Mesoblastic Nephroma in a 22 Years Old Woman.

Mesoblastic nephroma is an uncommon renal tumor of infancy and rarely occurs in adults. We report a case of mesoblastic nephroma in adult. A 22-year-old woman, who presented with left flank pain, was found to have a left renal mass by abdominal ultrasonography. Computed tomography revealed a heterogeneous tumor. Left radical nephrectomy was performed. The tumor was a creamy white solid mass. Microscopically, the tumor was composed of spindle cell proliferation. Atypia and mitoses were not identified. Among the tumor cells, there were tubular arranged epithelial elements. The patient was free of recurrence 18 months postoperatively. Mesoblastic nephroma is classified as a benign tumor but recurrence and malignant transformation of this tumor have been reported, so regular postoperative follow up is required.

Platelet Count as a Prognostic Factor in Stage IV Non-Small Cell Lung Cancer.

Increase platelet count can accompany various cancers including lung cancer. This finding has recently been suggested to indicate poor prognosis. In patients with malignancies, thrombocytosis has previously been related disease stage, histological type and survival. In this study, the prevalence of thrombocytosis and the prognostic information provided by platelet count were analyzed in patients with stage IV Non-Small Cell Lung Cancer (NSCLC) with an aim to assess elevated platelet count as a prognostic factor in patients with stage IV NSCLC and to investigate whether there is relationship between thrombocytosis, other clinico-pathologic factors and median survival. This prospective observational study was conducted in National Institute of Cancer Research and Hospital (NICRH), Dhaka, Bangladesh from September 2019 to August 2020. A total of 108 patients were enrolled purposively. Detail history taking, thorough physical examination was done along with relevant investigations. Data were collected by semi structured questionnaire and analysis was done with the help of Statistical Package for Social Science (SPSS), version 21.0. The mean age of the patients was found 56.4±12.2 years with range from 35 to 75 years. Majority (79.6%) patients were male, 52.8% patients came from low income and 36.1% were farmer. Majority (40.7%) were symptomatic; in bed >50.0% of day. Almost two third (59.3%) had <5.0% weight loss. Almost three fourth (69.4%) had squamous cell carcinoma. At the time of first assessment 75(69.4%) patients had normal and 33(30.6%) had elevated platelet count level. Age, sex and histological type were statistically not significant between normal and elevated platelet count level groups. But performance status, weight loss were statistically significant (p<0.05) between two groups. According to univariate analysis, age, performance status at presentation, weight loss more than 10.0% for 3 months and platelet count prior the start of treatment were all significant predictors for the overall survival. In multivariate analysis age, performance status at presentation and initial thrombocytosis were independent prognostic determinants for overall survival. Median survival time was significantly higher for the normal platelet count group and elevated platelet count group (7.5 months versus 5.5 months) respectively (95% CI, 5.5-7.5), p<0.001. The frequency of thrombocytosis in patients with stage-IV NSCLC at first presentation was 30.6% and median survival time in these patients was significantly shorter compared in patients without thrombocytosis. These results concluded that an elevated platelet count could be a useful prognostic factor for survival in patients with stage-IV NSCLC.

Clinical Outcomes in Non-Small-Cell Lung Cancer Patients Treated With EGFR-Tyrosine Kinase Inhibitors and Other Targeted Therapies Based on Tumor Versus Plasma Genomic Profiling.

PURPOSE: To compare clinical outcomes in a cohort of patients with advanced non-small-cell lung cancer (NSCLC) with targetable genomic alterations detected using plasma-based circulating tumor DNA (ctDNA) or tumor-based next-generation sequencing (NGS) assays treated with US Food and Drug Administration-approved therapies at a large academic research cancer center. METHODS: A retrospective review from our MD Anderson GEMINI database identified 2,224 blood samples sent for ctDNA NGS testing from 1971 consecutive patients with a diagnosis of advanced NSCLC. Clinical, treatment, and outcome information were collected, reviewed, and analyzed. RESULTS: Overall, 27% of the ctDNA tests identified at least one targetable mutation and 73% of targetable mutations were EGFR-sensitizing mutations. Among patients treated with first-line epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) therapies, there were no significant differences in progression-free survival of 379 days and 352 days (P value = .41) with treatment based on tissue (n = 40) or ctDNA (n = 40), respectively. Additionally, there were no differences in progression-free survival or objective response rate among those with low (n = 8, 0.01%-0.99%) versus high (n = 16, ≥ 1%) levels of ctDNA of the targetable mutation as measured by variant allele frequency (VAF). Overall, there was excellent testing concordance (n = 217 tests) of > 97%, sensitivity of 91.7%, and specificity of 99.7% between blood-based ctDNA NGS and tissue-based NGS assays. CONCLUSION: There were no significant differences in clinical outcomes among patients treated with approved EGFR-TKIs whose mutations were identified using either tumor- or plasma-based comprehensive profiling and those with very low VAF as compared with high VAF, supporting the use of plasma-based profiling to guide initial TKI use in patients with metastatic EGFR-mutant NSCLC.

Association of COPD with osteoporosis in male smokers: A case control study in a tertiary medical college hospital in Bangladesh.

OBJECTIVES: Chronic obstructive pulmonary disease (COPD) may increase the risk of osteoporosis and resulting fractures can contribute to disability and mortality of patients. We intended to evaluate the frequency of osteoporosis in male smokers with and without COPD and study whether any correlation existed between osteoporosis and COPD. MATERIALS AND METHODS: This case-control study was carried out in the Department of Medicine, Sylhet MAG Osmani Medical College Hospital, Sylhet, Bangladesh between July 2013 and June 2015. Seventy four male smokers with COPD and 66 age-matched male smokers without COPD were enrolled. All individuals underwent Bone Mass Densitometry (BMD) by Dual-Energy X-Ray Absorptiometry (DEXA). RESULTS: COPD and non-COPD groups did not differ regarding age and smoking pack-years. Osteoporosis at femoral neck (48.6% versus 16.7%; p< 0.001) and lumbar spine (68.9% versus 37.9%; p< 0.01) was significantly higher in COPD compared to controls. Osteopenia did not differ significantly. Patients with COPD were 4.5 times more likely to develop osteoporosis than controls after adjusting age, smoking-pack years and BMI (adjusted OR = 4.5; 95% CI = 1.8-11.5). CONCLUSIONS: Osteoporosis is more frequent in male smokers with COPD compared to smokers without COPD. COPD is a risk factor of osteoporosis independent of age, smoking and BMI.

Acute anti-obesity effects of intracerebroventricular 11ß-HSD1 inhibitor administration in diet-induced obese mice.

The hypothalamus is the regulatory centre of both appetite and energy balance and endoplasmic reticulum (ER) stress in the hypothalamus is involved in the pathogenesis of obesity. Recently, inhibition of 11 ß hydroxysteroid dehydrogenase type1 (11ß-HSD1) was reported to have an anti-obesity effect by reducing fat mass. However, the link between the role of 11ß-HSD1 in the hypothalamus and obesity has yet to be determined. In the present study, embryonal primary hypothalamic neurones and high-fat diet (HFD) fed mice were used to investigate the anorexigenic effects of 11ß-HSD1 inhibitors both in vitro and in vivo. In hypothalamic neurones, carbenoxolone (a non selecitve 11ß-HSD inhibitor) alleviated ER stress and ER stress-induced neuropeptide alterations. In HFD mice, i.c.v. administration of carbenoxolone or KR67500 (nonselective and selective 11ß-HSD1 inhibitors, respectively) was associated with less weight gain compared to control mice for 24 hours after treatment, presumably by reducing food intake. Furthermore, glucose regulated protein (Grp78), spliced X-box binding protein (Xbp-1s), c/EBP homologous protein (chop) and ER DnaJ homologue protein (Erdj4) expression was decreased in the hypothalami of mice administrated 11ß-HSD1 inhibitors compared to controls. Conversely, the phosphorylation of protein kinase B (PKB/Akt), signal transducer and activator of transcription 3 (Stat3), mitogen-activated protein kinase (MAPK/ERK) and S6 kinase1 (S6K1) in the hypothalamus was induced more in mice treated using the same regimes. In conclusion, acute 11ß-HSD1 inhibition in the hypothalamus could reduce food intake by decreasing ER stress and increasing insulin, leptin, and mammalian target of rapamycin complex 1 (mTORC1) signalling.

Admission Troponin I and Post Thrombolytic ST-Segment Resolution in Prediction of Early Risk Stratification in ST- Elevation Myocardial Infarction.

The prognostic value of admission troponin I (tnI) levels and the resolution of the ST-segment elevation in ST-elevation myocardial infarction (STEMI) is well established. However, the combination of these two early available markers for predicting the risk of early mortality has not been evaluated yet. This prospective analytical study conducted in the department of Cardiology, Sir Salimullah Medical College and Mitford Hospital, Dhaka and NICVD, Dhaka, Bangladesh from March 2004 to February 2005. We have evaluated 80 patients with streptokinase treated STEMI who had both admission troponin I and ST-monitoring. We used a prospectively defined cut-off value of troponin I of 0.1ng/ml. For ST-segment resolution, a cut-off of 50% measured after 90 minutes was used. Both a troponin I >0.1ng/ml and ST segment resolution <50% was related to higher early mortality; 16.7% vs. 14.3% (p<0.001) and 57.1% vs. 1.7% (p<0.001) respectively. In a multivariate analysis ST-segment resolution was and troponin I showed a strong trend to be independently related to early mortality. The combination of both further improved risk stratification. The early mortality in the group with elevation of troponin I and without ST-segment resolution compared to the group without troponin I elevation and with ST-segment resolution was 55.6% vs. 0%. Both troponin I on admission and ST-segment resolution after 90 minutes are strong predictors of early mortality. The combination of both gives additive early information about prognosis and further improves risk stratification.

Association of Low Level of High Density Lipoprotein cholesterol with Acute Coronary syndrome.

Incidence of coronary artery disease (CAD) is increasing in developing countries in Bangladesh with improvement of socioeconomic status, urbanization, changes of dietary habits and lifestyle. Dyslipidaemia is one of the major contributors increase CAD risk. This study was aimed to find out the association of low level HDL-C with acute coronary syndrome. This cross sectional study was conducted in the department of cardiology, Mymensingh Medical College Hospital, Mymensingh, Bangladesh from August 2009 to May 2010. Sociodemographic characteristics, smoking, hypertension, FBS, serum total cholesterol level, HDL-C, LDL-C, Triglyceride level were important variable considered. A total number of 100 respondents consisted of 50 cases (patient) Group I and 50 healthy people (control) Group II. Investigations included ECG, Troponin-I, FBS and Fasting Lipid Profile. The data was analyzed by computer with the help of SPSS. Chi-square test, T-test, ANOVA test used as test of significance. The mean level in cases of HDL-C 39.3±5.1 and in control level HDL-C 34.2±3.4 statistically significant (p<0.0001). In both group low concentration HDL-C (<40mg/dl) risk for CAD. Un-adjusted odds ratio 95% CI determinants of ACS, HDL-C of OR was 0.2. So, HDL-C is not protective factor. In multivariate logistic regression analysis that adjusted for confounders of HDL-C level (age, sex, smoking, hypertension, TC, LDL-C, TG) associated with ACS. HDL-C was strong predictor of ACS (RR in the highest) compared with lowest quarantile = 0.02; (95% CI=0.003-0.173; P for trend <0.0001). The study reflected that low HDL-C level associated with ACS. Categorization of patients with ACS on the basis HDL-C level may be helpful for risk stratification and management.

Dexamethasone-mediated oncogenicity in vitro and in an animal model of glioblastoma.

OBJECTIVEDexamethasone, a known regulator of mesenchymal programming in glioblastoma (GBM), is routinely used to manage edema in GBM patients. Dexamethasone also activates the expression of genes, such as CEBPB, in GBM stem cells (GSCs). However, the drug's impact on invasion, proliferation, and angiogenesis in GBM remains unclear. To determine whether dexamethasone induces invasion, proliferation, and angiogenesis in GBM, the authors investigated the drug's impact in vitro, in vivo, and in clinical information derived from The Cancer Genome Atlas (TCGA) cohort.METHODSExpression profiles of patients from the TCGA cohort with mesenchymal GBM (n = 155) were compared with patients with proneural GBM by comparative marker selection. To obtain robust data, GSCs with IDH1 wild-type (GSC3) and with IDH1 mutant (GSC6) status were exposed to dexamethasone in vitro and in vivo and analyzed for invasion (Boyden chamber, human-specific nucleolin), proliferation (Ki-67), and angiogenesis (CD31). Ex vivo tumor cells from dexamethasone-treated and control mice were isolated by fluorescence activated cell sorting and profiled using Affymetrix chips for mRNA (HTA 2.0) and microRNAs (miRNA 4.0). A pathway analysis was performed to identify a dexamethasone-regulated gene signature, and its relationship with overall survival (OS) was assessed using Kaplan-Meier analysis in the entire GBM TCGA cohort (n = 520).RESULTSThe mesenchymal subgroup, when compared with the proneural subgroup, had significant upregulation of a dexamethasone-regulated gene network, as well as canonical pathways of proliferation, invasion, and angiogenesis. Dexamethasone-treated GSC3 demonstrated a significant increase in invasion, both in vitro and in vivo, whereas GSC6 demonstrated a modest increase. Furthermore, dexamethasone treatment of both GSC3 and GSC6 lines resulted in significantly elevated cell proliferation and angiogenesis in vivo. Patients with mesenchymal GBM had significant upregulation of dexamethasone-regulated pathways when compared with patients with proneural GBM. A prognostic (p = 0.0007) 33-gene signature was derived from the ex vivo expression profile analyses and used to dichotomize the entire TCGA cohort by high (median OS 12.65 months) or low (median OS 14.91 months) dexamethasone signature.CONCLUSIONSThe authors present evidence that furthers the understanding of the complex effects of dexamethasone on biological characteristics of GBM. The results suggest that the drug increases invasion, proliferation, and angiogenesis in human GSC-derived orthotopic tumors, potentially worsening GBM patients' prognoses. The authors believe that careful investigation is needed to determine how to minimize these deleterious dexamethasone-associated side effects in GBM.

Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.

The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the chi 1 distribution for most side-chains in an alpha-helix showed an absence of the g- conformation and a shift towards the t conformation when compared to the non-alpha/beta structures. The exceptions to this tendency were for short polar side-chains that form hydrogen bonds with the main-chain which prefer g+. Shifts in the chi 1 preferences for residues in the beta-sheet were observed. Other side-chain dihedral angles (chi 2, chi 3, chi 4) were found to be influenced by the main-chain. This paper presents more accurate distributions for the side-chain dihedral angles which were obtained from the increased number of proteins determined to high resolution. The means and standard deviations for chi 1 and chi 2 angles are presented for all residues according to the secondary structure of the main-chain. The means and standard deviations are given for the most popular conformations for side-chains in which chi 3 and chi 4 rotations affect the position of C atoms.

Redefinition of the cleavage sites of DNase I on the nucleosome core particle.

DNase I has been widely used for the footprinting of DNA-protein interactions including analyses of nucleosome core particle (NCP) structure. Our understanding of the relationship between the footprint and the structure of the nucleosome complex comes mainly from digestion studies of NCPs, since they have a well-defined quasi-symmetrical structure and have been widely investigated. However, several recent results suggest that the established consensus of opinion regarding the mode of digestion of NCPs by DNase I may be based on erroneous interpretation of results concerning the relationship between the NCP ends and the dyad axis. Here, we have used reconstituted NCPs with defined ends, bulk NCPs prepared with micrococcal nuclease and molecular modelling to reassess the mode of DNase I digestion. Our results indicate that DNase I cuts the two strands of the nucleosomal DNA independently with an average stagger of 4 nt with the 3'-ends protruding. The previously accepted value of 2 nt stagger is explained by the finding that micrococcal nuclease produces NCPs not with flush ends, but with approximately 1 nt 5'-recessed ends. Furthermore we explain why the DNA stagger is an even and not an odd number of nucleotides. These results are important for studies using DNase I to probe nucleosome structure in complex with other proteins or any DNA-protein complex containing B-form DNA. We also determine the origin of the 10n +/- 5 nt periodicity found in the internucleosomal ladder of DNase I digests of chromatin from various species. The explanation of the 10n +/- 5 nt ladder may have implications for the structure of the 30 nm fibre.

Comparative computer graphics and solution studies of the DNA interaction of substituted anthraquinones based on doxorubicin and mitoxantrone.

1-[[(Diethylamino)ethyl]amino]- and 1,4-, 1,5-, and 1,8-bis[[(diethylamino)ethyl]amino]anthraquinones are shown to intercalate into DNA. Computer graphics modelling of their intercalation into the self-complementary deoxydinucleoside d(CpG) showed differences in binding properties. While the 1-substituted compound can bind from either groove, the 1,8-disubstituted compound binds with both substituents in the major groove. In the low-energy state of the complex with the 1,5-disubstituted compound, this ligand "straddles" the site with a substituent in each groove--to do this, the compound must bind to a non-base-paired region, so inducing base pairing. The 1,4-compound binds from the major groove; "straddling" is also possible if full minimization of deoxydinucleoside geometry is performed. The differences in binding mode and interaction energies are reflected in the affinities of interaction (1,5- greater than 1,4- much greater than 1,8- greater than 1-); also the antiproliferative effects in vitro are in general agreement with this ranking.

Experimental and computer graphics simulation analyses of the DNA interaction of 1,8-bis-(2-diethylaminoethylamino)-anthracene-9,10-dione, a compound modelled on doxorubicin.

The crystal structure of the anthraquinone derivative 1,8-bis-(2-diethylaminoethylamino)-anthracene-9,10-dione has been established. This compound was prepared as a potential DNA-intercalating agent based on the proven intercalators doxorubicin and mitoxantrone. Its DNA-binding properties have been examined experimentally by spectroscopic, thermal denaturation and ccc-DNA unwinding techniques: the results are consistent with an intercalative mode of binding to DNA. Computer graphics stimulation of the intercalative docking of this compound into the self-complementary dimer of d(CpG) has provided a minimum energy geometrical arrangement for the bound drug in the intercalation site comparable to that for proflavine when intercalated into the same d(CpG) model system. Entry of the compound into the site can only occur via the major groove.

Computer modelling studies of the covalent interactions between DNA and the enantiomers of anti-7,8-diol,9,10-epoxy-benzo[a]pyrene.

The molecular structures of adducts between the + and - enantiomers of 7,8-diol 9,10-epoxy benzo[a]pyrene and a double-stranded model for DNA, have been examined by empirical energy calculations. Low-energy structures were only obtained for A form, and not B form DNA. Both + and - adducts are of approximately equal energy. Some structural differences in the orientation of the BP chromophore in the two adducts were found.

Detection of arsenic in water, herbal and soil samples by neutron activation analysis technique.

Arsenic contamination of ground water is well understood while other environmental systems are rarely considered to be contaminated by arsenic. A vital issue is whether or not appreciable arsenic transmits through the food chain. Reportedly, ayurvedic herbal medicine products (AHMPs) manufactured in Asia were found to be contaminated by harmful level of Arsenic. This study was aimed to quantify the arsenic levels in water, herbal and soil samples collected from the same origin using highly accurate neutron activation analysis (NAA) technique. Harmful level of arsenic was detected in most of the water and soil samples. Moreover, a considerably harmful level of Arsenic was detected in herbal samples collected from the same origin. As a result, AHMPs manufactured in Asia might be contaminated by arsenic through arsenic contaminated herb plants.

Variation of folded polypeptide surface area with probe size.

Three types of polypeptide surface area (contact, accessible, and molecular) have been studied as a function of the radius of a probe sphere used to map the surface. The surfaces are: (1) three alpha-helices, the H-helix of myoglobin, the E-helix of leghemoglobin, and an artificial polyalanine helix, each with 26 residues; (2) two globins, myoglobin and leghemoglobin, each with 153 residues; and (3) a two-center model system for which the three types of surface area have been calculated analytically. The two globin helices have almost identical surface areas as a function of probe size as do the two globins. The polyalanine helix surface area is smaller but similar in shape to the globin helix areas. All three helix contact areas tend to the same limit as the probe size increases, and the globin contact areas behave similarly. Fractal dimensions were calculated for the helix and globin contact and molecular surfaces. All fractal dimensions showed strong dependence on probe size. The contact fractal dimension peaks at larger values for both the helices and globins. Most residues do not make contact with large probes (15 A).

Hemoglobin H disease in the eastern region of Saudi Arabia.

OBJECTIVE: Alpha-thalassemia is frequently encountered in eastern Saudi Arabia. We wanted to find out laboratory based incidence and laboratory features of Hemoglobin H disease in the Dammam region. METHODS: We retrospectively analyzed the results of Hemoglobin electrophoresis carried out during the last 5 years in our laboratory. Hemoglobin electrophoresis was performed on cellulose acetate, pH 8.6 using Helena or Biomidi kits. Hemoglobin S was confirmed by sickle solubility test. Variant hemoglobin if present, was confirmed by citrate agar (pH 6.0) electrophoresis. Helena rapid electrophoresis system was used for plate densitometry. The diagnosis of Hemoglobin H disease was made on the basis of the presence of Hemoglobin H on electrophoresis supplemented by demonstration of Hemoglobin H inclusions in red blood cells. RESULTS: Fifteen thousand, four hundred and ninety two blood samples were analyzed by Hemoglobin electrophoresis. We found 100 cases of Hemoglobin H disease, only one case was non-Saudi. The age ranged between 45 days to 85 years. There were 51 females and 49 males. Children (less than 12 years) were 35 and of adults there were 65. There were 35 adult females and 30 adult males. The mean +/- standard deviation of Hemoglobin H in children was 13.54 +/- 7, in adult females the mean +/- standard deviation of Hemoglobin H was 12 +/- 5.4, and in adult males it was 11.99 +/- 6.4. The Hemoglobin H inclusions seen in red blood cells ranged from 2.6-80 in children and 10-80 in adults. The sickle cell trait was co-existent in 7 cases. Hemoglobin Bart's along with Hemoglobin H was seen in 32 cases. Hemoglobin F was present, beyond first year of life in 34 cases. The Hemoglobin A2 as measured by densitometry was significantly low in all of the 3 age groups as compared to corresponding controls. The complete blood count results were available for analysis in only 26 cases of Hb H disease. The mean +/- SD values of Hb (g/dl), Hct (ratio), MCV (fl), MCH (pg) MCHC (g/dl), RDW-SD (fl) and RDW-CV (%) in these patients (all age groups together) were 8.15 +/- 1,.278 +/-.04, 59.4 +/- 5.8, 17.65 +/- 2.1, 29.4 +/- 1.7, 37.8 +/- 8.7 and 25.1 +/- 4.6. The mean Hb, Hct, MCV, MCH and MCHC were significantly reduced in all 3 age groups as compared to corresponding controls. RBC counts and RDW-CV were elevated in Hb H disease compared to corresponding controls. The blood film showed typical red cell morphology. CONCLUSION: Hb H disease is not infrequently encountered in the Dammam region. This condition should be kept in mind while evaluating patients for anemia. The genetic studies to determine the exact alpha-thalassemia determinants producing Hb H disease in eastern Saudi Arabia are needed.

Local protein sequence similarity does not imply a structural relationship.

A database search often will find a seemingly strong sequence similarity between two fragments of proteins that are not expected to have an evolutionary or functional relationship. It is tempting to suggest that the two fragments will adopt a similar conformation due to a common pattern of residues that dictate a particular substructure. To investigate the likelihood of such a structural similarity, local sequence similarities between proteins of known conformation were identified by a standard database search algorithm. Significant sequence similarity was identified as when the chance probability of obtaining the relatedness score from a scan of the entire database was less than 1%. In this region both true homologies and false homologies are detected. A total of 69 false homologies was located of length between 20 and 262 aligned positions. Many of these alignments had approximately 25% sequence identity and a further 25% of conservative changes. However, the results show in general these aligned fragments did not have a significant similarity in secondary or tertiary structure. Thus local sequence does not indicate a structural similarity when there is neither an evolutionary nor functional explanation to support this. Accordingly structure predictions based on finding a local sequence similarity with an evolutionary unrelated protein of known conformation are unlikely to be valid.

Molecular interactions in protein crystals: solvent accessible surface and stability.

The accessible surface areas of 58 monomeric and dimeric proteins, when measured in the crystalline environment, are found to be simply related to molecular weight. The loss of accessible surface when the proteins go from a free to their crystalline environment is well defined, implying that the hydrophobic interaction, which has been found to contribute to protein folding and stability in living systems, also contributes to protein crystal stability.

A relational database of protein structures designed for flexible enquiries about conformation.

A relational database of protein structure has been developed to enable rapid and flexible enquiries about the occurrence of many aspects of protein architecture. The coordinates of 294 proteins from the Brookhaven Data Bank have been processed by standard computer programs to generate many additional terms that quantify aspects of protein structure. These terms include solvent accessibility, main-chain and side-chain dihedral angles, and secondary structure. In a relational database, the information is stored in tables with columns holding the different terms and rows holding the different entries for the terms. The different relational base tables store the information about the protein coordinate set, the different chains in the protein, the amino acid residues and ligands, the atomic coordinates, the salt bridges, the hydrogen bonds, the disulphide bridges and the close tertiary contacts. The database was established under ORACLE management system. Enquiries are constructed in ORACLE using SQL (structured query language) which is simple to use and alleviates the need for extensive computer programs. A single table can be searched for entries that meet various criteria, e.g. all protein solved to better than a given resolution. The power of the database occurs when several tables, or the entries in a single table, are cross-correlated. For example the dihedral angles of proline in the fourth position in an alpha-helix in high resolution structures can be rapidly obtained. The structural database provides a powerful tool to obtain empirical rules about protein conformation. This database of protein structures is part of a joint project between Birkbeck College and Leeds University to establish an integrated data resource of protein sequences and structures (ISIS) that encodes the complex patterns of residues and coordinates that define protein conformation. The entire data resource (ISIS) will provide a system to guide all areas of protein modelling including structure prediction, site-directed mutagenesis and de novo protein design. The availability of ISIS is described in the paper.