Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases

Genomic blot analysis raised the possibility that uncharacterized tryptase genes reside on chromosome 17 at the complex containing the three genes that encode mouse mast cell protease (mMCP) 6, mMCP-7, and transmembrane tryptase (mTMT). Probing of GenBank's expressed sequence tag data base with these three tryptase cDNAs resulted in the identification of an expressed sequence tag that encodes a portion of a novel mouse serine protease (now designated mouse tryptase 4 (mT4) because it is the fourth member of this family). 5'- and 3'-rapid amplification of cDNA ends approaches were carried out to deduce the nucleotide sequence of the full-length mT4 transcript. This information was then used to clone its approximately 5.0-kilobase pair gene. Chromosome mapping analysis of its gene, sequence analysis of its transcript, and comparative protein structure modeling of its translated product revealed that mT4 is a new member of the chromosome 17 family of mouse tryptases. mT4 is 40-44% identical to mMCP-6, mMCP-7, and mTMT, and this new serine protease has all of the structural features of a functional tryptase. Moreover, mT4 is enzymatically active when expressed in insect cells. Due to its 17-mer hydrophobic domain at its C terminus, mT4 is a membrane-anchored tryptase more analogous to mTMT than the other members of its family. As assessed by RNA blot, reverse transcriptase-polymerase chain reaction, and/or in situ hybridization analysis, mT4 is expressed in interleukin-5-dependent mouse eosinophils, as well as in ovaries and testes. The observation that recombinant mT4 is preferentially retained in the endoplasmic reticulum of transiently transfected COS-7 cells suggests a convertase-like role for this integral membrane serine protease.

Psychosocial interventions and cancer patients: psychological and immune responses may depend on cancer type

Psychological and immunological responses of cancer patients to a psychosocial intervention program will be assessed over time. Previously it has been proposed that there are two large divisions in cancer histology (type I and II) and that the psychobiology of patients will vary accordingly.

Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome

The approach to annotating a genome critically affects the number and accuracy of genes identified in the genome sequence. Genome annotation based on stringent gene identification is prone to underestimate the complement of genes encoded in a genome. In contrast, over-prediction of putative genes followed by exhaustive computational sequence, motif and structural homology search will find rarely expressed, possibly unique, new genes at the risk of including non-functional genes. We developed a two-stage approach that combines the merits of stringent genome annotation with the benefits of over-prediction. First we identify plausible genes regardless of matches with EST, cDNA or protein sequences from the organism (stage 1). In the second stage, proteins predicted from the plausible genes are compared at the protein level with EST, cDNA and protein sequences, and protein structures from other organisms (stage 2). Remote but biologically meaningful protein sequence or structure homologies provide supporting evidence for genuine genes. The method, applied to the Drosophila melanogaster genome, validated 1,042 novel candidate genes after filtering 19,410 plausible genes, of which 12,124 matched the original 13,601 annotated genes. This annotation strategy is applicable to genomes of all organisms, including human.

Comparative protein structure modeling of genes and genomes

Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.

Crystal structures of ribosome anti-association factor IF6

Ribosome anti-association factor eIF6 (originally named according to translation initiation terminology as eukaryotic initiation factor 6) binds to the large ribosomal subunit, thereby preventing inappropriate interactions with the small subunit during initiation of protein synthesis. We have determined the X-ray structures of two IF6 homologs, Methanococcus jannaschii archaeal aIF6 and Sacchromyces cerevisiae eIF6, revealing a phylogenetically conserved 25 kDa protein consisting of five quasi identical alpha/beta subdomains arrayed about a five-fold axis of pseudosymmetry. Yeast eIF6 prevents ribosomal subunit association. Comparative protein structure modeling with other known archaeal and eukaryotic homologs demonstrated the presence of two conserved surface regions, one or both of which may bind the large ribosomal subunit.

Single and multiple cholesterol gallstones and the influence of bacteria

Single and multiple cholesterol gallstones constitute at least 80% of the gallstone population observed at cholecystectomy in Western countries. While supersaturation of bile with cholesterol is necessary for gallstone growth, the kinetic determinant of crystal nucleation is perhaps the critical factor leading to the incidence of gallstones. Nucleation involves aggregation of nidus-forming materials like pigment precipitates and mucus proteins. In combination with cholesterol precipitates and crystal formation, gallstone propagation is enhanced. Bacterial species may augment the process of nucleation and gallstone growth by contributing specific enzyme activities resulting in the formation of insoluble precipitates in bile, or by acting as a nidus upon which the deposition of cholesterol crystals may initiate gallstone formation. The utilization of Raman microscopic techniques permits detailed mapping of the distribution of the gallstone components leading to identification and characterization of the site of nucleation. This, when coupled to molecular genetic tools such as PCR DNA amplification, would permit elucidation of the role of bacteria in vivo gallstone propagation mechanisms.

Serotonin, noradrenaline and cognitive function: a preliminary investigation of the acute pharmacodynamic effects of a serotonin versus a serotonin and noradrenaline reuptake inhibitor

Comparisons of the behavioural side-effect profiles of antidepressants that inhibit either serotonin or both serotonin and noradrenaline reuptake, may reveal differences in cognitive and psychomotor functions, which may be attributed to their relative pharmacological selectivity for potentiating monoamine neurotransmission in the central nervous system. The aim of the present study was to determine the acute pharmacodynamic effects of citalopram and venlafaxine, on cognitive and psychomotor performance. Nine healthy male volunteers received a single clinical dose of citalopram, venlafaxine or amitriptyline (positive control) in a double-blind placebo-controlled design. Cognitive and psychomotor tests and a subjective measure of sedation were examined before and 1, 2 and 4 hours after drug administration. Citalopram improved psychomotor responses to sensory stimuli and sustained attention, with significant decreases in movement times of the choice reaction time test and an increase in critical flicker fusion threshold. Venlafaxine did not affect performances on any of the cognitive or psychomotor tests examined. Differences may be related to relative potencies of the compounds for monoamine reuptake inhibition.

Protein structure modeling for structural genomics

The shapes of most protein sequences will be modeled based on their similarity to experimentally determined protein structures. The current role, limitations, challenges and prospects for protein structure modeling (using information about genes and genomes) are discussed in the context of structural genomics.

Bacterial infections in terminally ill hospice patients

Terminally ill patients are very susceptible to infections, which are the result of disease-related processes and/or therapy-induced mechanisms. These patients are already subject to multiple severe symptoms and associated comorbid conditions, with much resultant distress. Infection increases this symptom burden and further reduces quality of life. We have retrospectively investigated the prevalence of infection and clinical course in 102 consecutive patients who died after admission to a tertiary palliative care unit and assessed the site-specific frequency of infection, pathogenic organisms involved, and the pattern of antibiotic agents used. The prevalence of symptoms and comorbid conditions on admission and during the progress phase of care were noted. Median overall survival of the total cohort was 12 days. The median survival of patients with infections was 22 days. Thirty-seven patients (36.3%) were diagnosed with 42 separate infections. The sites of infections were the urinary tract (42.5%), the respiratory tract (22.9%), blood (12.5%), skin and subcutaneous tissues (12.5%), and the eyes (10.0%). There were 20 separate positive cultures isolated from specimens obtained from 13 individual patients. Three isolates were obtained from 1 patient, 2 isolates obtained from 5 patients, and 1 isolate was obtained from each of the 7 remaining patients. Escherichia coli was the most common pathogen isolated. Eleven patients with infections (31.4%) were diagnosed on admission, and antibiotic treatment was commenced within 48 hours of admission in 21 patients (60%). Overall antibiotic response and symptom control of infections was observed to be a minimum of 40%. Psychological distress was common in this group of patients (P = 0.001) as were disabling symptoms on admission, such as pain, immobility, and weakness. Symptoms indicating poor survival, such as severe pain and dyspnea, were not significantly associated with infection. Decreased patient survival in this cohort was not significantly associated with the presence of bacterial infection (P = 0.07), irrespective of whether or not a positive culture isolate was obtained. We conclude that appropriate management of infection resulted in enhanced palliative symptom control.

Modeling of loops in protein structures

Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4-, 8-, and 12-residue loop predictions, respectively, had <2 A RMSD error for the mainchain N, C(alpha), C, and O atoms; the average accuracies were 0.59 +/- 0.05, 1.16 +/- 0.10, and 2.61 +/- 0.16 A, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 A, the average loop prediction error increased by 180, 25, and 3% for 4-, 8-, and 12-residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling.

Gallstones and gall bladder carcinoma

BACKGROUND

The present study reviewed the occurrence of gall bladder carcinoma in patients who underwent a cholecystectomy for gallstone disease.

METHODS

A retrospective study of demographical and clinical information for patients who underwent a cholecystectomy and operative cholangiogram for gallstones predominantly in three major hospitals located in the northern area of Melbourne was carried out.

RESULTS

Gall bladder carcinomas were observed in 14 patients (3.2%; 95% confidence interval (CI): 1.8-5.3%) consisting of 11 women and three men of median age 78.5 years (interquartile range: 77-81) from a series of 439 patients with a male-to-female ratio of 1-2. The results of the present study show that primary carcinoma of the gall bladder in this descriptive retrospective cohort was always associated with single or multiple cholesterol gallstones that were impacting on the gall bladder wall. Cholesterol 'solitaire' gallstones were ovoid in shape with diameters > 3 cm along their longest axis, whereas multiple cholesterol gallstones varied in size and number from two or three large stones (1-2 cm), to numerous smaller stones (variable size to 0.5 cm). No patient with gall bladder carcinoma had either brown or black pigment gallstones.

CONCLUSION

It is postulated that gall bladder carcinoma may be intimately associated with large or numerous cholesterol gallstones that in the first instance may interfere with the mechanical functioning of the gall bladder. The size as well as the number of gallstones present in the gall bladder may contribute significantly to the promotion of a gallstone filling defect of the gall bladder that may cause chronic mechanical damage to the gall bladder mucosa. The present report supports the hypothesis that gall bladder carcinoma is an age-dependent malignancy, present mostly in women, that may be intimately associated with long-standing benign gallstone disease of the gall bladder.

Core histones of the amitochondriate protist, Giardia lamblia

Genes coding for the core histones H2a, H2b, H3, and H4 of Giardia lamblia were sequenced. A conserved organism- and gene-specific element, GRGCGCAGATTTVGG, was found upstream of the coding region in all core histone genes. The derived amino acid sequences of all four histones were similar to their homologs in other eukaryotes, although they were among the most divergent members of this protein family. Comparative protein structure modeling combined with energy evaluation of the resulting models indicated that the G. lamblia core histones individually and together can assume the same three-dimensional structures that were established by X-ray crystallography for Xenopus laevis histones and the nucleosome core particle. Since G. lamblia represents one of the earliest-diverging eukaryotes in many different molecular trees, the structure of its histones is potentially of relevance to understanding histone evolution. The G. lamblia proteins do not represent an intermediate stage between archaeal and eukaryotic histones.

Understanding protein folding via free-energy surfaces from theory and experiment

The ability of protein molecules to fold into their highly structured functional states is one of the most remarkable evolutionary achievements of biology. In recent years, our understanding of the way in which this complex self-assembly process takes place has increased dramatically. Much of the reason for this advance has been the development of energy surfaces (landscapes), which allow the folding reaction to be described and visualized in a meaningful manner. Analysis of these surfaces, derived from the constructive interplay between theory and experiment, has led to the development of a unified mechanism for folding and a recognition of the underlying factors that control the rates and products of the folding process.

Identification and characterization of a p53 homologue in Drosophila melanogaster

The tumor suppressor gene p53 in mammalian cells plays a critical role in safeguarding the integrity of genome. It functions as a sequence-specific transcription factor. Upon activation by a variety of cellular stresses, p53 transactivates downstream target genes, through which it regulates cell cycle and apoptosis. However, little is known about p53 in invertebrates. Here we report the identification and characterization of a Drosophila p53 homologue gene, dp53. dp53 encodes a 385-amino acid protein with significant homology to human p53 (hp53) in the region of the DNA-binding domain, and to a lesser extent the tetramerization domain. Purified dp53 DNA-binding domain protein was shown to bind to the consensus hp53-binding site by gel mobility analysis. In transient transfection assays, expression of dp53 in Schneider cells transcriptionally activated promoters that contained consensus hp53-responsive elements. Moreover, a mutant dp53 (Arg-155 to His-155), like its hp53 counterpart mutant, exerted a dominant-negative effect on transactivation. Ectopic expression of dp53 in Drosophila eye disk caused cell death and led to a rough eye phenotype. dp53 is expressed throughout the development of Drosophila with highest expression levels in early embryogenesis, which has a maternal component. Consistent with this, dp53 RNA levels were high in the nurse cells of the ovary. It appears that p53 is structurally and functionally conserved from flies to mammals. Drosophila will provide a useful genetic system to the further study of the p53 network.

Subdural and intraventricular traumatic tension pneumocephalus: case report

Simple pneumocephalus most frequently arises as a complication of a head injury in which a compound basal skull fracture with tearing of the meninges allows entry of air into the cranial cavity. It can also follow a neurosurgical operation. Tension traumatic pneumocephalus with intraventricular extension is an extremely rare, potentially lethal condition that requires prompt diagnosis and treatment. We report the case of subdural and intraventricular accidental tension pneumocephalus occurring in a 26-year-old man as a result of skull fracture. This case is combined with rhinorrhea and meningitis that suggest some difficulties to treat. The operative procedure associated with medical treatment was performed and a good result was obtained.

Acute increases in night-time plasma melatonin levels following a period of meditation

To determine whether a period of meditation could influence melatonin levels, two groups of meditators were tested in a repeated measures design for changes in plasma melatonin levels at midnight. Experienced meditators practising either TM-Sidhi or another internationally well known form of yoga showed significantly higher plasma melatonin levels in the period immediately following meditation compared with the same period at the same time on a control night. It is concluded that meditation, at least in the two forms studied here, can affect plasma melatonin levels. It remains to be determined whether this is achieved through decreased hepatic metabolism of the hormone or via a direct effect on pineal physiology. Either way, facilitation of higher physiological melatonin levels at appropriate times of day might be one avenue through which the claimed health promoting effects of meditation occur.

A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing

We describe here the cloning and sequencing of a new auxiliary gene identified by Tn551 insertional mutagenesis of the highly and homogeneously methicillin-resistant Staphylococcus aureus strain COL. The insertionally inactivated mutant RUSA315 had intact mecA and normal amounts of PBP2A, but drastically reduced antibiotic resistance (drop in methicillin MIC from 1600 to 1.5 micrograms ml-1), a unique heterogeneous phenotype, and a compositional change in the cell wall characterized by the complete disappearance of the unsubstituted disaccharide pentapeptide from the peptidoglycan. Cloning in E. coli followed by sequencing located the Tn551 insert omega 720 in an open reading frame of 451 codons, provisionally called femR315, defining a polypeptide with a deduced amino acid sequence that showed over 26% sequence identity and 57% overall sequence similarity with the phosphoglucomutase (PGM) gene of E. coli. The Tn551 insertion site of a previously described mutant 12F (femD) also lies in the same gene as femR315. The wild-type form of femR315 subcloned in a shuttle vector fully restored expression of high level (parental) methicillin resistance in mutant RUSA315. The exact biochemical function of femR315 is not known. However, enzymes similar to PGM catalyze the isomerization of hexose and hexosamine phosphates leading to the formation of glucosamine-1-P, which is an obligate precursor in the biosynthesis of UDP-N-acetylglucosamine (UDP-NAGA). We propose that the suppression of methicillin resistance in RUSA315 is related to some functional or quantitative abnormality of UDP-NAGA metabolism.

Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface

Mouse mast cell protease (mMCP) 6 and mMCP-7 are homologous tryptases stored in granules as macromolecular complexes with heparin and/or chondroitin sulfate E containing serglycin proteoglycans. When pro-mMCP-7 and pseudozymogen forms of this tryptase and mMCP-6 were separately expressed in insect cells, all three recombinant proteins were secreted into the conditioned medium as properly folded, enzymatically inactive 33-kDa monomers. However, when their propeptides were removed, mMCP-6 and mMCP-7 became enzymatically active and spontaneously assumed an approximately 150-kDa tetramer structure. Heparin was not required for this structural change. When incubated at 37 degrees C, recombinant mMCP-7 progressively lost its enzymatic activity in a time-dependent manner. Its N-linked glycans helped regulate the thermal stability of mMCP-7. However, the ability of this tryptase to form the enzymatically active tetramer was more dependent on a highly conserved Trp-rich domain on its surface. Although recombinant mMCP-6 and mMCP-7 preferred to form homotypic tetramers, these tryptases readily formed heterotypic tetramers in vitro. This latter finding indicates that the tetramer structural unit is a novel way the mast cell uses to assemble varied combinations of tryptases.

MODBASE, a database of annotated comparative protein structure models

MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia coli, as well as all the available sequences from Arabidopsis thaliana and Homo sapiens. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the quality of the models. ModBase is accessible through a web interface at http://guitar.rockefeller.edu/modbase/

ModBase: a database of comparative protein structure models

ModBase is a database of evaluated and annotated comparative protein structure models. The database also includes fold assignments and alignments on which the models were based.

Challenges at the frontiers of structural biology

Knowledge of the three-dimensional structures of proteins is the key to unlocking the full potential of genomic information. There are two distinct directions along which cutting-edge research in structural biology is currently moving towards this goal. On the one hand, tightly focused long-term research in individual laboratories is leading to the determination of the structures of macromolecular assemblies of ever-increasing size and complexity. On the other hand, large consortia of structural biologists, inspired by the pace of genome sequencing, are developing strategies to determine new protein structures rapidly, so that it will soon be possible to predict reasonably accurate structures for most protein domains. We anticipate that a small number of complex systems, studied in depth, will provide insights across the field of biology with the aid of genome-based comparative structural analysis.