Antifungal activity of some coleus species growing in nilgiris

The in vitro antifungal activity of solvent extracts of Coleus forskohlii, Coleus blumei and Coleus barbatus were compared by testing against some pathogenic fungi like Aspergillus niger, Aspergillusfumigatus, Aspergillus ruantii, Proteus vulgaris and Candida albicans. The petroleum ether extract of Coleus forskohlii and Coleus barbatus exhibited significant antifungal activity against all the selected organisms. The extracts of Coleus blumei did not show any significant antifungal activity against the selected organisms.

Clinical Outcomes of 84 Children with Congenital Heart Disease Managed with Extracorporeal Membrane Oxygenation after Cardiac Surgery

The purpose of our research was to study the clinical outcomes of children with congenital heart disease (CHD) requiring extracorporeal membrane oxygenation (ECMO) support after cardiac surgery at a tertiary care children's hospital. Retrospective review of all patients with CHD who required postcardiotomy ECMO between January 2001 and September 2004 (45 months) was undertaken. Various outcome predictors were tested for any association with survival to hospital discharge using univariate analysis. A total of 84 children were placed on ECMO after CHD surgery; 39 (46.4%) were placed on ECMO in the operating room. Median age of the patients was 128 days (1 day to 5 years) and median weight was 4.53 kg (2-18 kg). Active cardiopulmonary resuscitation was ongoing at the time of cannulation in 27 children (32%). Fifty-two children (61.9) survived > 24 hours after decannulation and 31 (36.9%) survived to discharge. High arterial serum lactate levels at the time of ECMO initiation were strongly correlated with nonsurvival (p = 0.004). Nonsurvivors had longer duration on ECMO than survivors (p = 0.003). The odds of survival dropped significantly after 144 hours (day 6) of ECMO. ECMO support results in improved outcomes in patients who suffered hemodynamic collapse post cardiac surgery. Underlying cardiac lesion, age, weight, gender, initial arterial pH, location of ECMO initiation, need for hemofiltration and placement of ECMO after active ongoing cardiopulmonary resuscitation did not increase the mortality risk. Initial arterial serum lactate level and inability to wean off by 6 days were strongly correlated with nonsurvival.

Instability of the interface between thin fluid films subjected to electric fields

The effect of an externally applied electric field on the stability of the interface between two thin leaky dielectric fluid films of thickness ratio and viscosity ratio ris analyzed using a linear stability analysis in the long-wave limit. A systematic asymptotic expansion is employed in this limit to derive the coupled nonlinear differential equations describing the evolution of the position of the interface between the fluids and the interfacial free charge distribution. The linearized stability of these equations is determined and the effect of the ratio of the conductivities, dielectric constants, thicknesses, and viscosities on the wavenumber of the fastest growing mode, kmax, and the growth rate of the most unstable mode, smax, is examined in detail. Specific configurations considered in previous studies, such as a perfect dielectric-air interface, leaky dielectric-air interface, etc., emerge as limiting cases from the general formulation developed in this paper. Our results show that the viscosity ratio, mur, does not have any significant effect on kmax for the interface between perfect and leaky dielectric fluids. In marked contrast, however, mur is shown to have a significant effect on the interface between two leaky dielectrics. Increasing mur from 0.1 to 10 could decrease kmax up to a factor of 5. In general, our results show that the presence of nonzero conductivity in either one or both of the fluids has a profound influence on the length-scale characteristic of the linear instability: a reduction even by a factor of 1/50 in the length scale can be effected when compared to the interface between two perfect dielectrics. These predictions could have important implications in pattern formation applications in thin fluid films that employ electric fields. The variation of kmax and smax on the thickness ratio, beta, indicates in general that kmaxalpha(beta-apha), and smaxalpha(beta-theta), where the exponents alpha and theta (both >0) are found to depend only on the ratio of conductivities, and are largely independent of other system parameters.

Nuclease Rsn from Rhizopus stolonifer: specificity and mode of action

Nuclease Rsn from Rhizopus stolonifer catalyzes the hydrolysis of ss- and dsDNA in a ratio of approximately 2:1. Time course of 3' and 5' terminal analysis of the hydrolytic products of ss- and dsDNA showed that nuclease Rsn does not show any strict base preference and cleaves DNA in a non-specific manner. Moreover, separation of the hydrolytic products of ss- and dsDNA in the presence of Mg2+, Mn2+ or Co2+ showed the predominance of tetra-, tri-, and dinucleotides followed by mononucleotides, suggesting an endo mode of action.

Microheterogeneity of molecular forms of arginase in mammalian tissues

Two isoforms of arginase, A1 and A2, were found in rat liver, submaxillary gland and kidney as well as beef kidney. In beef liver, however, A2 was the only detectable form. Two additional forms, A3 and A4, found only in rat kidney were probably artifactitious. A1 and A2 exhibited chromatographic and immunological microheterogeneity. While A1 in rat liver and submaxillary gland was excluded by DEAE-cellulose (pH 8.3) and retained on CM-cellulose (pH 7.5), that (A'1) in beef and rat kidneys was excluded by both ion-exchangers. A2 in all tissues was retained on DEAE-cellulose, but not on CM-cellulose. Both A1 and A2 in rat liver and beef kidney, A1 from rat submaxillary gland and A2 from beef liver were precipitated by antibodies to rat and beef liver arginases. None of the forms in rat kidney (A1, A2, A3 and A4) showed any cross-reactivity to either antibody. Rat submaxillary gland A2 was precipitated by anti-rat liver arginase, but activated by anti-beef liver arginase. While the major molecular forms were A1 in rat liver and submaxillary gland and A2 in beef liver and rat kidney, the two forms occurred in equal proportions in beef kidney. It appears that different isoforms might function as components of the urea cycle in the liver of different mammals and of the arginine catabolic pathway in different extrahepatic tissues.

Bacterial glycoproteins: functions, biosynthesis and applications

Although widely distributed in eukaryotic cells glycoproteins appear to be rare in prokaryotic organisms. The prevalence of the misconception that bacteria do not glycosylate their proteins has been a subject matter of discussion for a long time. Glycoconjugates that are linked to proteins or peptides, generated by the ribosomal translational mechanism have been reported only in the last two to three decades in a few prokaryotic organisms. Most studied prokaryotic glycoproteins are the S-layer glycoproteins of Archeabacteria. Apart from these, membrane-associated, surface-associated, secreted glycoproteins and exoenzymes glycoproteins are also well documented in both, Archea and Eubacteria. From the recent literature, it is now clear that prokaryotes are capable of glycosylating proteins. In general, prokaryotes are deprived of the cellular organelles required for glycosylation. In prokaryotes many different glycoprotein structures have been observed that display much more variation than that observed in eukaryotes. Besides following similar mechanisms in the process of glycosylation, prokaryotes have also been shown to use mechanisms that are different from those found in eukaryotes. The knowledge pertaining to the functional aspects of prokaryotic glycoproteins is rather scarce. This review summarizes developments and understanding relating to characteristics, synthesis, and functions of prokaryotic glycoproteins. An extensive summary of glycosylation that has been reported to occur in bacteria has also been tabulated. Various possible applications of these diverse biomolecules in biotechnology, vaccine development, pharmaceutics and diagnostics are also touched upon.

Comparison of disc diffusion & E test methods with agar dilution for antimicrobial susceptibility testing of Haemophilus influenzae

BACKGROUND & OBJECTIVES

Reliable methods of detection of antimicrobial resistance are of paramount importance in the treatment and management of infections caused by Haemophilus influenzae. The objective of the present study was to compare and evaluate the performance of disc diffusion and E test (Epsilometer test) with agar dilution method for antimicrobial susceptibility testing of H. influenzae.

METHODS

A total of 46 isolates of H. influenzae from various invasive sites were included as test strains. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method for ampicillin, chloramphenicol, trimethoprim-sulphamethoxazole (TMP-SMZ) and cefotaxime. Minimum Inhibitory Concentration (MIC) determination was performed by E test and agar dilution for the same set of antimicrobials. All tests were performed on Haemophilus test medium (HTM).

RESULTS

Disc diffusion showed a very major (2%) and minor (4%) interpretative error with TMP-SMZ and minor interpretative errors to ampicillin (13%) and chloramphenicol (24%) when compared to agar dilution method. E test produced only minor interpretative errors to chloramphenicol (7%) and TMP-SMZ (2%) and no interpretative errors with ampicillin and cefotaxime as against agar dilution. E test showed good agreement with agar dilution for each of the antimicrobial tested.

INTERPRETATION & CONCLUSION

Disc diffusion test may be used as a preliminary screen for susceptibility testing of H. influenzae. E test is simple, easy to perform and a reliable method for determination of resistance in H. influenzae. However its cost and limited availability in India may limit its use. The reference agar dilution method can be used reliably in routine susceptibility testing of H. influenzae.

Comparison of IgM capture ELISA with a commercial rapid immunochromatographic card test & IgM microwell ELISA for the detection of antibodies to dengue viruses

BACKGROUND & OBJECTIVES

There is a need for a reliable test for the early diagnosis of dengue fever (DF), which is now active in many parts of India especially in the post monsoon months. This study evaluated two commercial tests with an assay available from a national laboratory in India to obtain information and to make a comparison among the three tests as to which will be the most suited for the detection of IgM antibodies to dengue virus.

METHODS

An IgM capture ELISA (National Institute of Virology, Pune, India) was compared with two commercial tests, the PanBio Rapid Immunochromatographic Card Test (Brisbane, Australia) and the PanBio Microwell IgM ELISA for the detection of IgM antibodies to dengue virus. We tested 154 samples from individuals with febrile illnesses having DF--like symptoms.

RESULTS

The NIV IgM capture ELISA (MAC-ELISA) showed a high positivity rate (38.9%) as compared to the PanBio Rapid (22.7%) and the PanBio IgM ELISA (20.7%). The true prevalence of disease, sensitivity and specificity of the three tests were estimated using 2LC latent class models using expectation-maximization (EM) algorithm. The NIV MAC-ELISA showed a high sensitivity (96%) as compared to PanBio Rapid (73%) and PanBio IgM ELISA (72%). A subset of 68 samples (of the 154 tested) were analyzed by the NIV MAC-ELISA for IgM antibodies additionally to Japanese encephalitis (JE) and West Nile (WN) of which 31 samples showed positivity to either one, two or all three flaviviruses. Out of the 8 samples which were positive for dengue IgM alone by the NIV MAC-ELISA, only 2 (25%) each were picked up by the other 2 tests. While out of 7 samples positive for IgM to all three flaviviruses IgM by the NIV MAC-ELISA, 5 (71%) were picked up by the other 2 tests. Of the 5 that were picked up by the PanBio tests, 3 had the highest absorbance values to WN by the NIV MAC-ELISA, indicating cross reactivity by PanBio tests.

INTERPRETATION & CONCLUSION

The MAC-ELISA though a 3 day procedure, would be a valuable screening test for the detection of IgM to dengue in routine diagnostic laboratories because of its high sensitivity and specificity rates. The test uses specific viral antigens to detect IgM antibodies not only to dengue but also to JE and West Nile as a result of which IgM antibodies to all the 3 commonly encountered flaviviruses can be detected in a single run. It also has the advantage in that depending on the strength of the antibody units obtained to a specific flaviviral antigen, presumptive diagnosis as to which particular arboviral infection has occurred can be made in conjunction with clinical presentation.

Sugar non-specific endonucleases

Sugar non-specific endonucleases are multifunctional enzymes and are widespread in distribution. Apart from nutrition, they have also been implicated in cellular functions like replication, recombination and repair. Their ability to recognize different DNA structures has also been exploited for the determination of nucleic acid structure. Although more than 30 non-specific endonucleases have been isolated to date, very little information is available regarding their structure-function correlations except that of staphylococcal and Serratia nucleases. However, during the past few years, the primary structure, nature of the active site based on sequence homology, and the probable mechanism of action have been postulated for some of the enzymes. This review describes the purification, characteristics, biological role and applications of sugar non-specific endonucleases.

Risk factors for post-transplant tuberculosis

BACKGROUND

Post-transplant tuberculosis (post-TxTB) occurs in 12 to 20% of patients in India and results in the death of 20 to 25% of those patients. Prospective studies on post-TxTB are few.

METHODS

Renal allograft recipients were studied prospectively for 3.1 (0 to 13.9) median (range) years for incidence, manifestations, risk factors, and prognosis for post-TxTB. Kaplan-Meier analysis was used to study the survival rates. The extended Cox proportional model for time-dependent covariates was used to measure the risk factors when the hazard was nonuniform.

RESULTS

Of the 1414 patients considered for inclusion, multiple-transplant subjects (N = 37) and patients who developed pre-transplant TB (pre-TxTB; N = 126) were excluded from the study. The prevalence of post-TxTB was 13.3% (N = 166). The risk of post-TxTB when on cyclosporine (CsA) therapy was 2.5 (P = 0.0311) and 1.9 (P = 0.0430) times at < or =6 and < or =12 months, respectively, compared with patients on prednisolone plus azathioprine (PRED + AZA). The risk of post-TxTB in the presence of diabetes mellitus, chronic liver disease, and other co-existing infections [including deep mycoses, cytomegalovirus (CMV), Pneumocystis carinii pneumonia (PCP), nocardia] was 2.2 (P = 0.0011), 1.7 (P = 0.0010) and 2.4 (P < 0.0001) times, respectively. Of the 166 patients with post-TxTB, 53 patients died, and of those deaths, 17 (32%) were due to post-TxTB; 11 (65%) of the 17 had co-existing infections. The factors associated with death were HLA mismatches, PRED + AZA immunosuppression, pre- and post-TxTB, diabetes mellitus, post-transplant diabetes (PTDM), and other co-existing infections. The extended Cox model for death as the outcome variable showed the following to be significant risk factors: post-TxTB> 2 years (P = 0.0036), chronic liver disease> 6 years (P = 0.0457), PTDM> 5 years (P = 0.0729), diabetes mellitus (P = 0.0091), human lymphocyte antigen match < or =1 antigen (P = 0.0134), two to three antigens (P = 0.0448), and the presence of other co-existing infections (P < 0.0001).

CONCLUSIONS

Cyclosporine therapy is associated with early post-TxTB. Diabetes mellitus and chronic liver disease are risk factors for post-TxTB. The occurrence of both pre-TxTB and post-TxTB (>2 years) along with hyperglycemia, liver disease, and other co-existing infections are important risk factors for death.

Viscoelasticity of dilute solutions of semiflexible polymers

We show using Brownian dynamics simulations and theory how the shear relaxation modulus G(t) of dilute solutions of relatively stiff semiflexible polymers differs qualitatively from that of rigid rods. For chains shorter than their persistence length, G(t) exhibits three time regimes: At very early times, when the longitudinal deformation is affine, G(t) approximately t(-3/4). Over a broad intermediate regime, during which the chain length relaxes, G(t) approximately t(-5/4). At long times, G(t) mimics that of rigid rods. A model of the polymer as an effectively extensible rod with a frequency dependent elastic modulus B(omega) approximately ((i)omega)(3/4) quantitatively describes G(t) throughout the first two regimes.

Nucleotide sequence analysis of varicella-zoster virus glycoprotein E epitope coding regions

Varicella-zoster virus (VZV) glycoprotein E [gE] contains 623 amino acid residues. Fifty percent of the gE gene, codons 39 to 344 that encompasses two epitope coding regions e1 and c1, was sequenced and analyzed for variation among the 30 VZV isolates. A total of eleven isolates showed variance when compared with Dumas VZV strain sequence through base substitutions, with two isolates showing an amino acid change of tryptophan to arginine outside the coding regions of the epitopes e1 and c1 that are recognized by monoclonal antibodies 4F9 and c1, respectively. The results suggest that these epitopes were stable in the various VZV isolates. Thus, VZV glycoproteins with conserved epitopes are suitable candidates for both primary and booster vaccines.

Ribonuclease Rs from Rhizopus stolonifer: lowering of optimum temperature in the presence of urea

RNase Rs showed an approx. 2-fold increase in its activity when incubated in the presence of 2 M urea at 37 degrees C. The increase in its activity, in the presence of urea, was comparable to the activity at its optimum temperature, i.e. 45 degrees C. Compared to the native enzyme at 37 degrees C, the K(m) and V(max) of RNase Rs at 45 degrees C and in the presence of 2 M urea at 37 degrees C showed an increase while k(cat)/K(m) decreased. Arrhenius plots in the presence and absence of urea showed a decrease in the activation energy in the presence of urea. Though there was no change in the secondary structure of the protein in the presence of urea, minor changes were observed in the tertiary structure. Hence, the increase in the activity of RNase Rs, in the presence of 2 M urea at 37 degrees C, is due to the lowering of the activation energy as a result of changes in the microenvironment of the active site.

Pathology of the diffuse variant of supravalvar aortic stenosis

Supravalvar aortic stenosis is a rare congenital heart anomaly, producing left ventricular outflow tract obstruction. Of the two anatomic variants that have been described, diffuse type is the rarest. We report five such cases in children between two months and nine years of age. None had features of Williams syndrome. The entire aorta was involved in three cases, with abdominal aortic coarctation in two cases. Stenosis was mainly due to involvement of the media, which showed smooth muscle hypertrophy, abnormal elastic fibers, and mild collagenization. Predominant intimal change was seen in one case. Pulmonary, coronary, arch, renal, and common iliac arteries were also involved.

Pre-transplant risk factors for renal allograft dysfunction at one year in Indian patients

BACKGROUND

Only a few patients with end-stage renal disease in the Indian subcontinent receive optimal treatment. Of these only a minority can afford a second renal transplant. Awareness of modifiable pre-transplant risk factors that influence allograft function is crucial before embarking on the first transplant. There are no reports from the Asian subcontinent describing the pre-transplant risk factors.

METHODS

We studied the effect of donor age, gender, and relation with the recipient, patient age, gender, HLA matching, native kidney disease and immunosuppression on one-year allograft function using data from 1177 consecutive primary living related donor renal transplants at the Christian Medical College Hospital, Vellore. We performed a univariate followed by a multivariate analysis using a logistic regression model to calculate the odds ratio for the effect of the above factors on two levels of graft function (serum creatinine > 1.4 mg/dl and > 2 mg/dl) at one year.

RESULTS

On univariate analysis, older donors, women donors, mother being the donor, men recipients, < 1 HLA antigen match, cyclosporine-based immunosuppression and patient age between 16 and 40 years were associated with serum creatinine levels > 1.4 mg/dl at one year. Multivariate analysis showed that donor-related factors, namely mother as donor, older donors, and a < or = 1 HLA antigen match, were risk factors for graft dysfunction (serum creatinine level > 1.4 mg/dl) at one year. Recipient-related risk factors were male patients and those between the age of 16 and 40 years.

CONCLUSION

In patients undergoing living related donor renal transplants from large extended families, a younger haplomatched donor, for instance, a brother, is a better choice than an older haplomatched donor, for instance, the mother, particularly in young male recipients at a higher risk of renal dysfunction.

Clinical manifestations and survival pattern of Wilson's disease

BACKGROUND

Wilson's disease usually presents in childhood. Early recognition and treatment is crucial to retard the progression of this disease, which can be debilitating, if not fatal. We analysed the clinical manifestations and survival pattern of patients admitted at our centre from 1993 to 1996.

METHODS

Hospital records of patients were reviewed to obtain the clinical manifestations. The survival status of patients was determined by a prospective follow up. The Kaplan-Meier survival curve and univariate Cox proportional hazards model were used to determine the survival pattern and risk for death in Wilson's disease.

RESULTS

A total of 60 patients were studied. The median age at onset of symptoms was 12 years (range 5-52 years). The log rank test showed a significant difference in the mean (SD) survival between patients who presented with hepatic [87.36 (15.26) months] and neurological symptoms [114.33 (9.14) months]. Cox proportional hazards analysis showed a hazard ratio of 4.9 for patients with a hepatic presentation compared to those with neurological presentation.

CONCLUSION

The presentation of Wilson's disease is not limited to the paediatric age group. Patients with a hepatic presentation had a five-fold higher risk of mortality when compared to those with a neurological presentation.

Purification and characterization of the single-strand-specific and guanylic-acid-preferential deoxyribonuclease activity of the extracellular nuclease from Basidiobolus haptosporus

An extracellular nuclease from Basidiobolus haptosporus (designated as nuclease Bh1) was purified to homogeneity by ammonium sulfate precipitation, heat treatment, negative adsorption on DEAE-cellulose, and chromatography on phenyl-Sepharose followed by FPLC on phenyl-Superose. The overall yield was 26%. The Mr of the purified enzyme, determined by gel filtration, was 41 000 whereas by SDS/PAGE (after deglycosylation) it was 30 000. It is a glycoprotein with a pI of 6.8. The optimum pH and temperature for DNA hydrolysis were 8. 5 and 60 degrees C, respectively. Nuclease Bh1 is a metalloprotein but has no obligate requirement for metal ions to be active, nor is its activity stimulated in the presence of metal ions. The enzyme was inhibited by Zn2+, Ag2+, Hg2+, Fe3+ and Al3+, inorganic phosphate, pyrophosphate, dithiothreitol, 2-mercaptoethanol, NaCl and KCl. It was stable to high concentrations of organic solvents and urea but susceptible to low concentrations of SDS and guanidine hydrochloride. Nuclease Bh1 is a multifunctional enzyme and its substrate specificity is in the order of ssDNA approximately 3'AMP >> RNA > dsDNA. Studies on its mode of action showed that it cleaved supercoiled pUC 18 DNA and phage M13 DNA, endonucleolytically, generating single base nicks. The enzyme hydrolyzed DNA with preferential liberation of 5'dGMP, suggesting it to be a guanylic acid preferential endoexonuclease. 5'dGMP, the end product of hydrolysis, was a competitive inhibitor of the enzyme. The absence of 5'dCMP as a hydrolytic product, coupled with the resistance of (dC)10 and deoxyribodinucleoside monophosphates having cytosine either at the 3' or the 5' end, indicates that C-linkages are resistant to cleavage by nuclease Bh1.

Stability of a varicella-zoster virus glycoprotein E epitope

The epitope stability of a varicella-zoster virus (VZV) glycoprotein E (gE) was analyzed with monoclonal antibodies (mAbs) in cells infected with different passages of various VZV strains and isolates. The gE-specific mAbs recognized same antigenic sites (epitopes) in VZV isolates with various passage history. All VZV strains and virus-isolates reacted with an anti-gE monoclonal antibody by immunoprecipitation, or indirect fluorescent antibody staining test. Sera from VZV seropositive individuals reacted with a truncated VZV gE glycoprotein, designated TgpI-511. Also, human mononuclear cells (MNCs) stimulated with TgpI-511 glycoprotein were shown to produce VZV-specific antibodies in vitro. The results demonstrated the stability of these gE epitopes tested in this study in TgpI-511 and among the VZV-isolates obtained from different passages. These results also suggest that VZV glycoproteins as well as live attenuated or killed varicella vaccines containing these epitopes could be used as therapeutic booster vaccines in adults and the elderly to prevent zoster.

Extracellular nuclease from Rhizopus stolonifer: purification and characteristics of - single strand preferential - deoxyribonuclease activity

An extracellular nuclease from Rhizopus stolonifer (designated as nuclease Rsn) was purified to homogeneity by chromatography on DEAE-cellulose followed by Blue Sepharose. The M(r) of the purified enzyme determined by native PAGE was 67¿ omitted¿000 and it is a tetramer and each protomer consists of two unidentical subunits of M(r) 21¿ omitted¿000 and 13¿ omitted¿000. It is an acidic protein with a pI of 4.2 and is not a glycoprotein. The purified enzyme showed an obligate requirement of divalent cations like Mg(2+), Mn(2+) and Co(2+) for its activity but is not a metalloprotein. The optimum pH of the enzyme was 7.0 and was not influenced by the type of metal ion used. Although, the optimum temperature of the enzyme for single stranded (ss) DNA hydrolysis in presence of all three metal ions and for double stranded (ds) DNA hydrolysis in presence of Mg(2+) was 40 degrees C, it showed higher optimum temperature (45 degrees C) for dsDNA hydrolysis in presence of Mn(2+) and Co(2+). Nuclease Rsn was inhibited by divalent cations like Zn(2+), Cu(2+) and Hg(2+), inorganic phosphate and pyrophosphate, low concentrations of SDS, guanidine hydrochloride and urea, organic solvents like dimethyl sulphoxide, dimethyl formamide and formamide but not by 3'- or 5'-mononucleotides. The studies on mode and mechanism of action showed that nuclease Rsn is an endonuclease and cleaves dsDNA through a single hit mechanism. The end products of both ssDNA and dsDNA hydrolysis were predominantly oligonucleotides ending in 3'-hydroxyl and 5'-phosphoryl termini. Moreover, the type of metal ion used did not influence the mode and mechanism of action of the enzyme.

Active site characterization of RNase Rs from Rhizopus stolonifer: involvement of histidine and lysine in catalysis and carboxylate in substrate binding

Chemical modification studies on purified RNase Rs revealed the involvement of a single histidine, lysine and carboxylate residue in the catalytic activity of the enzyme. RNA could not protect the enzyme against DEP- and TNBS-mediated inactivation whereas, substrate protection was observed in case of EDAC-mediated inactivation of the enzyme. K(m) and k(cat) values of the partially inactivated enzyme samples suggested that while histidine and lysine are involved in catalysis, carboxylate is involved in substrate binding. Active site nature of RNase Rs suggests that the inability of the enzyme to readily convert 2',3'-cyclic nucleotides to 3'-mononucleotides is probably due to the absence of catalytically active second histidine residue.

Extracellular deoxyribonuclease production by a thermophile, Streptomyces thermonitrificans

A thermophilic bacterial strain, Streptomyces thermonitrificans, produced high levels of extracellular deoxyribonuclease (DNase) when grown on NBG medium (containing 1% peptone, 0.3% beef extract, 1% glucose and 0.5% NaCl). Maximum DNase activity (140 U x ml(-1)) was obtained, in 24 h, when the culture was grown on modified NBG medium (containing 1.3% beef extract, 1% glucose, 0.5% NaCl and 50 microM Mn2+ at 45 degrees C. The crude enzyme showed higher activity on native DNA than on sonicated and heat denatured DNA. Moreover, addition of Mn2+ in the assay mixture resulted in a significant stimulation (10-15 fold) of the enzyme activity.

Infection-derived Enterococcus faecalis strains are enriched in esp, a gene encoding a novel surface protein

We report the identification of a new cell wall-associated protein of Enterococcus faecalis. Studies on the distribution of the gene encoding this novel surface protein, Esp, reveal a significant (P < 0.001) enrichment in infection-derived E. faecalis isolates. Interestingly, the esp gene was not identified in any of 34 clinical E. faecium isolates or in 4 other less pathogenic enterococcal species tested. Analysis of the structural gene among various E. faecalis isolates reveals the existence of alternate forms of expression of the Esp protein. The deduced primary structure of the Esp protein from strain MMH594, inferred to be 1,873 amino acids (aa) with a predicted mass of approximately 202 kDa, reveals a core region consisting of repeat units that make up 50% of the protein. Esp bears global organizational similarity to the Rib and C alpha proteins of group B streptococci. Identity among Esp, Rib, and C alpha proteins is strikingly localized to a stretch of 13 aa within repeats of similar length. The high degree of conservation of this 13-residue sequence suggests that it plays an important role in the natural selection for this trait among infection-derived E. faecalis and group B streptococcal isolates.

Extracellular ribonuclease from Rhizopus stolonifer: characteristics of an atypical--guanylic acid preferential--enzyme from ribonuclease T2 family

An extracellular ribonuclease from Rhizopus stolonifer (designated as RNase Rs) was purified to homogeneity by chromatography on DEAE-cellulose followed by CM-cellulose. The Mr of the purified enzyme determined by gel filtration and SDS-PAGE is 25,000 and 28,200, respectively. RNase Rs is a glycoprotein and contains 10.5% neutral sugar. It is an acidic protein with a pI of 5.0 and has a blocked N-terminus. The optimum pH and temperature are 5.5 and 45 degrees C, respectively. RNase Rs shows high stability between pH 6.0-10.0. Divalent cations like Zn2+, Hg2+ and Cu2+ inhibit the enzyme activity whereas, mononucleotides does not have any significant effect. The enzyme cleaves RNA to 3'-mononucleotides via 2',3'-cyclic nucleotides, with preferential liberation of 2',3'-cyclic GMP, suggesting that RNase Rs is a guanylic acid preferential cyclizing RNase. Moreover, cyclic nucleotides generated are highly resistant to further hydrolysis.

Modeling accident frequencies as zero-altered probability processes: an empirical inquiry

This paper presents an empirical inquiry into the applicability of zero-altered counting processes to roadway section accident frequencies. The intent of such a counting process is to distinguish sections of roadway that are truly safe (near zero-accident likelihood) from those that are unsafe but happen to have zero accidents observed during the period of observation (e.g. one year). Traditional applications of Poisson and negative binomial accident frequency models do not account for this distinction and thus can produce biased coefficient estimates because of the preponderance of zero-accident observations. Zero-altered probability processes such as the zero-inflated Poisson (ZIP) and zero-inflated negative binomial (ZINB) distributions are examined and proposed for accident frequencies by roadway functional class and geographic location. The findings show that the ZIP structure models are promising and have great flexibility in uncovering processes affecting accident frequencies on roadway sections observed with zero accidents and those with observed accident occurrences. This flexibility allows highway engineers to better isolate design factors that contribute to accident occurrence and also provides additional insight into variables that determine the relative accident likelihoods of safe versus unsafe roadways. The generic nature of the models and the relatively good power of the Vuong specification test used in the non-nested hypotheses of model specifications offers roadway designers the potential to develop a global family of models for accident frequency prediction that can be embedded in a larger safety management system.

Chromosomal localization of a human mucin gene (MUC8) and cloning of the cDNA corresponding to the carboxy terminus

A partial cDNA (pAM1) encoding a major airway mucin glycoprotein with novel tandem repetitive sequence has recently been cloned (Shankar, V., M. S. Gilmore, R. C. Elkins, and G. P. Sachdev. 1994. Biochem. J. 300:295-298). In this article, we report additional new sequence derived by 3'-rapid amplification of cDNA ends technique. The sequence corresponds to a stop codon, 3'-untranslated region of 458 bp, a polyadenylation signal, and poly A+ tail, and represents the extreme carboxy terminus of MUC8. A plasmid construct (pAM3) in pBluescript was generated by in-frame ligation of pAM1 to the 479-bp 3'UTR of MUC8. A 5'-end 325-bp fragment of this cDNA subcloned into the protein fusion and expression vector pET28b(+) was used to generate fusion protein under the control of T7 promoter. The purified fusion protein as well as synthetic peptide corresponding to the MUC8 repeat sequence (TSCPRPLQEGTPGS) were used to raise polyclonal antibodies in rabbits. The antiserum to the fusion protein and to the synthetic peptide reacted with the deglycosylated major tracheobronchial mucin. Immunohistochemical studies using the above antibodies localized the MUC8 protein product to submucosal glands in human tracheal epithelium. Furthermore, the gene from which this cDNA is derived, was mapped to chromosome 12 using DNA from a panel of human-mouse somatic cell hybrids. Fluorescence in situ hybridization was used to assign the regional localization to 12q24.3. Since the eight known human mucin genes map to other chromosomes, we have named this gene MUC8, in accordance with mucin gene nomenclature.

A recombinant vaccinia-rabies virus in the immunocompromised host: oral innocuity, progressive parenteral infection, and therapeutics

With the emergence of raccoons (Procyon lotor) as the primary rabies reservoir in the United States of America, a recombinant vaccinia-rabies glycoprotein (V-RG) virus vaccine was developed that protected raccoons by the oral route from rabies infection. Despite extensive laboratory evaluation, vaccine safety concerns remained about free-choice distribution for wildlife rabies control. In this study, the oral innocuity of V-RG virus was demonstrated in immunodeficient mice but parenteral exposure resulted in systemic and progressive infection, albeit significantly abrogated in severity in comparison to vaccinia virus. Treatment with vaccinia immune globulin and hydroxyphosphonylmethoxy-propyl-cytosine resulted in significantly longer survival and minimized V-RG viral gross lesions.

Statistical analysis of accident severity on rural freeways

The growing concern about the possible safety-related impacts of Intelligent Transportation Systems (ITS) has focused attention on the need to develop new statistical approaches to predict accident severity. This paper presents a nested logit formulation as a means for determining accident severity given that an accident has occurred. Four levels of severity are considered: (1) property damage only, (2) possible injury, (3) evident injury, and (4) disabling injury or fatality. Using 5-year accident data from a 61 km section of rural interstate in Washington State (which has been selected as an ITS demonstration site), we estimate a nested logit model of accident severity. The estimation results provide valuable evidence on the effect that environmental conditions, highway design, accident type, driver characteristics and vehicle attributes have on accident severity. Our findings show that the nested logit formulation is a promising approach to evaluate the impact that ITS or other safety-related countermeasures may have on accident severities.

Guillain Barre syndrome-electrodiagnostic features and therapeutic observations

Thirty seven patients with Guillain Barre syndrome were studied. The most common electrophysiologic abnormalities were delayed or absent Median nerve F wave (93.3%), increase in posterior tibial nerve distal latency (91.9%) and delayed or absent posterior tibial nerve F waves (83.9%). Slowing of nerve conduction was associated with the F wave abnormality and distal latency prolongation in most cases. There was no definite relationship between the results of electrophysiological studies and the clinical grade. 15 patients were treated with steroids, 10 with plasmapheresis, 8 with both steroids and plasmapheresis and 3 with immunoglobulins. There was a greater degree of improvement in patients treated with plasmapheresis.

Opioids contribute to hypoxia-induced pial artery dilation through activation of ATP-sensitive K+ channels

It has been previously observed that hypoxia increases cerebrospinal fluid (CSF) methionine enkephalin and leucine enkephalin levels, and these opioids contribute to hypoxia-induced pial artery vasodilation. The present study was designed to investigate whether the activation of ATP-sensitive K+ channels (KATP) mediates the contribution of opioids to the hypoxia-induced pial artery dilation. The closed-cranial window technique was used to measure pial diameter in newborn pigs. Glibenclamide (10(-6) M), a KATP inhibitor, attenuated the dilation resulting from moderate and severe hypoxia [23 +/- 1 and 33 +/- 2% vs. 7 +/- 1 and 18 +/- 2%, respectively, for moderate and severe hypoxia (arterial PO2 approximately 35 and 25 mmHg, respectively) in the absence vs. presence of glibenclamide]. In addition, glibenclamide attenuated the dilation produced by methionine enkephalin (10(-8) and 10(-6) M) (13 +/- 1 vs. 4 +/- 2% and 21 +/- 2 vs. 7 +/- 3%, respectively, for methionine enkephalin in the absence and presence of glibenclamide). Leucine enkephalin-induced dilation was similarly attenuated by glibenclamide. Cromakalim (10(-8) and 10(-6) M), a KATP agonist, produced dilation that was blocked by glibenclamide (12 +/- 1 and 25 +/- 1 vs. 3 +/- 1 and 5 +/- 1% before and after glibenclamide, respectively). These data show that activation of KATP contributes to methionine enkephalin- and leucine enkephalin-induced dilation. Furthermore, these observations suggest that opioids contribute to hypoxia-induced pial artery dilation via KATP activation.

S1 nuclease: immunoaffinity purification and evidence for the proximity of cysteine 25 to the substrate binding site

A simple procedure, involving heat treatment, gel filtration on Sephadex-G 100 followed by chromatography on anti-S1 nuclease antibodies bound to Sepharose, was developed for purification of S1 nuclease to homogeneity with an overall yield of 72%. S1 nuclease was rapidly inactivated, at pH 6.0 and 37 degrees C, in presence of o-phthalaldehyde. Kinetic analysis of o-phthalaldehyde medicated inactivation showed that the reaction followed pseudo-first-order kinetics and the loss of enzyme activity was due to the formation of a single isoindole derivative per molecule of the enzyme. Absorbance and fluorescence spectrophotometric data also gave similar results. The isoindole derivative formation, as a result of o-phthalaldehyde treatment is known to occur through crosslinking of the thiol group of cysteine and the epsilon-amino group of lysine, situated in close proximity in the native enzyme. Since, modification of the only available cysteine residue (Cys25) did not affect the catalytic activity of the enzyme, the o-phthalaldehyde mediated inactivation of S1 nuclease is due to the modification of lysine. Substrates of S1 nuclease, namely ssDNA, RNA, 3'AMP, could protect the enzyme against o-phthalaldehyde mediated inactivation. Moreover, the modified enzyme (having very little catalytic activity) showed a significant decrease in its ability to bind 5'AMP, a competitive inhibitor of S1 nuclease, suggesting that the modification has occurred at the substrate binding site. The above results point towards the presence of cysteine 25 in close proximity to the substrate binding site.

Effect of roadway geometrics and environmental factors on rural freeway accident frequencies

This paper explores the frequency of occurrence of highway accidents on the basis of a multivariate analysis of roadway geometrics (e.g. horizontal and vertical alignments), weather, and other seasonal effects. Based on accident data collected in the field, a negative binomial model of overall accident frequencies is estimated along with models of the frequency of specific accident types. Interactions between weather and geometric variables are proposed as part of the model specifications. The results of the analysis uncover important determinants of accident frequency. By studying the relationship between weather and geometric elements, this paper offers insight into potential measures to counter the adverse effects of weather on highway sections with challenging geometrics.

Do neonates with meconium aspiration syndrome require antibiotics?

A randomized clinical trial was conducted to evaluate the utility of antibiotics in the routine management of Meconium Aspiration Syndrome (MAS). Neonates diagnosed to have MAS were randomly allocated to either the antibiotic group (n = 20) receiving gentamicin for 7 days, or the control group (n = 20), receiving no antibiotic. All infants were given identical supportive care. The two groups were comparable with respect to birth weight, gestation, sex distribution, mode of delivery, Apgar scores, and initial clinical and radiological severity of the illness. Results showed that the mean duration and the severity of respiratory distress at 24 hours and 48 hours were similar in the two groups. No secondary infection was documented in either group. A single death occurred in the antibiotic group. It is concluded that empirical use of antibiotics in the routine management of meconium aspiration syndrome is of no benefit.

Single-strand-specific nucleases

Single-strand-specific nucleases, which act on single-stranded nucleic acids and single-stranded regions in double-stranded nucleic acids, are multifunctional enzymes and are ubiquitous in distribution. They find wide application as analytical tools in molecular biology research, although enzymes such as P1 nuclease are also used for production of flavor enhancers such as 5' IMP and 5' GMP. Because these enzymes are mainly used as analytical tools, very little attention was paid to aspects relating to their structure-function relationships. However, during the last few years considerable developments have taken place in this area. Single-strand-specific nucleases, their purification, characteristics, biological role, and applications have been reviewed.

Biophysical characterization of mucin components HTM-1 and HTM-2 from tracheobronchial secretions of cystic fibrosis patients

Mucins present in the tracheobronchial secretions are responsible for the viscoelastic properties of the mucus. Any changes in the mucin structure may alter the physical properties of mucus and hence its function. Previous studies from this laboratory have reported the isolation and characterization of a major mucin component (HTM-1) and a minor, novel mucin component (HTM-2) from the tracheobronchial secretions of cystic fibrosis (CF) individuals. In the present study, the macromolecular properties of the CF mucin components HTM-1 and HTM-2 were further investigated using biophysical methods. Dynamic light scattering studies showed that CF HTM-1 and HTM-2 had a greater extended structure in buffer containing 0.10 and 0.15 M NaCl than that observed in the presence of 0.03 M NaCl. Also, CF HTM-1 had a compact configuration in the presence of 5 and 10 mM Ca2+, while under similar experimental conditions, the structure of CF HTM-2 was unaffected, indicating differences in the macromolecular properties of CF mucin components. Fluorescent probe binding studies revealed that CF HTM-1 had more hydrophobic probe binding domains than those observed for CF HTM-2. In summary, both biochemical and biophysical characterization suggests structural differences between the CF HTM-1 and HTM-2 components.

A novel human airway mucin cDNA encodes a protein with unique tandem-repeat organization

Highly specific affinity-purified polyclonal antibodies against deglycosylated human tracheobronchial mucin was used to select immunoreactive clones from a Uni-ZAP cDNA expression library prepared from normal human tracheal mRNA. The largest of three positive clones, designated pAM1, which reacted strongly with the polyclonal antibodies, was further characterized. Sequence analyses revealed a partial 941 bp cDNA that encoded a 313-amino-acid polypeptide. Bases 3-892 consisted of imperfect 41-nucleotide tandem repeats (CCAGGAGGGGACACCGGGTTCACGAGCTGCCCACGCCCTCT) that encoded a unique polypeptide with two types of consensus repeats, TSCPRPLQEGTRV and TSCPRPLQEGTPGSRAAHALSRRGHRVHELPTSSPGGDTGF. The overall composition of the deduced amino acid sequence matched that expected for a mucin protein core and is rich in serine, threonine, proline, glycine and alanine (approximately 51%). Northern blots probed with the mucin cDNA exhibited intense polydisperse hybridization bands with RNA isolated from normal human trachea and cystic-fibrosis bronchus. The data indicate that mucin encoded by clone pAM1 represents a unique type of peptide organization which has not been described in mucin cDNAs reported thus far.

Peptide mapping reveals differences in the non-glycosylated domains of cystic fibrosis and normal tracheobronchial mucins

Tracheobronchial mucins from lung mucus secretions of healthy individuals and from patients with cystic fibrosis (CF) were purified according to a protocol established in our laboratory. Following digestion of the purified, reduced-alkylated mucin (free of 118 kDa and 70 kDa components) with trypsin-L-1-tosylamido-2-phenylethyl chloromethyl ketone, three fractions (TR-1, TR-2 and TR-3) were observed upon chromatography on a Superose 6 column using FPLC. TR-1 (glycosylated fraction) contained all of the carbohydrate, while TR-2 and TR-3 fractions had no detectable sugars. Comparison of the amino acid composition of TR-1 fractions from normal and CF individuals revealed no significant differences, while the TR-2 fractions from these mucins showed noticeable differences. Peptide mapping of TR-2 fractions from normal and CF mucins was performed on a C18 reverse phase column using FPLC. The peptide maps of normal mucins were markedly different from CF mucins. A greater number of peptides were seen in the TR-2 fractions of normal mucins when compared to CF mucin TR-2 fractions. In addition, normal TR-2 fractions appeared to be comprised of more hydrophobic peptides when compared to CF TR-2 fractions. These data provide evidence of possible structural differences in the non-glycosylated regions of CF and non-CF mucins, since the TR-2 fractions are essentially derived from the T-domains in the "naked" stretches of the mucin polypeptide backbone.

Preparation, properties and application of Aspergillus oryzae S1 nuclease covalently bound to aminobutyl-Bio-Gel P-2 through its carbohydrate moiety

Purified Aspergillus oryzae S1 nuclease, when covalently coupled to aminobutyl-(AB)-Bio-Gel P-2, via its carbohydrate moiety, retained 40-50% activity of the soluble enzyme. Optimization of coupling conditions showed that the most active immobilized preparations are obtained when 50-60 units of 1 mM periodate-oxidized enzyme are allowed to react with 1 ml (packed volume) of AB-Bio-Gel P-2 at 4 degrees C, in the presence of 20% (v/v) ethylene glycol, for 15 h. Immobilization did not change the pH and temperature optima of the enzyme, but it increased the temperature-stability. Immobilization brought about an approx. 2-fold increase in the Km and a slight decrease in the Vmax. On repeated use, the bound enzyme retained 60-65% of its initial activity after six cycles. Immobilized S1 nuclease could be stored, in a wet state, for more than 45 days without any significant loss in its initial activity. The application of AB-Bio-Gel- and concanavalin A-Sepharose-bound S1 nuclease in removing restriction-endonuclease-generated single-stranded tails in plasmid DNA is demonstrated.