Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India

A polyphasic approach was used to characterize a bacterium, GPTSA 11(T), isolated from a warm spring located in a reserve forest in Assam, India. The cells are Gram-variable, strictly aerobic, sporulating motile rods. The major fatty acids of the strain are C(15 : 0) anteiso (48.42 %), C(16 : 0) iso (11.59 %), C(16 : 1)omega11c (6.16 %), C(15 : 0) iso (6.03 %), C(17 : 0) anteiso (5.68 %) and C(16 : 1)omega7c alcohol (5.01 %). The presence of the fatty acid C(16 : 1)omega7c alcohol distinguishes this strain from other closely related species of the genus Paenibacillus. The strain contains MK-7 as the diagnostic menaquinone. The G+C content of the genomic DNA is 41.2 mol%. Analysis of the 16S rRNA gene sequence (1466 nt) revealed the presence of signature sequences PAEN 515F (5'-GAGTAACTGCTCTCGGAATGACGGTACTTGAGAAGAAAGCCCC-3') and PAEN 862F (5'-TCGATACCCTTGGTGCCGAAGT-3'), which were found in the species of the genus Paenibacillus surveyed by Shida et al. [Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997). Int J Syst Bacteriol 47, 289-298]. The sequence shows closest similarity (95.85 %) to that of Paenibacillus apiarius, followed by Paenibacillus alvei (94.34 %), Paenibacillus cineris (93.87 %), Paenibacillus favisporus (93.80 %), Paenibacillus chibensis (93.47 %) and Paenibacillus azoreducens (93.40 %). Biochemical, physiological, chemotaxonomic and phylogenetic analyses justify placement of the strain in the genus Paenibacillus but not within any existing species. It should, therefore, be considered as representing a novel species, for which the name Paenibacillus assamensis sp. nov. is proposed. The type strain is GPTSA 11T (=MTCC 6934T=JCM 13186T).

Single centre experience of umbilical cord stem cell transplantation for primary immunodeficiency

Primary immunodeficiencies (PID) are an important cause of childhood mortality. Haematopoietic stem cell transplantation (HSCT) is the best treatment for many PID. Umbilical cord stem cells are an alternative source of HSC. There is little data regarding outcome of umbilical cord stem cell transplantation (UCSCT) for PID. Our single centre experience is reported. A retrospective study of 14 of 148 patients transplanted for PID, who have received 15 UCSCT was performed, with specific regard to graft-versus-host disease (GvHD) and immune reconstitution. Eight patients with severe combined immunodeficiency (SCID), and six with other combined immunodeficiencies were treated. Of the patients, 12 received unrelated cords, and two had sibling transplants. Median age at transplant was 3.5 months, median nucleated cell dose was 0.8 x 10(8)/kg. All engrafted. Median time to neutrophil engraftment was 22 days, median time to platelet engraftment was 51 days. One developed significant grade III GvHD post transplantation. In total, 11 patients had full donor T and six full donor B-cell chimerism, six of nine patients >1 year post-BMT had normal IgG levels and specific antibody responses to tetanus and Hib vaccines; two are being assessed. Two patients died of multi-organ failure related to pre-existing infection and inflammatory complications respectively. UCSCT should be considered for patients requiring stem cell therapy for PID.

THE VESICOURETERAL REFLUX DYSPLASIA SYNDROME IN PATIENTS WITH POSTERIOR URETHRAL VALVES

PURPOSE

We retrospectively reviewed outcomes in children followed for posterior urethral valves and the vesicoureteral reflux dysplasia (VURD) syndrome.

MATERIALS AND METHODS

Of 65 patients with posterior urethral valves 13 fulfilled the criteria for the VURD syndrome. Patients were assessed with diethylenetriamine pentaacetic acid and dimercapto-succinic acid scans at followup to evaluate stability of renal function, presence of renal scarring and drainage of the contralateral kidney. Student's t test and the chi-square test were used for statistical analysis, with p < or = 0.05 considered significant.

RESULTS

Based on the dimercapto-succinic acid scan reports, patients were classified into group 1 (6 patients), in which the contralateral kidney had no evidence of scarring, and group 2 (7 patients), in which the contralateral kidney had evidence of scars. Patients in group 1 had no breakthrough urinary tract infections or history of urinary incontinence. There was no dilatation of the contralateral upper urinary tract, and 5 of 6 patients had prompt ureteral drainage on scans. They also attained a long-term serum creatinine of 0.6 +/- 0.0 mg/dl. Patients in group 2 had a significant incidence of breakthrough urinary tract infections (p < or = 0.03) and diurnal incontinence (p < or = 0.01). Hydroureteronephrosis and slow drainage were seen in 6 of 7 patients on scans. The long-term mean serum creatinine attained in this group was 0.9 +/- 0.3 mg/dl.

CONCLUSIONS

About half of the patients with the VURD syndrome had renal scarring in the contralateral kidney. These patients had evidence of hydroureteronephrosis, slow drainage of the ureter in association with breakthrough urinary tract infections and diurnal incontinence. Although serum creatinine in patients with the VURD syndrome and renal scarring in the contralateral kidney was not statistically different from that in children with a normal contralateral kidney in the short term, in the long term the deleterious effects of renal scarring, viz hypertension, proteinuria and renal failure, are likely to manifest. The presence of the VURD syndrome may not always be as good a prognostic indicator as believed previously.

Outcome of boost haemopoietic stem cell transplant for decreased donor chimerism or graft dysfunction in primary immunodeficiency

Haemopoietic stem cell transplants (HSCT) cure increasing numbers of primary immunodeficiencies (PID): residual recipient T-cell function increases risk of incomplete or decreasing immune reconstitution, which may resolve following a second, unconditioned, infusion from the same donor (boost infusion). We assessed the outcome of 20 boost infusions in 19/139 patients transplanted for PID patients at our centre since 1987. Boost infusion was given 64-1226 days after the original HSCT. Follow-up was 4-124 months. In all, 12 of 19 patients cleared viral infection (6), or showed sustained increase in donor chimerism, T- and B-cell numbers and function, or other markers (6). In 7/12 patients, immunoglobulin replacement has been discontinued. Four were partially successful with stable low-level chimerism (two patients) or improved T-cell function, but not B cell function (two patients). Four failed with no change in donor chimerism or cell number. No significant association with donor source, T-cell depletion, conditioning regimen, boost infusion stem cell dose or time from original HSCT to boost was found. One patient developed grade III acute graft-versus-host disease despite cyclosporine, and one developed severe pneumonitis; both have recovered. Boost infusion was successful or partially successful in 84% of patients. The risk of adverse effects is low.

Peritoneo-scrotal communication: Demonstration by 99mtechnetium sulphur colloid scintigraphy

Continuous ambulatory peritoneal dialysis is a widely used and convenient alternative to haemodialysis in patients with renal failure. Occasionally, a scrotal swelling may develop during this procedure because of fluid passing through a patent processus vaginalis. We present a case report to illustrate the diagnostic use of radionuclide scintigraphy in this group of patients.

Technetium-99m ciprofloxacin imaging in the diagnosis of postsurgical bony infection and evaluation of the response to antibiotic therapy: A case report

The use of radiolabelled antibiotics is fast emerging as a promising diagnostic test for the detection of infective lesions, because of their specific binding to the bacterial component. Ciprofloxacin is a broad-spectrum antibiotic that has been used as a radiolabelled antibiotic in both the diagnosis of infections in rabbits and in clinical trials on humans. The diagnosis of skeletal microbial infections remains a challenge, especially in orthopaedic patients with implants. We present a case report of a patient with undiagnosed and unrelenting pain in the lower third of the left leg, which had persisted for 6 months. A novel scintigraphy, which was developed in-house using a 99mTC ciprofloxacin single vial kit, was used for diagnosing the active bacterial infection. A 99mTC methylene diphosphonate bone scan was also performed to locate precisely the site of the lesion. Gradually increasing concentrations of both the radiotracers confirmed the presence of active bacterial infection in the distal third of the left tibia. Follow-up scanning after antibiotic therapy showed the disappearance of the pooling of 99mTC ciprofloxacin, indicating a good response. Therefore, 99mTC ciprofloxacin has good diagnostic and prognostic applications in deep-seated covert skeletal microbial infections. However, the persistence of a focal concentration detected by the 99mTC methylene diphosphonate scan was attributed to the inflammatory and not the infective pathology.

Electrostatic tuning of the superconductor-insulator transition in two dimensions

Superconductivity has been induced in insulating ultrathin films of amorphous bismuth using the electric field effect. The screening of the electron-electron interaction was found to increase with electron concentration in a manner correlated with the tendency towards superconductivity. This does not preclude an increase in the density of states being important in the development of superconductivity. The superconductor-insulator transition appears to belong to the universality class of the three dimensional XY model.

Evaluation of the concentration of HCH, DDT, HCB, PCB and PAH in the sediments along the lower stretch of Hugli estuary, West Bengal, northeast India

Detailed analyses of persistent organic pollutants (POPs) such as hexachlorocyclohexane (HCH) isomers (HCHs), dichlorodiphenyltrichloro ethane (DDT) and its metabolites (DDTs), hexachlorobenzene (HCB) and congeners of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) in surface sediments from the coastal estuarine environment of West Bengal, northeast India allowed the evaluation of the contamination status, distribution and possible pollution sources. HCH, DDT, HCB, PCB and PAH were identified compounds in all the samples, whereas the concentrations of chlorinated pesticides (trans-eptachlorepoxide, dieldrin, endrin, metaoxychlor and mirex) were below the detection limits and were not of great concern. The pesticides did demonstrate markedly different distributions reflecting different agricultural and domestic usage in the region. The range of concentrations of HCH, HCB, DDT and PCBs in the sediments were 0.11-0.40, <0.05-0.98, 0.18-1.93 and 0.18-2.33 ng/g dry wt, respectively. Overall elevated levels of HCB, DDT and PCB were recorded at Babughat, a very closely located site of the metropolitan megacity Calcutta. Fluoranthene (flu) and pyrene (py), the dominant 4-ring PAHs, also showed an abrupt elevated concentrations at Babughat with values of 214 and 144 ng/g dry wt, respectively. Among the isomers and metabolites of HCH, DDT and PCB, alpha-HCH, pp'-DDT and PCB (101), PCB (118), PCB(153) and PCB (138) were found to be dominant. High ratios of metabolites of DDT to SigmaDDTs reveal recent use of DDT in this coastal environment. Fluoranthene, pyrene, 1,2-benzo(a)anthracene and chrysene formed the dominant congeners out of 19 identified PAHs. The sources of contamination are closely related to human activities such as domestic and industrial discharge, automobile exhausts, street runoff, slum sewage, agricultural chemicals and soil erosion due to deforestation as well as atmospheric transport. This study is compared to other coastal and estuarine environments in India and abroad. The baseline data can be used for regular ecological monitoring, considering the industrial and agricultural growth around this important estuarine ecosystem.

Extrahepatic portal hypertension: quality of life and somatic growth after surgery

AIM

This study was carried out in order to determine whether children with extrahepatic portal hypertension show any improvement in growth parameters and quality of life after elective surgery.

PATIENTS AND METHODS

All patients with extrahepatic portal hypertension who underwent surgery between April 1999 and March 2002 were studied prospectively. Height and weight before and after surgery were converted into Z scores for comparison. The quality of life was assessed by changes in scholastic ability, physical activity, social interaction, and economic effects on the family.

RESULTS

At the end of a minimum follow-up period of 1 year, of the 30 children, 50 % and 76 % showed improvement in weight and height Z scores, respectively, compared to their scores while on medical management. Z scores below - 2 SD for weight and height were seen in 57 % and 37 % of patients prior to surgery, and only in 40 % and 20 %, respectively at the end of follow-up, which ranged from 1 - 4 years. The improvement in height and weight was more in those who had undergone splenectomy with either devascularization or central splenorenal shunt compared to those who had undergone side-to-side lienorenal shunt without splenectomy. The children, who had dropped out of school while on medical management, either rejoined school or attended vocational courses after surgery. There was an improvement in school performance and physical activity in 85 % of the children. Improvement in personality was seen in 73 % of the affected patients. The cost incurred for surgery was one-third of the amount spent while on medical management.

CONCLUSIONS

Growth parameters improved significantly in children after surgical intervention for portal hypertension. Overall improvement in scholastic abilities, physical activity, and social interaction was noted in a majority of the patients. As a one-time procedure in a developing country, surgery is also more cost effective.

Ambipolar gate effect and low temperature magnetoresistance of ultrathin La0.8Ca0.2MnO3 films

Ultrathin La(0.8)Ca(0.2)MnO(3) films have been measured in a field-effect geometry. The gate electric field produces a significant ambipolar decrease in resistance at low temperatures. This is attributed to the development of a pseudogap in the density of states and the coupling of localized charge to strain. Within a mixed phase scenario, the gate effect and magnetoresistance are interpreted in the framework of a "general susceptibility," which describes how phase boundaries move through a hierarchical pinning landscape.

Thyroid dysfunction after bone marrow transplantation for primary immunodeficiency without the use of total body irradiation in conditioning

Thyroid dysfunction, a common long-term complication following bone marrow transplantation (BMT), is frequently associated with total body irradiation (TBI) given in the pre-BMT conditioning protocol. We report our preliminary observation of the prevalence of thyroid dysfunction in children transplanted for primary immunodeficiency (PID) who were given cytoreductive conditioning with busulphan and cyclophosphamide, but without TBI. We evaluated thyroid-stimulating hormone (TSH) and free thyroxine (fT4) in 83 survivors transplanted between 1987 and 2002. We found nine children (10.8%) with clinical and/or biochemical thyroid dysfunction at 4 months to 4.5 years post-BMT of which three had positive antithyroid microsomal antibodies. Two patients were classified as primary and seven as compensated hypothyroidism (hyperthyrotropinaemia). Four patients with clinical features of hypothyroidism received replacement thyroxine, while five of the seven patients with compensated hypothyroidism remain off thyroxine because we suspect this may be a transient phenomenon. Abnormalities of thyroid function including severe primary hypothyroidism may occur post-BMT in children receiving chemotherapy conditioning without TBI. Thyroid function should be assessed regularly in this group of patients.

The clinical and biological overlap between Nijmegen Breakage Syndrome and Fanconi anemia

Fanconi anemia (FA), an autosomal recessive chromosomal instability syndrome, is characterized clinically by developmental abnormalities, growth retardation, progressive bone marrow failure, pancytopenia, and pronounced cancer predisposition. Nijmegen Breakage Syndrome (NBS) is a related disorder that shares overlapping clinical features, principally, developmental delay, microcephaly, and cancer predisposition. The diagnosis has relied on chromosomal instability following exposure to DNA cross-linking agents in FA and to ionizing radiation (IR) in NBS. We describe two patients who clinically had FA, but showed sensitivity to both DNA cross-linking agents and ionizing radiation, and who were found to have a rare mutation in the NBS gene. The importance of genetic diagnosis with respect to treatment and prognosis is discussed.

Progress: simultaneous searching of protein databases by sequence and structure

We consider the problem of similarity searches on protein databases based on both sequence and structure information simultaneously. Our program extracts feature vectors from both the sequence and structure components of the proteins. These feature vectors are then combined and indexed using a novel multi-dimensional index structure. For a given query, we employ this index structure to find candidate matches from the database. We develop a new method for computing the statistical significance of these candidates. The candidates with high significance are then aligned to the query protein using the Smith-Waterman technique to find the optimal alignment. The experimental results show that our method can classify up to 97% of the superfamilies and up to 100% of the classes correctly according to the SCOP classification. Our method is up to 37 times faster than CTSS, a recent structure search technique, combined with Smith-Waterman technique for sequences.

Posterior urethral valves: incidence and progress of vesicoureteric reflux after primary fulguration

This is a prospective study of 20 cases of posterior urethral valves (PUV) presenting between the ages of 12 days and 5.5 years (median 15 months) in order to determine the incidence and progress of vesicoureteric reflux (VUR), hydronephrosis (HN), and renal functional status. The efficacy of fulguration as the sole modality of treatment for PUV was assessed in terms of improvement or disappearance of VUR over a 6-month follow-up period. VUR was present in 60% of the patients, being unilateral in 41.7%. Out of 19 renal units with VUR, reflux subsided in 31.5% by 3 months and 78.94% by 6 months. The blood urea and serum creatinine levels, which were raised in 50% of the patients at presentation, came down to normal by 6 months in all the cases. Improvement in glomerular filtration rates (GFR) was noted in all the children at each follow-up and was found to be statistically significant ( p<0.01). HN was present in all the patients at presentation and was bilateral in 90%. It decreased significantly during the follow-up period, though its complete disappearance was seen only in one case. Vesicoureteric reflux dysplasia syndrome (VURD) was present in two cases. Our study showed that VUR disappeared in a majority of the cases by 6 months once adequate urethral patency was restored, although hydronephrosis persisted.

Experimental determination and system level analysis of essential genes in Escherichia coli MG1655

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.

Evaluation of cardiovascular status in severe leptospirosis

OBJECTIVES

To note incidence and profile of cardiac involvement in severe leptospirosis in South Gujarat.

METHODS

A study was carried out on twenty-five serologically proved leptospirosis patients referred to Government Medical College, New Civil Hospital, Surat between June 2002 to September 2002. In all the patients detailed history, physical examination and specific investigations were done to find out the incidence and profile of cardiac involvement in severe leptospirosis.

RESULTS

Out of twenty-five seropositive patients, 14(56%) had cardiovascular manifestations. Electrocardiography abnormalities were seen in 13(52%) patients. The commonest finding was first-degree AV block seen in II(44%) patients followed by ST-segment depression in four (16%) patients, T-wave inversion in leads II, III and avF in two (8%) patients, corrected QT-interval prolongation in three (12%) patients and ventricular premature beats in two (8%) patients. Atrial fibrillation was seen in only one patient. Left ventricular function as assessed by two-dimensional echocardiography was normal in all patients.

CONCLUSION

In cardiovascular involvement of leptospirosis, although electrocardiographic abnormalities were commonly seen, there was no left ventricular dysfunction.

Electrical transport of spin-polarized carriers in disordered ultrathin films

Slow, nonexponential relaxation of electrical transport accompanied by memory effects has been induced in quench-condensed ultrathin amorphous Bi films by the application of a parallel magnetic field. This behavior, which is very similar to space-charge limited current flow, is found in extremely thin films well on the insulating side of the thickness-tuned superconductor-insulator transition. It may be the signature of a collective state that forms when the carriers are spin polarized at low temperatures and in high magnetic fields.