DIP: The Database of Interacting Proteins: 2001 update

The Database of Interacting Proteins (DIP; http://dip.doe-mbi.ucla. edu) is a database that documents experimentally determined protein-protein interactions. Since January 2000 the number of protein-protein interactions in DIP has nearly tripled to 3472 and the number of proteins to 2659. New interactive tools have been developed to aid in the visualization, navigation and study of networks of protein interactions.

Metabolic hormones and tissue concentrations of mRNA for IGF-I in lines of sheep that differ in their protein synthesis response to feed intake

The rate of protein synthesis in the skin and muscle of sheep that have been genetically selected for high wool staple strength (SS) is less dependent on the level of dietary intake than that of low SS sheep. This study examined potential hormonal mediators of this difference in responsiveness. Sheep from SS+ and SS- genotypes were fed at 0.4, 1.1 or 1.8 times maintenance. Circulating concentrations of metabolic hormones and tissue concentrations of the mRNA for IGF-I were measured and compared with rates of protein synthesis measured previously. Plasma concentrations of GH, insulin, cortisol, thyroxine and IGF-I responded similarly to dietary intake in both genotypes, but SS+ sheep had higher plasma concentrations of IGF-I at all levels of nutrition (P<0.05). There were no interactions between diet and genotype. The concentration of mRNA for IGF-I was higher in the liver of SS+ sheep (P<0.05), and tended to increase (P=0.06) with nutrient intake, but there were no significant effects of genotype or nutrition in skin, muscle or gut. Concentrations of mRNA for IGF-I were not related to the rate of protein synthesis in any tissue examined. It was concluded that IGF-I did not drive the rate of protein synthesis directly, but it may mediate the responsiveness of protein synthesis rate, or protein degradation rate, to nutrient supply.

Fiber type-specific differential expression of angiogenic factors in response to chronic hindlimb ischemia

Alterations in endogenous levels of the angiogenic proteins basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF) were assessed in rabbit hindlimb muscles subjected to 1, 5, or 21 days of ischemia. In the glycolytic [tibialis anterior (TA)] and the oxidative [soleus (SOL)] muscles from the ischemic and contralateral (control) hindlimb, bFGF and VEGF protein expression was determined by ELISA and immunoblot analysis. Total VEGF protein expression was greater in oxidative than in glycolytic muscles after 5 days of hindlimb ischemia. In SOL muscle, total VEGF detected by ELISA in ischemic limbs was increased to 137, 300, and 220% of control at 1, 5, and 21 days, respectively. However, in TA, total VEGF expression by ELISA was increased only at 1 and 5 days of ischemia to 140 and 134% of control, respectively. By immunoblotting, the expression of the 165-amino acid isoform (VEGF(165)) was initially decreased to 55% of control in ischemic SOL at 1 day but was increased to 250% of control at day 5 and remained at 155% at day 21. In TA, VEGF(165) was increased to 260% of control at 1 day of ischemia but only to 150% of control by day 5. The only significant change in bFGF expression in either the oxidative or glycolytic muscles was a small increase (129% of control) at 21 days in SOL. This study demonstrates that the magnitude and direction of change in VEGF protein expression depend on VEGF subtype, muscle fiber type, and duration of ischemia. These findings suggest that strategies in therapeutic angiogenesis may need to differ depending on muscle fiber type.

Role of O6-alkylguanine-DNA alkyltransferase in the resistance of mouse spermatogenic cells to O6-alkylating agents

The O(6)-alkylguanine-DNA alkyltransferase inactivator O(6)-benzylguanine was administered to BALB/c mice either alone or before exposure to 1,3-bis(2-chloroethyl)-1-nitrosourea to study the role of the DNA repair protein O(6)-alkylguanine-DNA alkyltransferase in the protection of the testis against anti-cancer O(6)-alkylating agents. Exposure of the mice to 1, 3-bis(2-chloroethyl)-1-nitrosourea or O(6)-benzylguanine alone did not produce any marked testicular toxicity at the times studied. Testicular O(6)-alkylguanine-DNA alkyltransferase concentrations were assayed between 0 and 240 min after O(6)-benzylguanine treatment and were shown to be > 95% depleted 15 min after treatment with O(6)-benzylguanine and remained at > 95% at all the times assayed. Histological examination, the reduction in testicular mass and the induction of spermatogenic cell apoptosis showed that this depletion significantly potentiated 1, 3-bis(2-chloroethyl)-1-nitrosourea-induced testicular damage after treatment. Major histological damage was apparent 42 days after treatment, demonstrating that the stem spermatogonia were significantly affected by the combination. These results demonstrate that O(6)-alkylguanine-DNA alkyltransferase plays a significant role in protecting the spermatogenic cells from damage caused by DNA alkylation and indicate that the observed toxicity may result from damage to stem spermatogonia.

Deeply Penetrating Banded Zonal Flows in the Solar Convection Zone

Helioseismic observations have detected small temporal variations of the rotation rate below the solar surface that correspond to the so-called "torsional oscillations" known from Doppler measurements of the surface. These appear as bands of slower- and faster-than-average rotation moving equatorward. Here we establish, using complementary helioseismic observations over 4 yr from the GONG network and from the MDI instrument on board SOHO, that the banded flows are not merely a near-surface phenomenon: rather, they extend downward at least 60 Mm (some 8% of the total solar radius) and thus are evident over a significant fraction of the nearly 200 Mm depth of the solar convection zone.

Dynamic variations at the base of the solar convection zone

We have detected changes in the rotation of the sun near the base of its convective envelope, including a prominent variation with a period of 1.3 years at low latitudes. Such helioseismic probing of the deep solar interior has been enabled by nearly continuous observation of its oscillation modes with two complementary experiments. Inversion of the global-mode frequency splittings reveals that the largest temporal changes in the angular velocity Omega are of the order of 6 nanohertz and occur above and below the tachocline that separates the sun's differentially rotating convection zone (outer 30% by radius) from the nearly uniformly rotating deeper radiative interior beneath. Such changes are most pronounced near the equator and at high latitudes and are a substantial fraction of the average 30-nanohertz difference in Omega with radius across the tachocline at the equator. The results indicate variations of rotation close to the presumed site of the solar dynamo, which may generate the 22-year cycles of magnetic activity.

A combined algorithm for genome-wide prediction of protein function

The availability of over 20 fully sequenced genomes has driven the development of new methods to find protein function and interactions. Here we group proteins by correlated evolution, correlated messenger RNA expression patterns and patterns of domain fusion to determine functional relationships among the 6,217 proteins of the yeast Saccharomyces cerevisiae. Using these methods, we discover over 93,000 pairwise links between functionally related yeast proteins. Links between characterized and uncharacterized proteins allow a general function to be assigned to more than half of the 2,557 previously uncharacterized yeast proteins. Examples of functional links are given for a protein family of previously unknown function, a protein whose human homologues are implicated in colon cancer and the yeast prion Sup35.

Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability

Understanding the molecular determinants of protein thermostability is of theoretical and practical importance. While numerous determinants have been suggested, no molecular feature has been judged of paramount importance, with the possible exception of ion-pair networks. The difficulty in identifying the main determinants may have been the limited structural information available on the thermostable proteins. Recently the complete genomes for mesophilic, thermophilic and hyperthermophilic organisms have been sequenced, vastly improving the potential for uncovering general trends in sequence and structure evolution related to thermostability and, thus, for isolating the more important determinants. From a comparative analysis of 20 complete genomes, we find a trend towards shortened thermophilic proteins relative to their mesophilic homologs. Moreover, sequence alignments to proteins of known structure indicate that thermophilic sequences are more likely than their mesophilic homologs to have deletions in exposed loop regions. The new genomes offer enough comparable sequences to compute meaningful statistics that point to loop deletion as a general evolutionary strategy for increasing thermostability.

Assigning protein functions by comparative genome analysis: protein phylogenetic profiles

Determining protein functions from genomic sequences is a central goal of bioinformatics. We present a method based on the assumption that proteins that function together in a pathway or structural complex are likely to evolve in a correlated fashion. During evolution, all such functionally linked proteins tend to be either preserved or eliminated in a new species. We describe this property of correlated evolution by characterizing each protein by its phylogenetic profile, a string that encodes the presence or absence of a protein in every known genome. We show that proteins having matching or similar profiles strongly tend to be functionally linked. This method of phylogenetic profiling allows us to predict the function of uncharacterized proteins.

The coupling of NAD(P)+-producing reactions to a semiautomated bioluminescent reaction

Many cellular metabolites can be measured with high sensitivity using bioluminescent techniques. These metabolites are coupled to an appropriate enzyme to produce NAD(P)H, which can then be coupled to the bioluminescent reactions. The sensitivity of bioluminescence cannot be readily applied to methods in which cellular metabolites consume NAD(P)H because of the difficulty in measuring, with sufficient sensitivity, decreases in the concentration of NAD(P)H against a high background NAD(P)H concentration. We have overcome these technical difficulties by developing a bioluminescent reagent to measure the production of NAD(P)+. Assays for creatine/creatine phosphate, pyruvate, and succinate, as well as the kinetic measurement of lactate, are described for a range of biological material. The assays are highly sensitive, quantitative, and reproducible and show no sample-specific inhibition. The range of assays and the diverse biological material tested suggests that NAD(P)+ bioluminescence has a wide potential for application.

Influence of O6-benzylguanine on the anti-tumour activity and normal tissue toxicity of 1,3-bis(2-chloroethyl)-1-nitrosourea and molecular combinations of 5-fluorouracil and 2-chloroethyl-1-nitrosourea in mice

Previous studies have demonstrated that novel molecular combinations of 5-fluorouracil (5FU) and 2-chloroethyl-1-nitrosourea (CNU) have good preclinical activity and may exert less myelotoxicity than the clinically used nitrosoureas such as 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU). This study examined the effect of O6-alkylguanine-DNA-alkyltransferase (ATase) depletion by the pseudosubstrate O6-benzylguanine (BG) on the anti-tumour activity and normal tissue toxicity in mice of three such molecular combinations, in comparison with BCNU. When used as single agents at their maximum tolerated dose, all three novel compounds produced a significant growth retardation of BCNU-resistant murine colon and human breast xenografts. This in vivo anti-tumour effect was potentiated by BG, but was accompanied by severe myelotoxicity as judged by spleen colony forming assays. However, while tumour resistance to BCNU was overcome using BG, this was at the expense of enhanced bone marrow, gut and liver toxicity. Therefore, although this ATase-depletion approach resulted in improved anti-tumour activity for all three 5-FU:CNU molecular combinations, the potentiated toxicities in already dose-limiting tissues indicate that these types of agents offer no therapeutic advantage over BCNU when they are used together with BG.

Microsatellite instability, chemosensitivity and mutant frequency in a series of 1,2-dimethylhydrazine induced murine colon adenocarcinoma models

Loss of DNA mismatch repair has been described in a number of tumour types such as colorectal adenocarcinoma and leads to microsatellite instability. This may have clinical relevance due to mismatch repair defects altering chemosensitivity towards certain classes of anti-tumour agent. This study has examined microsatellite instability of eight murine colon adenocarcinoma tumour models induced by 1,2-dimethylhydrazine. Four microsatellite regions were examined suggesting that four of the tumour models exhibit a low level of microsatellite instability. Loss of heterozygosity was found in 5/8 tumours, suggesting that allelic loss may be a relatively common step in the carcinogenesis of these tumour models. Three of the allelic losses involved the D11MIT4 locus which is situated very close to the p53 tumour suppressor locus. Four tumour models are routinely cultured in vitro and these were used to examine whether there was any association between microsatellite instability, mutant frequency and chemo-sensitivity of these tumour models, comparing them with four human adenocarcinoma cell lines of known mismatch repair status. Two cell lines (MAC26 and MAC16) were found to be more chemoresistant towards cisplatin but not 6-thioguanine. No association was found between microsatellite instability and chemosensitivity for either the human or mouse cell lines.

Characteristics of the intron involvement in the mitogen-induced expression of Zfp-36

Zfp-36, the gene encoding the putative zinc finger protein tristetraprolin (TTP), is rapidly induced in fibroblasts by a variety of growth factors. Recent gene knockout experiments have shown that TTP-deficient mice developed arthritis, cachexia, and autoimmunity, all apparently mediated by an excess of tumor necrosis factor alpha. We recently showed that full serum inducibility of Zfp-36 requires elements in the promoter; in addition, removal of the single intron strikingly inhibited serum-induced TTP expression. We show here that replacement of the intron with unrelated sequences, or removal of 95% of the intron but retention of the splice sites, each resulted in the maintenance of approximately 45 and 19%, respectively, of full serum-induced expression. In addition, deletion of intron sequences base pairs 601-655 decreased the serum-induced expression of TTP by 65%. Sequence base pairs 618-626 bound specifically to the transcription factor Sp1; mutation of this binding motif decreased TTP expression by 70%, suggesting that Sp1 binding to this motif contributes to serum induction of Zfp-36. We conclude that full serum-induced expression of Zfp-36 depends on the activation of conventional promoter elements as well as elements in the single intron, and that the presence per se of the intron in its natural location also contributes significantly to the regulated expression of this gene.

Bioluminescent methods for determining metabolites in micro-samples of pig plasma

A highly sensitive and simplified method for the luminometric determination of plasma metabolites has been developed. Furthermore, the technique has been automated for the Dynatech ML2250 Microtiter Plate Luminometer and can be applied to the measurement of any plasma metabolite which may be coupled to a reaction involving the reduction of NAD+. Assays are described for lactose/galactose, beta-hydroxybutyrate and D-lactate, and have been validated with plasma samples. The assays require 1-2 microliters of plasma, and are capable of detecting concentrations below 5 mumol/l. Since luminometry is based on the kinetics of the luciferase/oxidoreductase enzyme system, components of complex biological samples may interfere with the rate of the reaction; necessitating the use of internal standards for individual samples. However, the need for internal standards to account for sample to sample variation in the luminescent response, has been eliminated with the present technique.

Predicting protein secondary structure with probabilistic schemata of evolutionarily derived information

We demonstrate the applicability of our previously developed Bayesian probabilistic approach for predicting residue solvent accessibility to the problem of predicting secondary structure. Using only single-sequence data, this method achieves a three-state accuracy of 67% over a database of 473 non-homologous proteins. This approach is more amenable to inspection and less likely to overlearn specifics of a dataset than "black box" methods such as neural networks. It is also conceptually simpler and less computationally costly. We also introduce a novel method for representing and incorporating multiple-sequence alignment information within the prediction algorithm, achieving 72% accuracy over a dataset of 304 non-homologous proteins. This is accomplished by creating a statistical model of the evolutionarily derived correlations between patterns of amino acid substitution and local protein structure. This model consists of parameter vectors, termed "substitution schemata," which probabilistically encode the structure-based heterogeneity in the distributions of amino acid substitutions found in alignments of homologous proteins. The model is optimized for structure prediction by maximizing the mutual information between the set of schemata and the database of secondary structures. Unlike "expert heuristic" methods, this approach has been demonstrated to work well over large datasets. Unlike the opaque neural network algorithms, this approach is physicochemically intelligible. Moreover, the model optimization procedure, the formalism for predicting one-dimensional structural features and our previously developed method for tertiary structure recognition all share a common Bayesian probabilistic basis. This consistency starkly contrasts with the hybrid and ad hoc nature of methods that have dominated this field in recent years.

Prediction of requirement for, and outcome of, prolonged mechanical ventilation following cardiac surgery

The prediction of requirement for, and short- and long-term outcome of, prolonged mechanical ventilation after cardiac surgery is ill-defined. The aims of this study were to isolate any predictive indices which might identify those groups of patients who may require prolonged ventilation postoperatively and to determine which factors significantly affect outcome in the prolonged-ventilation group. Following case note review of 139 consecutive cardiac surgical patients ventilated for > or = 7 days following surgery, 43 factors were recorded on each patient, including smoking, pulmonary function, chest infection, and chronic obstructive airways disease. Of 139 patients, 89 were discharged from hospital (64% survival); of these, 52 were alive at long-term follow-up (58% long-term survival). Statistical analysis identified urban residence, chronic obstructive airways disease, prolonged operation, and bypass time as significant predictors of requirement for prolonged ventilation postoperatively. On multivariate analysis five factors were predictive of increased intensive care mortality, including urban residence, inotrope days, sepsis, perioperative cerebrovascular accident and coagulopathy requiring fresh frozen plasma transfusion postoperatively. Following discharge from hospital, four factors were found to be significant predictors of increased mortality: these are impaired preoperative ejection fraction, increasing age, impaired preoperative pulmonary function, and abscence of preoperative aspirin medication. These factors should be considered in intensive care planning, long-term follow-up and importantly on clinical decision making in the individual patient.

Establishment and characterisation of new cell lines from human breast tumours initially established as tumour xenografts in NMRI nude mice

Human breast cancer cell lines are required as models for use in the understanding of breast carcinoma, and for improving the ability of cell screens to detect appropriate anti-cancer agents. Four human breast cancer cell lines (MT-1, MaTu. MT-3 and MC4000) were established from human tumour xenografts grown in nude mice. All the lines were shown to be of human origin by karyotype analysis, were epithelial in morphology by both light and electron microscopy, were positive for cytokeratin 18, and were free from mycoplasma, bacterial, yeast and fungal contamination. All of the new lines were shown to be ER and PgR negative, while using the same procedures (i.e. radioligand binding and immunohistochemical staining) the positive control cell line MCF-7 was shown to be positive. MaTu had been previously reported as ER and PgR positive in vivo and it may be that this characteristic had been lost due to in vitro selection pressures. The growth rates of all the new breast cancer cell lines were similar and within the limits required for incorporation into a panel for screening anti-cancer drugs by a microtetrazolium based, colorimetric growth inhibition assay. Three of the lines (MT-1. MaTu and MC4000) were also able to grow into macroscopic colonies for use in a non-agar clonogenic assay. In addition, both MT-1 and MaTu formed spheroids and were clonogenic in soft-agar. The new lines demonstrated a wide range of sensitivities to anticancer agents commonly used in the treatment of breast cancer, and together with their corresponding xenografts are providing additional systems for the evaluation of new compounds.

Cloning and characterization of two yeast genes encoding members of the CCCH class of zinc finger proteins: zinc finger-mediated impairment of cell growth

Members of the CCCH zinc finger (Zf) protein family have in common two or more repeats of a novel Zf motif consisting of Cys and His residues in the form Cx8Cx5Cx3H [where x is a variable amino acid (aa)]. We used a degenerate polymerase chain reaction (PCR) strategy to clone members of this gene family from Saccharomyces cerevisiae. The deduced aa sequences encoded by these genes, designated CTH1 and CTH2, share 46% overall identity and 59% similarity, largely due to the two highly conserved Zf domains. We found readily detectable expression of a 1.4-kb mRNA encoding Cth1p. The 1.1-kb mRNA encoding Cth2p was barely detectable under normal growth conditions; however, disruption of CTH1 resulted in at least a threefold increase in CTH2 mRNA accumulation. No change in phenotype was detected following disruption of CTH1 and CTH2, either singly or together. In contrast, overexpression of the CTH genes or one of the related mammalian genes, tris-tetraprolin (TTP), caused delayed entry of cell cultures into exponential growth, and a decrease in final cell density. Removal of the Zf domain of Cth1p by truncation or deletion completely reversed this slow growth phenotype, indicating that it was mediated through this highly conserved structural motif.

Maintenance of villus height and crypt depth, and enhancement of disaccharide digestion and monosaccharide absorption, in piglets fed on cows' whole milk after weaning

The aims of the present study were (a) to maintain the structure and function of the small intestine of the piglet after weaning, and (b) to compare the capacity in vivo of sucking and weaned piglets to digest oral boluses of lactose and sucrose and absorb their monosaccharide products. Piglets were fed on cows' whole milk ad libitum every 2 h for 5 d after weaning. Physiological doses of lactose plus fructose (treatment LAC+FRU) and sucrose plus galactose (treatment SUC+GAL) were administered on day 27 of lactation and on the fifth day after weaning, after which time piglets were killed. Villus height and crypt depth were maintained (P > 0.05) by feeding cows' milk after weaning. The areas under the curves (AUC) for galactose and glucose, adjusted for live weight and plasma volume, increased (P < 0.05) after weaning. Despite the enhancement of gut function after weaning, the galactose index (GalI:AUC for galactose ingested as lactose divided by the AUC for the same dose of galactose ingested as the monosaccharide) and fructose index (FruI: AUC for fructose ingested as sucrose divided by the AUC for the same dose of fructose ingested as the monosaccharide), which are indices of digestive and absorptive efficiency, both decreased after weaning. This apparent anomaly may be reconciled by increased growth, and hence surface area, of the small intestine between weaning and slaughter such that 'total' digestion and absorption most probably increased despite apparent decreases in GalI and FruI. Positive correlations (P < 0.05) between villus height and GalI are consistent with the maximum activity of lactase occurring more apically along the villus. Significant linear relationships (P < 0.05) were recorded between villus height at the proximal jejunum and adjusted AUC for galactose and glucose following treatment LAC+FRU, and between villus height at the proximal jejunum and adjusted glucose AUC following treatment SUC+GAL. These relationships suggest that maximum digestion and absorption occurs at increasing distances along the crypt:villus axis in the weaned pig.

Distribution of systemically administered ampicillin, benzylpenicillin, and flucloxacillin in excisional wounds in diabetic and normal rats and effects of local topical vasodilator treatment

The present study assessed the suitability of the streptozotocin-treated diabetic rat as a model for the study of diabetes-impaired wound healing. The distribution of three antibiotics, ampicillin, benzylpenicillin, and flucloxacillin, in wound and adjacent tissue sites on the abdomens and legs of normal and diabetic rats was determined 30 min after intravenous administration of a single bolus containing 50 mg of all three antibiotics per kg of body weight. Tissue/plasma ratios showed that antibiotic tissue penetration appeared to be related to protein binding. The treatment of wound sites with vasodilators (1% solution) to increase local blood flow and antibiotic delivery to the site was then determined and appeared to be more effective with endothelium-independent sodium nitroprusside than with endothelium-dependent acetylcholine in diabetic rats. These results suggest that coadministration of topical vasodilators to wound sites in neuropathic diabetic patients undergoing antibiotic therapy for infected ulcers could increase antibiotic delivery to wound tissue sites.