The role ofAcidithiobacillus ferrooxidansin alleviating the inhibitory effect of thiosulfate on the growth of acidophilicAcidiphiliumspecies isolated from acid mine drainage samples from Garubathan, India

Several acidophilic chemolithoautotrophic and heterotrophic strains were isolated from acid mine drainage samples from Garubathan, West Bengal, India. The strains, chemolithoautotrophic DK6.1 and heterotrophic DKAP1.1, used in this study were assigned to the species Acidithiobacillus ferrooxidans and Acidiphilium cryptum , respectively. Unamended filtered and subsequently autoclaved elemental sulfur spent medium of A. ferrooxidans was used as the medium to study heterotrophic growth of A. cryptum DKAP1.1. While characterizing the heterotrophic strain, an inhibitory effect of thiosulfate on A. cryptum DKAP1.1 was identified. The lethality of thiosulfate broth was directly related to the concentration of thiosulfate in the medium. Nonviability of A. cryptum DKAP1.1 in the presence of thiosulfate was alleviated by A. ferrooxidans DK6.1 in co-culture. Microbiological data on a positive growth effect for A. ferrooxidans DK6.1 caused by co-culturing in solid media in the presence of A. cryptum DKAP1.1 is also presented.

The effect of parity on placental weight and birth weight: Interaction with placental alkaline phosphatase polymorphism

The effect of parity on placental weight and birth weight is examined through a series of birth records from an Indian population in Calcutta. Placental weight and birth weight increase with parity, the maximum increment occurring between parities 1 and 2. This is compatible with a hypothesis of sensitization of the mother to foetal, paternally derived, antigens. The three common placental alkaline phosphatase enzymic genotypes have no effect on determining foetal development.

Income Level and Food Intake Patterns among Male Bengalee Slum Dwellers in Kolkata, India

This cross-sectional study explored the relationships between income levels and food intake patterns among slum dwellers in Kolkata, India. A total of 284 male subjects of Bengalee ethnicity participated in the study. The mean (SD) age, monthly family income and monthly per capita income of the subjects were 40.8 years (14.2), Indian Rupees (Rs.) 3259 (1574) and Rs. 700 (416) respectively. Potatoes, fresh vegetables, sweets and eggs were among the most frequently consumed food items on a daily basis. Butter, soft drinks, milk and ghee were least frequently consumed. The frequency of consumption of snacks, sweets and fruits showed strong significant correlations (p < 0.001). Principal component analysis of the frequency of consumption of different foods showed five components that explained a cumulative variance of 56%. Eigen values of components one to five were: 1.49 for fruit, sweets and snacks; 1.36 for fish and soft drinks; 1.16 for ghee and butter; 0.65 for fresh vegetables; and 1.02 for milk. Individually, these components explained 14, 12, 11, 10 and 9% of the variations respectively. Regression analyses showed monthly per capita income to be significantly associated with frequency of consumption of soft drinks (F = 6.79, p < 0.001) and fish (F = 7.90, p< 0.005). Age showed a significantly positive association with butter consumption (F = 9.41, p<0.002), and was negatively associated with intake of soft drinks and fried snacks (F = 10.10, p< 0.002). Using regression equations to predict the impact of increased income on consumption patterns, it was found that a 10% increase in income is associated with 1% increase in consumption of fish, which carries traditional prestige. A similar increase in income would also lead to 10% increase in consumption of soft drinks that has connotations of brand associated prestige.

Effect of copper-hydroquinone complex on oxidative stress-related parameters in human erythrocytes (in vitro)

The effect of in vitro exposure of human erythrocytes to micromolar concentrations of hydroquinone and copper simultaneously on oxidative status-related biochemical parameters was studied. Hydroquinone is a component of cigarette smoke and serum copper level is increased in smokers. Copper forms a complex with hydroquinone and enhances its auto-oxidation to benzoquinone which covalently binds to sulfhydryl group containing compounds like reduced glutathione. In this study, copper increased H(2)O(2) production by hydroquinone. Hydroquinone either alone or in the presence of copper produced a decrease of reduced glutathione level without altering methemoglobin concentration and erythrocyte lipid peroxidation. Catalase inhibition by sodium azide depleted reduced glutathione level further. Copper-hydroquinone complex mediated glutathione depletion in the catalase containing RBC was not decreased by antioxidant, butylated hydroxytoluene. From the known facts and above findings, it is suggested that depletion of reduced glutathione by hydroquinone in the presence of copper in catalase active RBC may be due to the formation of 1, 4 benzoquinone adduct of reduced glutathione and to some extent due to binding of copper to the thiol group of reduced glutathione rather than conversion to oxidized glutathione via reactive oxygen species. Depletion of reduced glutathione by N-ethylmaleimide pretreatment followed by copper-hydroquinone treatment had no effect on methemoglobin level or lipid peroxidation. Furthermore, copper-hydroquinone complex did not increase erythrocyte susceptibility to oxidative stress. This suggests hydroquinone in the presence of copper does not contribute to erythrocyte membrane lipid peroxidation seen in smokers. Criteria for ideal antioxidant supplementation in smokers were suggested.

Correlation analyses reveal a substantial influence of allelic gaps on the investigation of genetic diversity of modern human populations with microsatellites

High intra-population genetic diversity and multiple measures of genetic variability at STR loci are useful in inferring past evolutionary history. However, STRs, categorized by their repeat motif size, differ in a number of aspects, requiring separate analyses. We analyzed 783 STRs in 36 worldwide populations to examine marker suitability as well as correlations between various measurements, to evaluate the extent of genomic diversity present in modern human populations. The loci were grouped by type and analyzed separately for each population group. Genetic variation defined by gene diversity and allele size variance, shows different trends of variation across four types of STRs. Additionally, there is little variation of genetic diversity, but there is decreased allelic size variance with increasing repeat motifs. A poor correlation between genetic diversity and allelic size variance across loci in all groups for Di-STRs is probably caused by the presence of allelic size gaps. In contrast, allelic size variance, genetic diversity, and number of alleles are strongly correlated with both tri- and tetra-STRs. The positive correlation of allelic size variance and presence of gaps within the range of allelic sizes in Di-STRs alone explains these observations. An unexpected high imbalance index (beta) at Di-STRs due to high allelic size variance also supports this assertion.

Quorum sensing in metal tolerance of Acinetobacter junii BB1A is associated with biofilm production

Acinetobacter junii strain BB1A, a novel metal-tolerant bacterium, produced biofilm in the presence of added ions such as Ni(2+), AsO(2)(-), Cd(2+) and Hg(2+) on surfaces such as glass and polystyrene. Generation of a metal-sensitive and adhesion-deficient mutant by transposition of Tn5-mob in the A. junii genome has putatively confirmed the association of metal tolerance with the production of biofilm. The requirement of a critical cell density for biofilm formation and presence of acyl-homoserine lactone-like autoinducer molecules in the cell-free supernatant indicated the phenomenon of quorum sensing. Addition of a natural quorum-sensing inhibitor (garlic extract) or synthetic quorum-sensing inhibitor (4-nitro-pyridine oxide) significantly inhibited cell growth and biofilm formation in the presence of metal/metalloid ions.

Conjugation potential and class 1 integron carriage of resident plasmids in river water copiotrophs

Plasmid content was investigated in hundred copiotrophic Gram-negative river water isolates that exhibited resistance to four or more antibiotics. A total of seventy-seven isolates were found to carry plasmids of varying sizes. These isolates were primarily grouped as Pseudomonads and members of Enterobacteriaceae on the basis of physiological and biochemical tests. Fifty-six isolates that were rifampicin-sensitive and belonged to Enterobacteriaceae family were chosen as donors for the conjugal transfer assay. Eighteen of the isolates successfully transferred conjugable plasmids to the E. coli DH5alpha recipient. Countable multiple antibiotic resistant transconjugants arose readily and conjugal transfer frequency was in the range of 3.75 x 10(-6) to 1.0 x 10(-1). The most common carriage of resistances conferred by transmissible R plasmids was against ampicillin, cefotaxim and cephalexin. The residence of class 1 integrons on conjugative R plasmids was confirmed in only six transconjugants. Gene cassettes borne on the integrons were identified to be dihydrofolate reductases (dhfrs). The major concern of this study was about the copiotrophs containing self-transmissible R plasmids which may be potential reservoirs of antibiotic-resistance genes and instrumental in dissemination of the same in the environment.

Fluctuation in recoverable nickel and zinc resistant copiotrophic bacteria explained by the varying zinc ion content of Torsa River in different months

Heavy metal content analysis of River Torsa in India did not indicate any alarming level of toxicity for human consumption but revealed variation at the ppb level in different months. The variation in recoverable nickel and zinc resistant copiotrophic (or eutrophic) bacterial counts was explained by the variation of the zinc content (34.0-691.3 ppb) of the river water in different sampling months. Growth studies conducted with some purified nickel and/or zinc resistant strains revealed that pre-exposure of the cells to ppb levels of Zn(2+), comparable to the indigenous zinc ion concentration of the river, could induce the nickel or zinc resistance. A minimum concentration of 5-10 microM Zn(2+ )(325-650 ppb) was found effective in inducing the Nickel resistance of the isolates. Zinc resistance of the isolates was tested by pre-exposing the cells to 4 microM Zn(2+ )(260 ppb). The lag phase was reduced by 6-8 h in all the cases. Biochemical characteristics and phylogenetic analysis based on 16S rDNA sequence indicated that some of the Torsa River isolates, having inducible nickel and zinc resistance, are members of the genus Pseudomonas, Acinetobacter, Bacillus, Enterobacter, Serratia and Moraxella.

Clinical predictors and risk of optic pathway glioma (OPG) in Neurofibromatosis-1 (NF-1)

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Background: NF-1 is a progressive disease with wide spectrum of phenotype and unpredictability in clinical course. NF-1 patients are at significantly increased risk for development of a variety of neoplasms that cause morbidity and limited mortality, including OPG. There are limited data identifying risk factors predictive of subsequent OPG development. Objective: To identify key early clinical features which predict subsequent risk for development of OPG. Methods: Case-control study of NF-1 patients with and without OPG from Cincinnati Children’s Hospital NF-1 and Cancer Registries. Predictor variables were clinical risk factors (age at diagnosis of NF-1, race/ethnicity, gender, and history of familial NF-1, macrocephaly, plexiform neurofibroma, developmental delay, seizure disorder,), and the dependent variable was development of OPG by imaging. Patients received screening head MRI at the time of presentation with NF-1. Odds ratios (O.R.) were calculated with 75 cases (NF-1 and OPG) and 215 controls (NF-1 only) and statistically/clinically significant factors were further analyzed by logistic regression method. Results: Prevalence of OPG in NF-1 was 15.6%. Almost half had familial NF-1. Median age at diagnosis of NF-1 was 1.6 yrs (cases) and 2.4 yrs (controls). OPG was diagnosed at median age 4 yrs. Patients with T2 hyperintense lesions on imaging (UBOs) and age 4 years or less at diagnosis of NF-1 were at significantly increased risk of developing OPG (O.R=3.1, p=0.006 and O.R=3.1, p=0.002 respectively). In addition, presence of seizure disorder and developmental delay were borderline significant (O.R=2.8, p=0.07 and O.R=1.7, p=0.04 respectively). Race (Caucasian) appeared to have disease modifying effect on development and progression of OPG. Conclusions: Patients with T2 lesions on presentation MRI, developmental delay, seizures, and age 4 years or less at NF-1 diagnosis appear to be at an increased risk of developing OPG. Caucasian race appears to have a modifying effect on disease progression. Patients with these risk factors may be stratified as “high risk” and may benefit from close surveillance for early detection of OPG. The association of developmental delay and seizures may suggest a pathophysiologic relationship.

No significant financial relationships to disclose.

Characterization of ‘Schizokinen’; a dihydroxamate-type siderophore produced by Rhizobium leguminosarum IARI 917

The Rhizobia comprise one of the most important groups of beneficial bacteria, which form nodules on the roots (rarely on the stems) of leguminous plants. They live within the nodules and reduce atmospheric nitrogen to ammonia, which is further assimilated by plants into required nitrogenous compounds. The Rhizobia in return obtain nutrition from the plant. Rhizobia are free-living soil bacteria and have to compete with other microorganisms for the limited available iron in the rhizosphere. In order to acquire iron Rhizobia have been shown to express siderophore-mediated iron transport systems. Rhizobium leguminosarum IARI 917 was investigated for its ability to produce siderophore. It was found to produce a dihydroxamate type siderophore under iron restricted conditions. The siderophore was purified and chemically characterized. The ESMS, MS/MS and NMR analysis indicate the dihydroxamate siderophore to be 'schizokinen', a siderophore reported to be produced by Bacillus megaterium that shares a similar structure to 'rhizobactin 1021' produced by Sinorhizobium meliloti 1021. This is the first report of production of schizokinen by a strain of R. leguminosarum, therefore it was carefully investigated to confirm that it is indeed 'schizokinen' and not a degradation product of 'rhizobactin 1021'. Since ferric-siderophore complexes are transported across the outer membrane (OM) into the periplasm via an OM receptor protein, R. leguminosarum IARI 917 was investigated for the presence of an OM receptor for 'ferric-schizokinen'. SDS PAGE analysis of whole cell pellet and extracted OM fractions indicate the presence of a possible iron-repressible OM receptor protein with the molecular weight (MW) of approximately 74 kDa.

Incidence of class 1 integrons in multiple antibiotic-resistant Gram-negative copiotrophic bacteria from the River Torsa in India

The presence of class 1 integrons in multiple-antibiotic-resistant (MAR) Gram-negative copiotrophic bacteria from the River Torsa in India was detected using a polymerase chain reaction (PCR)-based screening method. Among 100 isolates that were resistant to at least five of the twelve antibiotics tested, 40 carried class 1 integrons, with inserted DNA regions of 0.7-3.2 kb. Carriage of integrons in strains of higher MAR index was found to be statistically significant. DNA sequencing was used to identify the genetic content of the integron-variable regions. In addition to the identification of gene cassettes dfrA1, dfrA5, dfrA7, dfrA17 and a variant of dfrA12 for trimethoprim, aac(6')-Ib for amikacin and tobramycin and aadA1 and aadA6 for streptomycin and spectinomycin resistance, a novel ORF predicted from a sequence of Morganella sp. TR 90 bearing homology with the Vibrio cholerae dfrA1 gene cassette was characterized. To our knowledge, this is the first report of the incidence and abundance of class 1 integrons in copiotrophic river water bacteria from India.

nef gene sequence variation among HIV-1-infected African children*

BACKGROUND

There are few data on African children infected with nonclade B HIV-1 in endemic settings, which limits generalizations about pathogenesis and progression. Genotypic and phenotypic variations in host immunogenetics and HIV-1 negative factor (nef) accessory protein may influence disease progression and have frequently been characterized in subjects infected with clade B HIV-1.

METHODS

In this descriptive study, we report nef gene sequence variation and host genetic polymorphisms in 32 Kenyan children, including 12 slow progressors.

RESULTS

Phylogenetic analysis identified HIV-1 clades A, C and D and a recombinant A/D subtype. Grossly defective nef genes or significant changes from relevant clade reference sequences were not identified in children with delayed disease progression.

CONCLUSIONS

nef sequence variations may not be common in perinatally infected African children. Further studies are warranted in HIV-1-infected subjects in settings where infection is endemic.

G(2) chromosomal radiosensitivity in Danish survivors of childhood and adolescent cancer and their offspring

In order to investigate the relationship between chromosomal radiosensitivity and early-onset cancer, the G(2) chromosomal radiosensitivity assay was undertaken on a group of 23 Danish survivors of childhood and adolescent cancer, a control group comprising their partners and a group of 38 of their offspring. In addition, the previously reported in-house control group from Westlakes Research Institute (WRI) was extended to 27 individuals. When using the 90th percentile cutoff for the WRI control group, the proportion of individuals with elevated radiosensitivity was 11, 35, 52 and 53% for the WRI control, partner control, cancer survivor and the offspring groups, respectively, with significant differences between the WRI control group and the cancer survivor group (P=0.002) and the offspring group (P<0.001). However, while the comparisons with the WRI control group support an association of chromosomal radiosensitivity with cancer predisposition, when the partner control group was used to define the radiosensitivity cutoff point, no significant differences in radiosensitivity profiles were found between the partner control group and either the cancer survivor group or the offspring group. The failure to distinguish between the G(2) aberration profiles of the apparently normal group of partners and the cancer survivor group suggests that any association with cancer should be viewed with caution, but also raises questions as to the suitability of the partners of cancer survivors to act as an appropriate control group. Heritability of the radiosensitive phenotype was examined by segregation analysis of the Danish families and suggested that 67.3% of the phenotypic variance of G(2) chromosomal radiosensitivity is attributable to a putative major gene locus with dominant effect.

Serratia ureilytica sp. nov., a novel urea-utilizing species

A Gram-negative, rod-shaped, urea-dissolving and non-spore-forming bacterium, designated strain NiVa 51(T), was isolated from water of the River Torsa in Hasimara, Jalpaiguri district, West Bengal, India. On the basis of 16S rRNA gene sequence similarity, strain NiVa 51(T) was shown to belong to the gamma-Proteobacteria and to be related to Serratia marcescens subsp. sakuensis (98.35%) and S. marcescens subsp. marcescens (98.30%); however, strain NiVa 51(T) exhibited only 43.7% similarity to S. marcescens by DNA-DNA hybridization. The G+C content of the genomic DNA of the isolate was 60 mol%. Both biochemical characteristics and fatty acid analysis data supported the affiliation of strain NiVa 51(T) to the genus Serratia. Furthermore, strain NiVa 51(T) was found to utilize urea as nitrogen source. The results of DNA-DNA hybridization as well as physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NiVa 51(T) from recognized Serratia species. Strain NiVa 51(T) therefore represents a novel species, for which the name Serratia ureilytica sp. nov. is proposed, with type strain NiVa 51(T) (=LMG 22860(T)=CCUG 50595(T)).

Haplotype diversity in 11 candidate genes across four populations

Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.

A method to detect excess risk of disease in structured data: Cancer in relatives of retinoblastoma patients

It is often of interest to know whether there is increased occurrence of a trait in a pedigree or other structured set of epidemiological data. In answering such questions most current methods use aggregate measures, such as relative risk, that may not relate the outcome for each individual to that individual's risk. In this paper we present a simple method, and its computational algorithm, to overcome this limitation. This new method also permits one to identify high-risk families or subsets of a collection of data, which is not always possible using other approaches. In a study of cancer risk among relatives of retinoblastoma patients, by applying this new method it was found that 11 of 33 families each obtained through a unilateral retinoblastoma patient are at statistically high risk of cancer at all sites combined, while there are 15 of 47 such families obtained through a bilaterally affected proband. These results are unlikely to have occurred by chance, indicating an overall excess risk in the ancestors of these retinoblastoma cases. The proposed test procedure does not specify the cause of elevated risk; however, a method is proposed that provides some indication regarding possible causal mechanisms under some circumstances.