Percutaneous treatment of stone containing calyceal diverticula: Strategies and outcomes from a University teaching hospital in a developing country

INTRODUCTION

There is a dearth of research available on the outcomes, complications, and recurrence rates of the modalities employed in treatment of diverticula after stone clearance by PCNL. We present our experience of various approaches employed in our institute for treatment of caliceal diverticulum after stone clearance by PCNL. We aimed to review the outcomes, complications, and recurrence rates of these procedures which can provide valuable insights into the effectiveness of these techniques in the treatment of stone containing caliceal diverticulum.

METHODS

A retrospective analysis of a prospectively maintained database of patients diagnosed with caliceal diverticular stone was conducted. The primary outcome was the stone-free rate (SFR) at the time of hospital discharge, determined by a combined nephroscopic/fluoroscopic assessment, and the obliteration of the diverticular sac. Secondary outcomes included the evaluation of operative time, duration of hospital stay and postoperative complications.

RESULTS

A total of 53 patients were evaluated. The mean diverticulum size was 23.2 mm, most common location was the superior calyx (30 (56.7%)). Group 1 (diverticular neck treatment + DJ stent) included 27 patients, group 2 (diverticular wall fulguration + PCN) included 18 patients and group 3 (PCN alone) included 8 patients. Mean operating time was highest in group 1 (80 min). Stone clearance was 100% in group 1, 91% in group 2 and 88% in group 3. Obliteration of caliceal diverticulum was highest in group 1 (90%). Mean duration of hospital stay was lowest in group 1 (3.2 days). Overall complications were lowest in group 2 (3/18).

CONCLUSION

PCNL followed by combination of diverticular wall fulguration and PCN or treatment of diverticular neck and DJ stenting is safe and effective in causing diverticular obliteration. Placement of nephrostomy tube alone was not found to be effective in causing diverticular obliteration in our study.

Interaction of Pd and PdCl2 with cellulose: a theoretical investigation

The pyrolytic fragmentation of cellulose in the presence of atomic palladium (Pd) and palladium(II) chloride (PdCl2) has been studied with use of hybrid density functional theory and cellobiose as a model for cellulose. The configuration changes in the host, rearrangement of geometries of the products, and the respective reaction energetics for different fragmentation pathways are analyzed. While Pd is found to undergo insertion at the beta-1,4-linkage oxygen (O1)-carbon (C-1) of the rings, Pd(II) chloride is observed to promote the cleavage of the chain as well as rearrangement of the rings. A detailed mechanism for the formation of levoglucosan from one of the fragments following the interaction with PdCl2 is also highlighted.

Self-stimulated NO reduction and CO oxidation by iron oxide clusters

It is shown that a bare Fe2O3 cluster can oxidize CO to form CO2 and reduce NO to form N2 by undergoing compositional changes between Fe2O2 and Fe2O3 states. Investigations based on density functional theory reveal that the above reactions occur through an interesting sequence. An initial CO or NO adsorbed on the Fe2O3 weakens one of the O-Fe bonds to create a loosely attached O site. A subsequent CO gets oxidized by this O and transforms the cluster to a reduced Fe2O2 that now reduces NO via multiple oxidation and reduction steps that return the cluster to the oxidized Fe2O3 state. It is shown that the small size allows geometrical rearrangements that eliminate reaction barriers, allowing energetics and not barriers to be the primary motor for catalysis. Detailed reaction paths and the corresponding energetics are presented to illustrate the viability of the proposed mechanisms.

Acute and sub-acute effects of 2-butenoic acid-3-(diethoxy phosphinothioyl) methyl ester (RPR-II) on testis of albino rat

Acute and sub-acute toxic effects of a novel phosphorothionate coded as RPR-II on testis of albino rats were studied. In acute study rats received a single dose of 12.3 mg/kg of RPR-II and sacrificed after 24 hr. For sub-acute study 0.58 mg/kg/day was administered orally to rats for 10 and 21 days. Acute exposure of rats to RPR-II brought no change either in the gonadosomatic index (GSI) or in the structure of testis or in the serum levels of testosterone. Testis glutathione (GSH) level and glutathione S-transferase (GST) activity was significantly decreased whereas, acid phosphatase (AcP) levels increased significantly at 24 hr post-treatment. On 7th day (withdrawal period) after the cessation of the treatment the GSH, GST, AcP, and AkP levels reached to near control. The sub-acute study revealed a significant decrease in GSI on 10th and 21st day of the treatment. In contrast, a time-dependent and significant increased in GSH level and GST activity was observed on 100th and 21st day of post-treatment, except GSH level on 10th day, which was declined. Due to RPR-II treatment the testis AcP and alkaline phosphatase (AkP) levels were significant at both 10th and 21st day of medication but AcP levels were increased whereas AkP levels decreased. The histopathological studies on day 10th showed considerable loss of spermatozoids in testis and at 21st day complete derangement of cellular organization was observed. Testosterone levels decreased significantly on 10th day and remained significantly low at 21st day. However, withdrawal studies showed a recovery in testis of rat treated with RPR-II. GST, GSH, GSI, AcP and AkP values recovered, testosterone levels were also well recovered but recovery in testis structure remained at a low profile. The present study suggests that RPR-II may cause testicular toxicity in rats affecting the normal functioning of testis and it also gave some new information in withdrawal studies.

Effects of phosphorothionate on the reproductive system of male rats

Acute and Sub-acute toxic effects of a new pesticide phosphorothionate coded as RPR-V on testis of albino rat were studied. For the acute study, rats received a single dose of 30 mg/kg of RPR-V and sacrificed after 24 hours. For the Subacute study, 1.42 mg/kg/day was administered orally to rats for 10 days and 21 days. Acute exposure of rats to RPR-V brought no change either in the Gonadosomatic Index (GSI) or in the structure of testis or in the serum levels of Testosterone. Similarly, no significant change was observed in the Glutathione S-transferase (GST) activity. But, in testis there was significant increased in the reduced Glutathione (GSH) and Acid Phosphatase (AcP), whereas Alkaline Phosphatase (AkP) levels decreased significantly at 24hr post treatment. On 7th day (withdrawal period) after the cessation of the treatment the GSH, AcP, and AkP levels reached to near control. The sub-acute study revealed a significant post treatment. Due to RPR-V treatment the testis AcP levels increased significantly at 21st day of medication but AkP levels decreased both at 10th and 21st day of post treatment. Histopathological studies showed that after 10th day testis showed considerable loss of spermatozoids and at 21st day complete derangement of cellular organization was observed. Testosterone levels decreased significantly after 10th day and remained significantly low at 21st day. However, withdrawal studies showed a recovery in testis of rat treated with RPR-V. GST, GSH, GSI, AcP and AkP values were recovered, testosterone levels were also recovered but recovery in testis structure remained at a low profile.

LiBF4-mediated C-glycosylation of glycals with allyltrimethylsilane: a facile synthesis of allyl C-glycosylic compounds

The treatment of glycals with allyltrimethylsilane in the presence of lithium tetrafluoroborate in acetonitrile gave the corresponding allyl 2,3-unsaturated C-glycosylic compounds in excellent yields with high anomeric selectivity.

Macromolecular assemblages. Theory and simulation

A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology.

Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins

An all-against-all protein structure comparison using the Combinatorial Extension (CE) algorithm applied to a representative set of PDB structures revealed a gallery of common substructures in proteins (http://cl.sdsc.edu/ce.html). These substructures represent commonly identified folds, domains, or components thereof. Most of the subsequences forming these similar substructures have no significant sequence similarity. We present a method to identify conserved amino acid positions and residue-dependent property clusters within these subsequences starting with structure alignments. Each of the subsequences is aligned to its homologues in SWALL, a nonredundant protein sequence database. The most similar sequences are purged into a common frequency matrix, and weighted homologues of each one of the subsequences are used in scoring for conserved key amino acid positions (CKAAPs). We have set the top 20% of the high-scoring positions in each substructure to be CKAAPs. It is hypothesized that CKAAPs may be responsible for the common folding patterns in either a local or global view of the protein-folding pathway. Where a significant number of structures exist, CKAAPs have also been identified in structure alignments of complete polypeptide chains from the same protein family or superfamily. Evidence to support the presence of CKAAPs comes from other computational approaches and experimental studies of mutation and protein-folding experiments, notably the Paracelsus challenge. Finally, the structural environment of CKAAPs versus non-CKAAPs is examined for solvent accessibility, hydrogen bonding, and secondary structure. The identification of CKAAPs has important implications for protein engineering, fold recognition, modeling, and structure prediction studies and is dependent on the availability of structures and an accurate structure alignment methodology. Proteins 2001;42:148-163.

CKAAPs DB: a conserved key amino acid positions database

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) PROTEINS:, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly-peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

Refolding, structural transition and spermatozoa-binding of recombinant bonnet monkey (Macaca radiata) zona pellucida glycoprotein-C expressed in Escherichia coli

An internal cDNA fragment (978 bp) corresponding to bonnet monkey (Macaca radiata) zona pellucida glycoprotein-C (bmZPC), excluding the N-terminal signal sequence and the C-terminal transmembrane-like domain, was cloned in pQE-30 vector and the protein expressed as inclusion bodies in Escherichia coli. Recombinant bmZPC (r-bmZPC) was solubilized from purified inclusion bodies in the absence of a high concentration of chaotropic agents and was subsequently refolded. Use of a low concentration of urea (2 M) during solubilization of r-bmZPC helped to minimize the extent of protein aggregation during refolding of the recombinant protein, and retain the existing native-like secondary structure that was essential for proper folding. Purified r-bmZPC appeared as a dominant band of 43 kDa on SDS/PAGE and Western blot. Although it lacked carbohydrate moieties, the purified and refolded r-bmZPC bound to the head region of bonnet monkey spermatozoa, confirming the existence of a native-like conformation. CD revealed a maximum at 200 nm and a single broad minimum extending from 209 to 216 nm, indicating the presence of both alpha-helical and beta-sheet conformations in the refolded r-bmZPC. Two different phases of transition were observed by urea-gradient electrophoresis, suggesting the existence of multiple intermediate stages during the unfolding of r-bmZPC. The availability of refolded r-bmZPC will help in elucidating its role during the complex cascade of events during fertilization.

Oral lesions and conditions associated with human immunodeficiency virus infection in 300 south Indian patients

BACKGROUND

Human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) is a major health problem in India. The National AIDS Control Organisation (NACO) of India reports a seropositivity of 25.03 per thousand for the whole country, as of October 1999. In spite of this high prevalence there are very few reports of oral lesions and conditions in Indian HIV/AIDS patients, which are important in early diagnosis and management of these patients.

OBJECTIVE AND SETTING

The present report describes the oral lesions in 300 HIV positive symptomatic patients presenting to us at RAGAS-YRG CARE, a non-governmental organisation in Chennai, South India, over a period of 9 months in 1998.

METHOD

Lesions were diagnosed on clinical appearance using international criteria.

RESULTS

Of the 300 patients 89% had acquired the infection through heterosexual contact. There were 205 males and 95 females, aged from 7 months to 72 years. Forty-seven percent of the patients were in the age group 21-30 years. CD4 counts were ascertained for 105 patients, 64 (62%) had CD4 counts < or = 200. A total of 217 (72%) of the 300 patients had some oral lesion when examined. Gingivitis (47%) and pseudomembranous candidiasis (33%) were the most common oral lesions. The other oral lesions seen were oral mucosal pigmentation (23%), erythematous candidiasis (14%), periodontitis (9%), angular cheilitis (8%), oral ulcers (3%), oral hairy leukoplakia (3%), hyperplastic candidiasis (1%), oral submucous fibrosis (2%) and one case of leukoplakia.

CONCLUSIONS

Oral lesions occur commonly in HIV infection. A comprehensive oral examination may not only suggest HIV disease but may also be useful in monitoring the disease progression. This is a cost-effective procedure, which may be useful in screening large populations in developing countries like India.

Nitric oxide synthase in toxic epidermal necrolysis and Stevens-Johnson syndrome

Toxic epidermal necrolysis and Stevens-Johnson syndrome are severe cutaneous drug reactions of unknown mechanism. Nitric oxide can cause apoptosis and necrosis. The inducible form of nitric oxide synthase generates large amounts of nitric oxide and has been described in human skin. We propose that a large burst of nitric oxide in toxic epidermal necrolysis and Stevens-Johnson syndrome may cause the epidermal apoptosis and necrosis. Skin biopsies were taken from seven patients with actively progressing Stevens-Johnson syndrome or toxic epidermal necrolysis. Expression of inducible nitric oxide synthase was examined by reverse transcription-polymerase chain reaction and by immunoperoxidase staining for inducible nitric oxide synthase protein. Messenger RNA for inducible nitric oxide synthase was detected by reverse transcription-polymerase chain reaction and confirmed by the sequencing of polymerase chain reaction products. Strong staining for inducible nitric oxide synthase was observed in inflammatory cells in the lower epidermis and upper dermis. Diffuse, weaker staining was observed in keratinocytes. Expression of inducible nitric oxide synthase is consistent with the hypothesis that nitric oxide mediates the epidermal necrosis in toxic epidermal necrolysis and provides a potential target for therapeutic intervention.

Analysis and prediction of inter-strand packing distances between beta-sheets of globular proteins

Any two beta-strands belonging to two different beta-sheets in a protein structure are considered to pack interactively if each beta-strand has at least one residue that undergoes a loss of one tenth or more of its solvent contact surface area upon packing. A data set of protein 3-D structures (determined at 2.5 A resolution or better), corresponding to 428 protein chains, contains 1986 non-identical pairs of beta-strands involved in interactive packing. The inter-axial distance between these is significantly correlated to the weighted sum of the volumes of the interacting residues at the packing interface. This correlation can be used to predict the changes in the inter-sheet distances in equivalent beta-sheets in homologous proteins and, therefore, is of value in comparative modelling of proteins.

An iterative structure-assisted approach to sequence alignment and comparative modeling

Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http:/(/)www-cryst.bioc.cam.ac.uk/ approximately homstrad) and protein superfamilies (CAMPASS, http:/(/)www-cryst.bioc.cam.ac.uk/ approximately campass), in which structure-based alignments are analyzed and formatted with the program JOY (http:/(/)www-cryst.bioc.cam.ac.uk/ approximately joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.

Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins

An alpha-helix and a beta-strand are said to be interactively packed if at least one residue in each of the secondary structural elements loses 10% of its solvent accessible contact area on association with the other secondary structural element. An analysis of all such 5,975 nonidentical alpha/beta units in protein structures, defined at < or = 2.5 A resolution, shows that the interaxial distance between the alpha-helix and the beta-strand is linearly correlated with the residue-dependent function, log[(V/nda)/n-int], where V is the volume of amino acid residues in the packing interface, nda is the normalized difference in solvent accessible contact area of the residues in packed and unpacked secondary structural elements, and n-int is the number of residues in the packing interface. The beta-sheet unit (beta u), defined as a pair of adjacent parallel or antiparallel hydrogen-bonded beta-strands, packing with an alpha-helix shows a better correlation between the interaxial distance and log(V/nda) for the residues in the packing interface. This packing relationship is shown to be useful in the prediction of interaxial distances in alpha/beta units using the interacting residue information of equivalent alpha/beta units of homologous proteins. It is, therefore, of value in comparative modeling of protein structures.

Use of propensities of amino acids to the local structural environments to understand effect of substitution mutations on protein stability

Advances in site-directed mutagenesis and other genetic engineering techniques have made it possible to create novel proteins of interest. A challenging aspect of these studies is to understand the effect of substitution mutations on folding and stability of natural proteins. We present an analysis of protein structure data, available from the literature, for which substitution mutations have been made and changes in stability characteristics are reported. Amino acid structural environment parameters have been computed for a set of 304 non-homologous best resolved protein structures. The structural environment parameters were used to calculate each of the 20 amino acid propensities to a given structural environment. The observed increase or decrease in stability upon mutation was found to be correlated with the average residue structural environment propensity of wild-type residue versus mutant residue. The analysis presented here helps identification of less optimally placed residues in a given protein structure, and suggests possible substitution mutations to a residue with higher propensity to the corresponding local structural environment. We propose that such substitution mutations, suggested based on amino acid propensities to local structural environments, should bestow higher stability to the protein structure.

MEICPS: substitution mutations to engineer intracellular protein stability

In MEICPS, results from earlier analyses are utilized to suggest possible substitution point mutations to engineer intracellular stability using a given sequence or structure of the protein.

AVAILABILITY

From bvbreddy@ccmb.ap.nic.in. This program needs data from other software, PSA and SSTRUC, available from sali@tamika.rockefeller.edu and tom@cryst.bioc.cam.ac.uk, respectively.

CONTACT

bvbreddy@ccmb.ap.nic.in

Oral tolerization to adenoviral proteins permits repeated adenovirus-mediated gene therapy in rats with pre-existing immunity to adenoviruses

Exposure to wild-type adenoviruses is common in humans and results in immune response against adenoviruses. The pre-existing antibodies and a strong secondary humoral and cellular immune response would interfere with gene transfer using recombinant adenoviral vectors. To test whether the secondary immune response can be abrogated by oral tolerization to adenoviral antigens, we immunized bilirubin-UDP-glucuronosyltransferase (BUGT)-deficient jaundiced Gunn rats with a recombinant adenovirus (5 x 10(9) pfu/rat) expressing the human UDP-glucouronosyltransferase (BUGT1) gene (Ad-hBUGT). Transgene expression was shown by reduction of mean serum bilirubin levels from 7.0 mg/dL to 2.3 mg/dL in 14 days, which then increased gradually to pretreatment levels in 6 weeks. All recipients developed antibodies (1:2[10]) and cytotoxic lymphocytes against the adenovirus. For oral tolerization, we administered to the immunized rats protein extracts of a recombinant adenovirus type 5 (1-1.5 mg/day) via duodenostomy tubes 10 to 40 days after the initial virus injection; control rats received bovine serum albumin. In rats fed adenoviral proteins and the BSA-fed controls, the antibody titers decreased to 1:2(7) and 1:2(9), respectively, in 70 days. Lymphocytes from the tolerized rats expressed TGF-beta1 upon exposure to antigen-presenting cells primed with adenoviral antigens, whereas IFN-gamma expression was undetectable. In contrast, lymphocytes from the BSA-treated control rats expressed IFN-gamma but not transforming growth factor beta1 (TGF-beta1). Seventy days after the first injection in the orally tolerized rats, but not in the controls, a second Ad-hBUGT injection caused human BUGT1 expression again, reducing serum bilirubin levels to those observed after the first injection. In the tolerized rats, serum antibody titers and anti-adenoviral cytotoxic lymphocyte activities continued to decline despite the second injection, whereas the antibody levels were boosted in the non-tolerized group. This results show that by preventing the secondary booster response, oral tolerization permits repeated adenovirus-directed gene transfer despite the presence of a residual antibody titer from a previous adenoviral exposure.

Forskolin delays the ethanol-induced desensitization of hypothalamic beta-endorphin neurons in primary cultures

Ethanol and its metabolite acetaldehyde have been shown to stimulate immunoreactive beta-endorphin (IR-beta-EP) secretion from hypothalamic neurons in primary cultures. Also, chronic ethanol and acetal-dehyde have been shown to cause the development of tolerance and desensitization of these neurons. In this study, we determined some of the cellular events leading to desensitization of the function of beta-endorphin (beta-EP) secretory neurons. The fetal hypothalamic cells were treated with various doses of ethanol (25 and 50 mM) or acetaldehyde (6.25, 12.5, and 25 mM) for 6 hr or treated with these drugs at 12 hr intervals for 72 hr. Determination of IR-beta-EP concentrations in the media revealed that ethanol increased IR-beta-EP secretion from these cultures for 12 hr, after this period, the cultured cells did not respond to ethanol. Acetaldehyde stimulated IR-beta-EP secretion from this culture for a period of 48 hr, but the IR-beta-EP secretory response to acetaldehyde reduced gradually with time during the first 48-hr period and reached the basal level at 72 hr. The desensitization of beta-EP neurons 12 hr after treatment with alcohol did not seem to be related to the loss of viable cells, because chronic ethanol exposures did not produce any effect on cell viability. However, reduced IR- beta-EP secretory response to acetaldehyde with time was associated with the time-dependent increase in cell death. Pretreatment of cultures with a cAMP analog, forskolin, increased the activity of functional beta-EP neurons and delayed the ethanol desensitization effects on these neurons. Pretreatment of forskolin did not delay the acetaldehyde desensitization of beta-EP neurons, but protected these cells from acetaldehyde toxicity. These results suggest that (i) chronic treatment with ethanol desensitizes beta-EP-secreting neurons due to reduced cellular functions and (ii) chronic acetaldehyde reduces beta-EP neurotransmission due to cell death. Furthermore, data suggest for the first time that cAMP pretreatments delay the ethanol-induced desensitization of opioid neurons and partly protect against the neurotoxic action of acetaldehyde on opioid neurons.

Recognition of promoter DNA by subdomain 4.2 of Escherichia coli sigma 70: a knowledge based model of -35 hexamer interaction with 4.2 helix-turn-helix motif

In Escherichia coli, subdomains 2.4 and 4.2 of the primary transcription factor sigma 70 are the most highly conserved regions and are responsible for the recognition of -10 and -35 promoter elements respectively. Mutational studies provide evidence to this end and indicate that the side chains of subdomain 4.2 make specific contacts with the nucleotides at -35. Subdomain 4.2 is highly conserved among group-1 sigma factors and is strongly homologous to the classical helix-turn-helix (HTH) motif shared by bacteriophage lembda cl, Cro, the CAP protein and other homeodomain proteins, suggesting that sigma factor also belongs to the HTH class of proteins. In this study, a single point mutation of the conserved hydrophobic residue valine at position 576, in the 4.2 subdomain results in a mutant that is transcriptionally inefficient although conformationally similar to wild-type sigma. The mutant sigma, like wild-type, migrates as a 87 kDa protein on SDS gels and has 50% helicity. However, transcription at "extended -10 promoter' by RNA polymerase containing mutant sigma 70-V576G, synthesized appreciable amount of RNA product, when compared with that generated by sigma 70-W434G, a mutation in -10 DNA binding domain. A model of HTH motif for the conserved 20 residue region of 4.2 domain of E. coli sigma 70 as well as its mutant sigma 70-V576G and sigma 70-V576T were constructed based on five other homologous HTH motifs from DNA-protein complexes for which X-ray or NMR structure is available. A B-DNA structure was designed for -35 region using sequence dependent base pair parameters. The modeled HTH structure was docked into the major groove formed by the -35 hexamer DNA using the DNA-recognition rules and amino acid-nucleotide base contact information of homologous DNA-protein complexes. Analysis of the residue contact information of the model was tested and found to have good agreement with the experimental reports.

Structural distribution of dipeptides that are identified to be determinants of intracellular protein stability

The dipeptides that had been previously implicated as determinants of in vivo protein stability (Guruprasad, K., Reddy, B.V.B. and Pandit, M.W., 1990. Protein Eng. 4, 155-161) have been reassessed on a latest data set and about 25% dipeptide combinations (102 dipeptides) were found to play significant role in determining the intracellular protein stability. These were classified as stabilizing dipeptides (Stb), destabilizing dipeptides (Dst) and normal dipeptides (Nor). By different theoretical approaches we have investigated the global localization of these dipeptides in a set of 303 best resolved (< or = 2.0A) non-homologous X-ray defined protein structures. The Dst dipeptides are found to be more of hydrophilic combinations where as Stb dipeptides are more of hydrophobic combinations. We observed a significant difference in overall frequency of occurrence of Stb and Dst dipeptides in different secondary structural regions. The sensitive dipeptides (Stb + Dst) are less in beta-strands and more in coils. A high frequency of occurrence of Stb are observed in the regions closer to the molecular surface compared to the Dst and Nor dipeptides. A significantly high dipole interactions are observed in the Dst dipeptides. The studies indicate that though the Dst dipeptides are more of hydrophilic nature they are localized significantly more in the buried regions of protein structures, on the other hand Stb are more of hydrophobic nature but relatively more accessible to the solvent. These dipeptides therefore increasing sensitivity of the protein to external environment, any alteration in their occurrence in the sequence could increase or decrease intracellular stability of the protein. These observations are useful to select mutations to alter intracellular stability of a given protein and therefore have implications in protein engineering.

Modification of the sialic acid residues of choriogonadotropin affects signal transduction

Human choriogonadotropin (hCG) is a glycoprotein hormone that activates adenylyl cyclase. The carbohydrate moieties of hCG are required for biological activity, but not for binding to the gonadotropin receptors. We modified N-acetylneuraminic acid (NeuAc) on the oligosaccharide moieties of hCG, and determined the effect on its biological activity by measuring hormone-stimulated adenylyl cyclase. Treating hCG with sodium periodate to remove two carbon atoms from NeuAc or quantitatively removing NeuAc from hCG reduced its biological activity by 36% and 50%, respectively. The galactose residues of asialo-hCG were reacted with NeuAc-hydrazone or a hydrazone of the oligosaccharide from the ganglioside GM1 (Gal(beta 1-3)GalNAc(beta 1-4) [NeuAc(alpha 2-3)]Gal(beta 1-4)Glc). The gonadotropin receptor had high affinity for both derivatives, but their biological activity was less than that of hCG. These results suggest that several structural aspects of NeuAc including carbon side chain, an intact ring structure, and the position of NeuAc relative to other carbohydrate residues are important for full biological activity of hCG.

Contextual constraints in the choice of synonymous codons

From EMBL Nucleotide Sequence Database, protein coding sequences of all E. coli and its DNA phages, were extracted using our computer programme. Same programme has been used to form a database of sequence of oligonucleotides of length 18 nucleotides on both sides of each of the 61 codons. From analysis of this database and study of variations in twist parameter (Tw) values, as an indicator of sequence dependent variations in B-DNA helix, a method is developed to fix the codon among the set of synonymous codons. The accuracy of the method was checked on enlarged data set by adding data from more prokaryotes. Our method assign the codon 85-90% times correctly if the selection has to be made between codons having different sequence in terms of R and Y. The accuracy of the method is somewhat lower when choice of the codon has to be made between codons having same codes in terms of R and Y. This study points out that the major factors which decide the choice of a codon from a set of synonymous codons are contextual constraints arising from flanking regions.

Effect of ethanol, propanol, butanol, and catalase enzyme blockers on beta-endorphin secretion from primary cultures of hypothalamic neurons: evidence for a mediatory role of acetaldehyde in ethanol stimulation of beta-endorphin release

Previously, we have shown that low doses of ethanol (12.5-100 mM) and acetaldehyde (12.5-50 microM), but not salsolinol, enhanced immunoreactive beta-endorphin (IR-beta-EP) secretion from fetal hypothalamic neurons in primary culture. In this study, the effects of ethanol, propanol, and butanol, as well as the effect of catalase inhibitors on IR-beta-EP secretion were studied in vitro to determine the role of membrane fluidization and ethanol metabolism on ethanol-induced IR-beta-EP secretion. The primary cultures of fetal hypothalamic neurons were maintained for 8-9 days in chemically defined medium and treated for 5 hr with ethanol (50 mM), propanol (25 and 50 mM), and butanol (25 and 50 mM). Determination of hourly secretion of IR-beta-EP from the cultures revealed that only 50 mM ethanol caused stimulation of IR-beta-EP secretion, whereas propanol and butanol did not alter IR-beta-EP response at any given concentration. Pretreatment of these cultures with the catalase inhibitors, 3-amino-1,2,4-triazole (3-AT; 1, 5, and 10 mM), caused a dose-dependent inhibition of ethanol-stimulated IR-beta-EP secretion, but did not inhibit dibutyryl cAMP (dcAMP)-stimulated IR-beta-EP secretion. Another catalase inhibitor, sodium azide (5 mM), also inhibited ethanol-stimulated IR-beta-EP secretion. Measurement of acetaldehyde production in cultured cells and media after ethanol or dcAMP treatments revealed that cultured cells produce acetaldehyde only after ethanol treatment and at levels of acetaldehyde (8-24 microM) that are known to evoke IR-beta-EP release. The catalase inhibitor 3-AT (10 mM) treatment reduced ethanol-evoked acetaldehyde production.(ABSTRACT TRUNCATED AT 250 WORDS)

A statistical analytical approach to decipher information from biological sequences: application to murine splice-site analysis and prediction

A simple statistical approach for the analysis of biological sequences, such as splice-sites, promoter regions, helices and extended structure forming regions or any other sequence dependent functional entities in proteins, is presented. The approach has been proved useful to develop a method for prediction of such entities in newly available sequences. We first search for invariant sequence features of each functional entity from the experimentally available sequences and identify a set of 'like' sequences with similar sequence features. In the next step, concrete features of sequence entities in terms of occurrences of smaller subsequences are identified at various positions which are used as a knowledge base to select potential functional entities from the identified 'like' sequences. The third step consists of refinement of this pattern learning, statistical improvements of the knowledge base weight matrices, and finally its application to predict functional entities in newly available sequences. Such an analysis is operationally described for murine splice-site predictions. Regions comprising -30 to +30 nucleotides from the splice-junction at the murine splice-sites (donors and acceptors), reported earlier, were analyzed. Invariant sequence-specific features in terms of monomer frequency average were used to identify splice-site-like sequences in the EMBL murine DNA sequence data base. The frequencies of occurrence of mono-, di-, tri- and tetranucleotides in the known splice-sites were studied in comparison with the splice-site-like sequences; the significant differences in their occurrences were extracted as statistical knowledge coded in weight matrices for computer to identify potential splice-sites. The algorithm was refined and a method was developed to predict potential splice-sites in a given murine DNA; the analysis was also extended to human DNA. The success rate of the method to predict correct splice-sites in these species is found to be 80% and 85%, respectively. The major strength of this method lies in reducing significantly the number of false positives which are normally picked up in such analysis.

Cyclic AMP and ethanol interact to control apoptosis and differentiation in hypothalamic beta-endorphin neurons

In this study we have determined the role of cyclic AMP on the function and differentiation of beta-endorphin (beta-EP) neurons in rat fetal hypothalamic cell cultures. Addition of Bt2cAMP or the cAMP elevating agent, forskolin, in cultures, dose and time dependently increased beta-endorphin secretion. The increased beta-EP secretion after Bt2cAMP or forskolin treatment was associated with proopiomelanocortin gene expression, enhanced neurite growth, and increased neuronal viability. Determination of internucleosomal cleavage of DNA by agarose gel electrophoresis revealed that apoptosis occurred in hypothalamic neurons during the first 6-8 days in culture. Addition of Bt2cAMP during this developmental period inhibited DNA degradation in hypothalamic neurons. Furthermore, incubation with various doses of ethanol, which is known to reduce intracellular levels of Bt2cAMP, increased DNA degradation in these cells. Ethanol-induced DNA degradation was blocked by concomitant incubation with Bt2cAMP. Histochemical identification of apoptotic cells following ethanol and Bt2cAMP treatments further revealed that apoptosis occurred in beta-EP neurons during the developmental period, and that ethanol increased and Bt2cAMP reduced apoptotic beta-EP cell numbers. These results suggest that ethanol neurotoxicity on beta-EP neurons during early neuronal differentiation involves an apoptotic process and that the cAMP signaling system plays an important role in controlling apoptosis and differentiation of the beta-EP neuronal system.

Ultrastructural immunolabeling: a unique diagnostic tool in monoclonal light chain-related renal diseases

Ultrastructural labeling can play a key role in the evaluation of morphologic expressions of monoclonal light chain-related renal diseases in cases where light microscopy, electron microscopy, and immunofluorescence data, even when combined, are not definitive in conveying a diagnosis and, in other cases, in clarifying the findings by providing immunomorphologic correlation. The important role of ultrastructural labeling is highlighted by the fact that in some of these cases bone marrow aspirates and biopsy specimens obtained at the time of the evaluation of the renal specimens are often unable to establish unequivocally a diagnosis of plasma cell dyscrasia. This is in part because renal manifestations commonly precede overt diagnostic bone marrow alterations. Overt bone marrow findings and clinical manifestations may be preceded for as long as 16 years by the renal manifestations. Determination or confirmation of monoclonality and detection of early deposition of monotypical light chains before the finding of ultrastructural morphologic correlates (ie, subendothelial, punctate, granular, electron-dense material) represent unique attributes of this technique. The increased sensitivity of ultrastructural immunolabeling compared with other available diagnostic techniques and its exquisite immunomorphologic correlative capabilities result in a comprehensive evaluation. Sixteen monoclonal light chain-related renal disease cases with early, unusual, or equivocal immunomorphologic manifestations that may have not been characterized properly if ultrastructural labeling had not been performed are presented. The crucial role played by ultrastructural labeling in evaluating these cases and establishing an accurate diagnosis is illustrated and emphasized.

Proline-protein interactions: protection of structural and functional integrity of M4 lactate dehydrogenase

A well defined labile isozyme, rabbit muscle M4-lactate dehydrogenase was denatured under freeze-thaw, heat and GuHCl treatment in the presence and absence of proline, and the corresponding structural changes of the enzyme were monitored through fluorescence and CD spectral studies. The data reveal that proline confers protection to the structural integrity of the enzyme, thereby protecting its activity. This was attributed to its property of forming hydrophilic colloids in aqueous media with a hydrophobic backbone interacting with protein. Unlike other osmolytes, proline is proposed to act on the enzyme stability not only by inducing preferential hydration of proteins but also through the interactions of its multimeric hydrophobic backbone with the solvent-accessible hydrophobic regions of the enzyme.

Effect of alcohol, acetaldehyde, and salsolinol on beta-endorphin secretion from the hypothalamic neurons in primary cultures

The effect of ethanol, acetaldehyde, and salsolinol on hypothalamic beta-endorphin secreting neurons is studied by using rat fetal hypothalamic neurons in primary culture. Exposure of these neuronal cells to different concentrations of ethanol (12.5-50 mM) and acetaldehyde (12.5-50 microM) caused a concentration-dependent increase in the secretion of beta-endorphin. Salsolinol (12.5-50 microM) did not cause any significant change in the secretion of beta-endorphin. Ethanol's effect was short-lasting (2 hr). Acetaldehyde's effect on beta-endorphin secretion was greater and longer lasting, as compared with ethanol. Ethanol and salsolinol do not have any effect on cell viability, whereas higher concentrations of acetaldehyde appear to reduce the number of viable cells after 6 hr of treatment. None of the above treatments has any effect on cellular DNA content. These results suggest that ethanol is a potent stimulator of hypothalamic beta-endorphin. These results also show for the first time that ethanol's metabolite acetaldehyde is more potent in stimulating beta-endorphin secretion and may be significant in the ethanol regulated beta-endorphin secretion.

Packing of secondary structural elements in proteins. Analysis and prediction of inter-helix distances

Interacting helix pairs were defined as those in which each member has one residue which undergoes a fractional loss of 0.10 solvent accessible contact area on association. Analysis of 1095 such pairs of helices, selected from the Brookhaven Data Bank, confirms that helix pairs in proteins can pack interactively at all angles with preferential packing observed in the angle intervals (omega), -160 degrees to -140 degrees, -100 degrees to -20 degrees, 10 degrees to 40 degrees, and 50 degrees to 160 degrees. The distance (d) between the helix axes in the contact region of two interactively packed helices is linearly correlated with the volume-dependent function, log(V/nda), of the residues in this region. The correlation is used to predict inter-helix distances in equivalent helix pairs of homologous proteins and is therefore of value in comparative modelling of protein three-dimensional structures.

Electronic, Magnetic, and Geometric Structure of Metallo-Carbohedrenes

The energetics and the electronic, magnetic, and geometric structure of the metallocarbohedrene Ti(8)C(12) have been calculated self-consistently in the density functional formulation. The structure of Ti(8)C(12) is a distorted dodecahedron with a binding energy of 6.1 electron volts per atom. The unusual stability is derived from covalent-like bonding between carbon atoms and between titanium and carbon atoms with no appreciable interaction between titanium atoms. The density of states at the Fermi energy is high and is derived from a strong hybridization between titanium 3d and carbon sp electrons. Titanium sites carry a small magnetic moment of 0.35 Bohr magneton per atom and the cluster is only weakly magnetic.

Effect of chronic insecticide, phosalone, toxicity on haem synthesis and blood gas composition in the rat

The influence of multiple sublethal concentrations of phosalone on whole animal and kidney oxygen consumption, haem synthesis and blood gases of rat, were carried out over a 90 day dosed period. The results indicate the existence of hypoventilation and a hypoxic condition in the animals which lead to the disruption of neuromuscular transmission in respiratory muscles and increase of erythropoiesis and haemoglobin synthesis. The changes were most pronounced when animals were exposed for the 90 day dosed period.

Impact of chronic phosalone toxicity on Bohr factor and oxygen equilibrium curves of rat

The multiple sublethal doses of phosalone induced changes in haemodynamics, maximum absorption spectra, oxygen equilibrium curves (OEC), half saturation tension (P50), degree of interaction (n), pH of blood, Bohr factor and circulatory gases of blood in rat, Rattus norvegicus. The results have obviously shown that increase the activation of pyridoxal phosphate, shift of OEC to right and decrease in the affinity of haemoglobin for oxygen at tissue level.

Impact of chronic phosalone toxicity on erythropoietic activity of fish, Oreochromis mossambicus

Effect of multiple sublethal concentrations of Phosalone on whole animal and kidney oxygen consumption, haematological indices and serum enzymes of freshwater fish, Oreochromis mossambicus, were carried out over a 90 day exposure period. Significant changes were observed which have been indicating that the presence of hypoxic condition in the biosystem, gradual increase in the rate of synthesis of haemoglobin and disruption of liver function during the toxicity of phosalone.

Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence

Statistical analysis of 12 unstable and 32 stable proteins revealed that there are certain dipeptides, the occurrence of which is significantly different in the unstable proteins compared with those in the stable ones. Based on the impact of these dipeptides on the unstable proteins over the stable ones, a weight value of instability is assigned to each of the dipeptides. For a given protein the summation of these weight values normalized to the length of its sequence helps to distinguish between unstable and stable proteins. Results suggest that the in vivo instability of proteins is possibly determined by the order of certain amino acids in its sequence. An attempt is made to correlate metabolic stability of proteins with features of their primary sequence where weight values of instability for a protein of known sequence could thus be used as an index for predicting its stability characteristics.

Testosterone response in arginine vasopressin desensitized immature rat testis

Direct injection of arginine vasopressin into immature rat testis inhibited basal testosterone synthesis. Simultaneous injection of arginine vasopressin with luteinizing hormone, norepinephrine or cholera toxin inhibited these agonists - induced testosterone response. In arginine vasopressin - desensitized testis, cAMP response to luteinizing hormone, norepinephrine and cholera toxin was not disturbed. However, testosterone response to luteinizing hormone, norepinephrine or cholera toxin was drastically reduced in arginine vasopressin-desensitized testis. This shows that the increased cAMP generated by luteinizing hormone, norepinephrine or cholera toxin in arginine vasopressin desensitized testis did not cause increase in steroidogenesis. This could be due to a lesion in steroidogenic pathway beyond cAMP generation caused by arginine vasopressin.

Effects of vanadyl sulphate on ornithine decarboxylase and progesterone levels in the ovary of rat

The effects of vanadyl sulphate in vitro on the levels of ODC activity and progesterone synthesis in ovaries were studied. The levels of ODC in the ovaries were stimulated with high concentration of vanadyl sulphate and at low concentrations there was no change in the levels of ODC activity. On the contrary progesterone levels were stimulated with low concentrations of vanadyl sulphate and were inhibited at higher concentrations. Vanadyl sulphate showed additional stimulation of ODC activity, when it was added with hCG and caused inhibition of hCG induced progesterone biosynthesis. These results show that the effects of vanadyl sulphate on ODC and progesterone are different.

Desensitization of immature rat testicular ornithine decarboxylase to arginine vasopressin

Prior exposure of immature rat testis to arginine vasopressin caused the testis refractory at 24 h in terms of ornithine decarboxylase activity. Arginine vasopressin caused desensitization both in Leydig cells and seminiferous tubules. Arginine vasopressin induced desensitization was found to be both time and dose-dependent. Arginine vasopressin desensitized testis was refractory to luteinizing hormone, follicle stimulating hormone, norepinephrine, dibutyryl cAMP, phorbol-myristate acetate and cholera toxin at 24 h. Arginine vasopressin desensitized testis showed recovery of response to norepinephrine at 48 h after the first injection. On the contrary arginine vasopressin could stimulate ornithine decarboxylase in luteinizing hormone desensitized testis. These results indicate that in arginine vasopressin desensitized testis the block is at post cAMP step which is common to both cAMP dependent and protein kinase C-diacylglycerol system in stimulating testicular ornithine decarboxylase.

Stimulation of testicular ornithine decarboxylase activity by arginine vasopressin

Intratesticular injection with arginine vasopressin caused stimulation of ornithine decarboxylase activity in the testes of immature rats. The increase in ornithine decarboxylase activity in response to arginine vasopressin was dose and time dependent. Maximal stimulation of ornithine decarboxylase activity occurred at 2 h after injection with 0.1 micrograms of arginine vasopressin. It was observed that stimulation of ornithine decarboxylase activity occurred in seminiferous tubules and in Leydig cells of the testis in response to arginine vasopressin.

Contextual constraints on codon pair usage: structural and biological implications

Complementary DNA sequence data of 278 protein coding genes from prokaryotic systems have been analysed at the level of near neighbour codon pairs. Our analysis points out that constraints exist even at the level of near neighbour codon pairs. These constraints are in addition to those which arise due to relative levels of tRNA. Codon pairs, which in the data base have different occurrence values from their expected values, neither have common secondary structure nor do have better stabilization due to high base stacking. Our study points out that there are strong interaction between constituent codons in these codon pairs. These strongly interacting codon pairs, we suggest, are involved in the formation of three dimensional structural elements of cDNA/mRNA and interact with ribosome and thus modulate translation.

A method to locate protein coding sequences in DNA of prokaryotic systems

cDNA sequence data from E. coli phages, for which complete genome sequences are known, have been analysed, From this analysis thirteen triplets have been identified as markers to distinguish protein-coding frames from fortuitous open reading frames. The region of -18 to +18 nucleotides around ATG/GTG, has been analysed and used to identify initiator codons from internal ATG/GTG. With the aid of criteria defined above a method has been developed to locate protein coding sequences by a combination of 'gene search by signal' and 'gene search by content' approaches. Application of this method to prokaryotic systems including those which were not part of our data base indicates that it is quite accurate and general in nature.

Influence of age on motor nerve conduction

Motor nerve conduction velocity (MNCV) has been determined in seventy five normal healthy male subjects in different age groups in Right ulnar and median nerves respectively. It is observed that MNCV decreases in the older age group. Further it is seen that MNCV is less in the distal than in the proximal segment, the results being significant in the median nerve.

Serum lipoproteins in lepromatous leprosy

Serum total cholesterol and the lipoprotein fractions were studied in forty subjects of lepromatous leprosy and age matched controls. The study revealed a significant decrease in serum cholesterol in the disease group as compared to control group. The decrease in cholesterol was 28.76% An alteration in serum lipoprotein fractions was observed in disease group. The beta-lipoprotein fraction showed a significant decrease along with a rise in alpha-lipoprotein fraction. A positive correlation was also observed between total cholesterol and beta-lipoproteins. The significance of the above findings are discussed.

Electrophoretic pattern of proteins in lepromatous leprosy

Serum total proteins and the various protein fractions were studied in fifty cases of lepromatous leprosy and in eleven cases of lepromatous leprosy with lepra reaction. The study revealed a significant increase in serum total proteins in both lepromatous leprosy and lepra reaction groups, when compared with normal healthy subjects. The percentage rise was found to be 14.5% and 22.95% for lepromatous leprosy and lepra reaction respectively. The globulin fraction showed a significant elevation, while albumin showed a decrease. Thus a reversal of A/G ratio was observed in both the disease groups. Alpha-1 and Alpha-2 globulins were found to be significantly increased in both the disease groups. Beta globulins did not reveal any significant alteration. It was interesting to note the presence of an additional globulin fraction in seventeen patients of lepromatous leprosy and two cases of lepra reaction. Gammaglobulin showed a significant rise in lepromatous leprosy (56.16%) and in lepra reaction (60.72%). The significance of the above findings are discussed in the light of available literature.