ERbeta). Association of ERbeta with male infertility has not been analyzed to date except for genotyping of known polymorphisms in two different studies, which yielded controversial interpretation. Hence, we performed sequencing of all the exons and untranslated regions of ERbeta gene in 300 infertile and 255 fertile control Indian men. We identified eight novel mutations and four known single nucleotide polymorphisms (SNPs). Of the eight novel mutations, four were non-synonymous, of which one was detected only in infertile men, whereas the other three mutations were detected only in fertile men. Using different bioinformatics tools, we predicted that non-synonymous mutations were benign and they neither altered the structure nor the function of the protein. Among synonymous novel mutations, one was detected in both fertile and infertile men, two were exclusive to infertile men and one was exclusive to fertile men. None of the known SNPs or novel mutations showed statistically significant difference between infertile and fertile men. Moreover, infertile men having ERbeta mutations had normal reproductive tract and serum hormone levels. Our results suggest that the SNPs and mutations in ERbeta gene are not a common cause of spermatogenesis failure in Indian men, although mutations specifically found in infertile men can affect transcription, translation or have synergic effect with other variants in causing infertility.

A large cholera outbreak due to a new cholera toxin variant of the Vibrio cholerae O1 El Tor biotype in Orissa, Eastern India

A total of 32 Vibrio cholerae isolates were collected during a recent large cholera outbreak in Eastern India. Biochemical and serological studies revealed that all of the isolates belonged to serogroup O1, biotype El Tor, serotype Ogawa. Two multiplex PCR assays confirmed the presence of various toxigenic and pathogenic genes - ace, ctxAB, hlyA, ompU, ompW, rfbO1, rtx, tcp, toxR and zot - in all of the isolates. Sequencing of the ctxB gene from the isolates revealed a novel mutation in the gene. Sequencing also confirmed the presence of altered cholera toxin B of the classical biotype in all of the El Tor isolates, suggesting infection of isolates by classical CTXPhi. The molecular diversity of V. cholerae isolates studied by enterobacterial repetitive intergenic consensus sequence PCR, BOX-PCR and randomly amplified polymorphic DNA analysis uniformly showed the clonal relationship among the outbreak V. cholerae O1 isolates. The results of this study suggest that cholera-causing V. cholerae strains are constantly evolving in epidemic areas, highlighting the potential of the emergence of more virulent strains.

Whole body protection against lethal ionizing radiation in mice by REC-2001: a semi-purified fraction of Podophyllum hexandrum

The current study has concentrated on assessment of the radioprotective potential of REC-2001, a semi-purified fraction of rhizomes of Podophyllum hexandrum, in Swiss albino Strain 'A' mice exposed to 10 Gy whole-body gamma radiation. Animals were treated with 10 and 15 mg/kg b wt (i.p.) of REC-2001 1h prior to exposure to a lethal dose of gamma-radiation (10 Gy) and observed upto 30 days. For analysis of maximum tolerable dose (MTD), LD(50) and acute toxic dose, different concentrations of the extract were administered to animals and their mortality and morbidity status was observed upto 72 h and one week, respectively. Dose reduction factor (DRF) was determined by exposing REC-2001 pre-treated mice to supra-lethal doses of gamma-radiation. Endogenous spleen colony forming units (CFU), DNA strand breaks in thymocytes (alkaline halo assay) and lipid degradation was studied to understand the mechanism of radioprotection. A single dose of REC-2001 (10 and 15 mg/kg b wt i.p.) exhibited >90% survival in the pre-treated irradiated group versus no survival in radiation control group. Single doses of upto 75 mg/kg b wt (i.p.) did not cause any mortality (MTD) in mice. REC-2001, a dose of 90 mg/kg b wt, resulted in 50% mortality (LD(50)), while the LD(100) was 115 mg/kg b wt REC-2001 exhibited a DRF of 1.62. CFU counts in the REC-2001 treated group were found significantly high (5.33/spleen) as compared to controls. Exposure of thymocytes to 10 Gy radiation resulted in increased halo diameter (45+/-3 microm) in comparison to untreated controls (8+/-1 microm). REC-2001 administration (500 microg/ml) decreased the halo diameter to 15+/-2 microm. Radiation-induced lipid degradation was also inhibited by REC-2001. The present study has revealed that REC-2001 is a promising radioprotective fraction that can be effectively used against lethal doses of gamma-radiation after further investigations in higher animal models.

CA repeat and RsaI polymorphisms in ERbeta gene are not associated with infertility in Indian men

Oestrogen Receptor beta (ERbeta) gene plays an important role in the regulation of fertility in both males and females. Polymorphism in CA repeat located in the flanking region of ERbeta has been shown to be associated with several diseases, but its association with male infertility has not been analysed so far. However, RsaI polymorphism (rs1256049) in exon 5 of ERbeta has been shown to be associated with male infertility in Caucasian patients. Hence, we have analysed 695 Indian men, including 443 infertile and 252 fertile men to evaluate the association of CA repeat length and RsaI polymorphisms in male infertility. Our results revealed no significant difference in the distribution of CA repeat length between infertile (mean +/- SD 23.24 +/- 2.06, median 24) and fertile men (mean +/- SD 23.16 +/- 2.27, median 24). The analysis of dosage effect by classifying samples into SS (short/short), SL (short/long) and LL (long/long) groups also did not show any significant difference between infertile and fertile men. Similarly, RsaI polymorphism also did not show any significant difference between infertile and fertile men. Furthermore, the combined analysis of CA repeat and RsaI polymorphisms by haplotyping showed that the distribution of haplotypes was not significantly different between fertile and infertile men. Our results suggest that CA repeat length and RsaI polymorphisms in ERbeta are not associated with infertility in Indian men.

Expression of interferon-gamma- inducible protein-10 and its receptor CXCR3 in chronic pancreatitis

AIM

The role of CXC chemokine, interferon-gamma-inducible protein-10 and its receptor CXCR3 in pathophysiology of chronic pancreatitis (CP) is not very clear. Hence, this study was carried out to analyze the expression of CXCL10 and CXCR3 in CP tissues.

METHODS

Pancreatic tissues from 25 histopathologically graded CP cases (11 alcohol associated CP, 5 confirmed idiopathic and 9 of undefined nature) and 10 normal cases were studied. Tissues were subjected to real-time PCR, immunohistochemistry, and Western blot analysis for CXCL10 and CXCR3 expression.

RESULTS

Real-time (RT)-PCR revealed increased expression of CXCL10 (13-fold) and CXCR3 (7-fold) in CP tissue. The immunohistochemistry and Western blot analysis of the same showed significant increased protein expression and correlated well with the histopathological grades. The CXCL10 was localized mainly in the cytoplasm of pancreatic acinar cells and expression increased from grade I to grade II and declined in grade III while no expression was recorded in normal. The CXCR3 was expressed strongly at the acinar cell membrane in CP as compared to normal. Further, comparative analysis by semiquantitative RT-PCR analysis was performed for other CXC/CC chemokines (CXCL9, CXCL11, CCL3, CCL4, CCL5) and receptor (CCR5) which revealed their upregulation in the diseased state.

CONCLUSION

The existence of CXCL10 and CXCR3 with other CXC/CC chemokine signature in CP is suggestive of their vital role in the progression of chronic inflammation.

Single multiplex polymerase chain reaction for environmental surveillance of toxigenic-pathogenic O1 and non-O1 Vibrio cholerae

A multiplex PCR assay was developed for the detection of toxigenic and pathogenic V. cholerae from direct water sources using specific primers targeting diverse genes, viz. outer membrane protein (ompW), cholera toxin (ctxB), ORF specific for O1 (rfbG), zonula occludens (zot) and toxin co-regulated pilus (tcpB); among these genes, ompW acts as internal control for V. cholerae, the ctx gene as a marker for toxigenicity and tcp for pathogenicity. The sensitivity of multiplex PCR was 5 x 10(4) V. cholerae cells per reaction. The procedure was simplified as direct bacterial cells were used as template and there was no need for DNA extraction. The assay was specific as no amplification occurred with the other bacteria used. Toxigenic V. cholerae were artificially spiked in different water samples, filtered through a 0.45 microm membrane, and the filters containing bacteria were enriched in APW for 6 h. PCR following filtration and enrichment could detect as little as 8 V. cholerae cells per mL in different spiked water samples. Various environmental potable water samples were screened for the presence of V. cholerae using this assay procedure. The proposed method is rapid, sensitive and specific for environmental surveillance for the presence of toxigenic-pathogenic and nonpathogenic V. cholerae.

Surgical treatment of pulmonary aspergilloma: a series of 72 cases

BACKGROUND

The objective of this study was to evaluate the immediate and long-term result of resectional surgery in pulmonary aspergilloma.

METHODS

Seventy-two patients who underwent pulmonary resectional surgery for symptomatic aspergilloma between 1990 to 2002 were studied. Seventy-nine definitive operations were carried out, including one bilateral lobectomy for recurrent lesions and six thoracoplasties to deal with post-operative complications, besides 21 pneumonectomies and 51 lobectomies. There were 10 bilobectomies as well, included in the lobectomy group.

RESULTS

At a mean follow-up of 3.5 years, there were two post-operative deaths and a few complications occurred in 20 cases translating into a morbidity of 28.57% and a mortality of 2.77 percent. Major complications included were persistent air leak, persistent pleural space, empyema, bronchopleural fistula and massive haemorrhage. All events were seen in cases of complex aspergilloma; cases of simple aspergillomas had an uneventful course.

CONCLUSIONS

Surgery offers definitive and long-term symptom-free survival in cases of pulmonary aspergilloma at a negligible risk; though almost one-third of those undergoing surgery develop some complications, these are largely manageable.

A to G transitions at 260, 386 and 437 in DAZL gene are not associated with spermatogenic failure in Indian population

The autosomal DAZL (Deleted-in-Azoospermic-Like) gene, mapped to the short arm of the human chromosome 3, is the precursor for the Y-chromosomal DAZ cluster, which encodes for putative RNA-binding proteins. Mutations in the DAZL have been reported to be associated with spermatogenic failure in Taiwanese population but not in Caucasians. As there was no study on Indian populations, we have analysed the entire coding sequences of exons 2 and 3 of DAZL in a total of 1010 men from Indian subcontinent, including 660 infertile men with 598 non-obstructive azoospermia, 62 severe oligozoospermia and 350 normozoospermic fertile control men, to investigate whether mutation(s) in the DAZL is associated with male infertility. Interestingly, none of our samples (1010) showed A386G (T54A) mutation, which was found to be associated with spermatogenic failure in Taiwanese population. In contrast, A260G (T12A) mutation was observed in both infertile and normozoospermic fertile control men, without any significant association with infertile groups (chi2= 0.342; p = 0.556). Similarly, we have found a novel A437G (I71V) mutation, which is also present in both infertile and normozoospermic fertile control men without any significant difference (chi2 = 0.476; p = 0.490). Our study clearly demonstrates the complete absence of the A386G (T54A) mutation in Indian subcontinent and the other two mutations --A260G (T12A) and A437G (I71V)--observed are polymorpic. Therefore, we conclude that these mutations in the DAZL gene are not associated with male infertility in Indian subcontinent.

Novel mitochondrial mutation in the ND4 gene associated with Leigh syndrome

We analyzed the complete mitochondrial genome of a 3-month-old female child with basal ganglionic lesions and other clinical features suggestive of Leigh syndrome, which is caused by variations in mitochondrial and nuclear genes. Our study revealed a novel, homoplasmic T11984C missense mutation in ND4 gene, which replaces a highly conserved amino acid tyrosine with histidine. Computational analysis showed that this mutation alters the secondary structure of ND4 subunit. As the mutation observed in this study was novel and homoplasmic, we speculate that there could be interplay of this mitochondrial mutation along with nuclear gene(s) in the pathogenesis.

Coat protein gene diversity among Chrysanthemum virus B isolates from India

The complete coat protein (CP) sequences from 29 Indian isolates of Chrysanthemum virus B (CVB) were determined and analysed in relation to other previously characterized carlaviruses. The CP genes of the Indian CVB isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98%. Based on phylogenetic analyses, the isolates formed three groups potentially representing either two or three major CVB strain groupings. Recombination analysis revealed at least one definite recombination event involving the exchange of sequences between members of different groups. To our knowledge this is the first reported evidence of homologous recombination in carlaviruses.

Association of cathepsin B gene polymorphisms with tropical calcific pancreatitis

BACKGROUND AND AIMS

Tropical calcific pancreatitis (TCP) is a type of chronic pancreatitis unique to countries in the tropics. Mutations in pancreatic secretory trypsin inhibitor (SPINK1) rather than cationic trypsinogen (PRSS1) explain the disease in only 50% of TCP patients. As cathepsin B (CTSB) is known to activate cationic trypsinogen, we attempted to understand the role of CTSB mutations in TCP. Evidence of epistatic interaction was investigated with the previously associated N34S SPINK1 allele, a variant considered to be a modifier rather than a true susceptibility allele.

SUBJECTS AND METHODS

We sequenced the coding region of CTSB gene in 51 TCP patients and 25 controls and further genotyped 89 patients and 130 controls from the same cohort for Leu26Val, C595T, T663C, and Ser53Gly polymorphisms. The positive findings observed in the earlier cohort were re-examined in an ethnically matched replication cohort comprising 166 patients and 175 controls. Appropriate statistical analyses were performed and Bonferroni correction for multiple testing was applied.

RESULTS

We found a statistically significant association of the Val26 allele at Leu26Val polymorphism with an odds ratio (OR) of 2.15 (95% confidence interval (CI) 1.60-2.90 (p = 0.009)), after Bonferroni correction (corrected p value = 0.025). This significant association of Leu26Val with TCP was replicated in another cohort (OR 2.10 (95% CI 1.56-2.84); p = 0.013). Val26 allele also showed significantly higher frequency in N34S positive and N34S negative patients than in controls (p = 0.019 and 0.013, respectively). We also found significant differences in the mutant allele frequencies at Ser53Gly and C595T single nucleotide polymorphisms between N34S positive patients and controls (p = 0.008 and 0.001, respectively). Although haplotype analysis did not complement the results of allelic association, it did uncover a unique haplotype protective for TCP (p = 0.0035).

CONCLUSION

Our study suggests for the first time that CTSB polymorphisms are associated with TCP. As PRSS1 mutations are absent in TCP and the N34S SPINK1 mutation is proposed to play a modifier role, these variants may be critical as a trigger for cationic trypsinogen activation.

Unique origin of Andaman Islanders: insight from autosomal loci

Our mtDNA and Y chromosome studies lead to the conclusion that the Andamanese "Negrito" mtDNA lineages have survived in the Andaman Islands in complete genetic isolation from other South and Southeast Asian populations since the initial settlement of the region by the out-of-Africa migration. In order to obtain a robust reconstruction of the evolutionary history of the Andamanese, we carried out a study on the three aboriginal populations, namely, the Great Andamanese, Onge and Nicobarese, using autosomal microsatellite markers. The range of alleles (7-31.2) observed in the studied population and heterozygosity values (0.392-0.857) indicate that the selected STR markers are highly polymorphic in all the three populations, and genetic variability within the populations is significantly high, with a mean gene diversity of 77%. The Andaman "Negrito" populations do not show particular affinities either with the African populations or with the Indian populations, confirming their unique origin. In contrast, Nicobarese show close affinities with the Southeast Asian populations, suggesting their recent entry in the Islands.

Autosomal STR data on the enigmatic Andaman Islanders

We have analyzed nine autosomal STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820) in 97 samples of enigmatic Andaman islanders including: 15 Great Andamanese, 46 Onge and 36 Nicobarese. Data was compared with the available data on Indian and South East Asian populations. Heterozygosity (H), power of discrimination (PD), probability exclusion (PE), typical paternity index (TPI), polymorphism information content (PIC), AMOVA and Arlequin analysis were carried out. Average heterozygosity observed was high and almost equal in all the populations. Similarly, PD, PE, TPI and PIC have been almost equal in all the populations.

Mutational analysis of the betaglycan gene-coding region in susceptibility for ovarian failure

BACKGROUND

Elevation of FSH is frequently a consequence of impaired ovarian follicle growth. Down-regulation of the FSH levels by inhibins is mediated through its receptor betaglycan in the gonadotrophs. Understanding of germline status of the betaglycan gene (TGFBR3) is essential for ovarian failure pathophysiology.

METHODS

Sequence analysis was performed for the coding region of TGFBR3 gene in a cohort of 196 ovarian failure cases that include 133 premature ovarian failure (POF) cases, 63 primary amenorrhoea (PA) cases compared with 200 controls.

RESULTS

Forty-six variants including six novel exonic variants and 16 novel intronic variants were revealed. Two variants were missense: (i) p.Iso184Val in a control and (ii) p.Pro775Ser in a POF case. Genotypic distribution of three variants (c.382-81C>T, c.382-77T>C and c.1200G>A) was significantly different in the patients as compared with the controls. Five variants c.382-81C>T, c.382-77T>C, c.566-216G>A, c.1200G>A and c.2022T>C were chosen for haplotyping. The CCAAT haplotype was significantly higher in the patient population as compared with the controls (P = 0.00007).

CONCLUSION

This study establishes the first mutational report of the TGFBR3 gene in correlation with ovarian failure. Significant diversity of genotype distribution and haplotype analysis suggested susceptibility of the TGFBR3 gene for ovarian failure aetiology.

Direct immunofluorescence assay for rapid environmental detection of Vibrio cholerae O1

An immunofluorescence assay for direct detection of V. cholerae O1 was developed using polyclonal antibodies raised against outer membrane proteins (OMPs) of V. cholerae O1. Production of OMPs varied with growth media used; maximum production was found in tryptic soy broth. The detection system was specific because no cross-reactivity was observed with other bacteria including V. cholerae O139, E. coli, S. dysenteriae and Salmonella enterica subsp. enterica serovar Typhi. The technique was able to detect 240 CFU/mL of V. cholerae O1 suspended in phosphate-buffered saline. The assay coupled with bacterial enrichment in APW for 6 h detected as few as 5 CFU of V. cholerae in spiked samples. Moreover, a 2-h incubation of enriched bacterial cells in 0.1% yeast extract with 10 ppm nalidixic acid enhanced the bacterial size and helped in morphological identification of V. cholerae. Among 32 potable water samples from afflicted hand pumps and wells collected from a cholera-plagued area 12 were found to be contaminated with V. cholerae by immunofluorescence assay as well as by conventional culture methods. The proposed method could thus be employed in environmental surveillance of V. cholerae O1.

Asian and non-Asian origins of Mon-Khmer- and Mundari-speaking Austro-Asiatic populations of India

In the present study, we analyzed 1,686 samples from 31 tribal populations of India for the mitochondrial DNA 9-base-pair deletion/insertion polymorphism, and characterized them based on the relevant mitochondrial DNA coding-region single nucleotide polymorphisms and hypervariable region I motifs, to test the genetic origins of the ethnically and linguistically heterogeneous Austro-Asiatic tribes of India. A comparative analysis of our results with the existing data suggests multiple origins of Austro-Asiatic tribes in India, and particularly the Asian and non-Asian origins of the Mon-Khmer and the Mundari populations. We also identified a novel subclade of haplogroup B in the Mon-Khmer Khasi tribes that distinguishes them from the Nicobarese, indicating two different waves of migration of the Mon-Khmer tribes in India.

Major histocompatibility complex class I polymorphism in Asiatic lions

Asiatic lions (Panthera leo persica), whose only natural habitat in the world is the Gir forest sanctuary of Gujarat State in India, are highly endangered and are considered to be highly inbred with narrow genetic diversity. An objective assessment of genetic diversity in their immune loci will help in assessing their survivability and may provide vital clues in designing strategies for their scientific management and conservation. We analyzed the comparative sequence polymorphism at exon 2 and exon 3 of major histocompatibility complex (MHC) class I in three groups of lions, i.e. wild Asiatic (from Gir forest), captive-bred Asiatic (from zoological parks in India), and Afro-Asiatic hybrid groups (from zoological parks in India) through polymorphism chain reaction-assisted sequence-based typing. The two exons were amplified, cloned, sequenced, and analyzed for polymorphism at nucleotide and putative translated product level. The analysis revealed extensive sequence polymorphism not only between clones derived from different lions but also the clones derived from a single lion. Furthermore, the wild Asiatic lions of Gir forest exhibited abundant sequence polymorphism at MHC class I comparable with that of Afro-Asiatic hybrid lions and significantly higher than that of captive-bred Asiatic lions. We hypothesize that Asiatic lions of Gir forest are not highly inbred as thought earlier and they possess abundant sequence polymorphism at MHC class I loci. During this study, 52 new sequences of the multigene MHC class I family were also identified among Asiatic lions.