Supra-domains: Evolutionary Units Larger than Single Protein Domains

Domains are the evolutionary units that comprise proteins, and most proteins are built from more than one domain. Domains can be shuffled by recombination to create proteins with new arrangements of domains. Using structural domain assignments, we examined the combinations of domains in the proteins of 131 completely sequenced organisms. We found two-domain and three-domain combinations that recur in different protein contexts with different partner domains. The domains within these combinations have a particular functional and spatial relationship. These units are larger than individual domains and we term them "supra-domains". Amongst the supra-domains, we identified some 1400 (1203 two-domain and 166 three-domain) combinations that are statistically significantly over-represented relative to the occurrence and versatility of the individual component domains. Over one-third of all structurally assigned multi-domain proteins contain these over-represented supra-domains. This means that investigation of the structural and functional relationships of the domains forming these popular combinations would be particularly useful for an understanding of multi-domain protein function and evolution as well as for genome annotation. These and other supra-domains were analysed for their versatility, duplication, their distribution across the three kingdoms of life and their functional classes. By examining the three-dimensional structures of several examples of supra-domains in different biological processes, we identify two basic types of spatial relationships between the component domains: the combined function of the two domains is such that either the geometry of the two domains is crucial and there is a tight constraint on the interface, or the precise orientation of the domains is less important and they are spatially separate. Frequently, the role of the supra-domain becomes clear only once the three-dimensional structure is known. Since this is the case for only a quarter of the supra-domains, we provide a list of the most important unknown supra-domains as potential targets for structural genomics projects.

The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity

Drosophila melanogaster is an arthropod with a much more complex anatomy and physiology than the nematode Caenorhabditis elegans. We investigated one of the protein superfamilies in the two organisms that plays a major role in development and function of cell-cell communication: the immunoglobulin superfamily (IgSF). Using hidden Markov models, we identified 142 IgSF proteins in Drosophila and 80 in C. elegans. Of these, 58 and 22, respectively, have been previously identified by experiments. On the basis of homology and the structural characterisation of the proteins, we can suggest probable types of function for most of the novel proteins. Though overall Drosophila has fewer genes than C. elegans, it has many more IgSF cell-surface and secreted proteins. Half the IgSF proteins in C. elegans and three quarters of those in Drosophila have evolved subsequent to the divergence of the two organisms. These results suggest that the expansion of this protein superfamily is one of the factors that have contributed to the formation of the more complex physiological features that are found in Drosophila.

The SUPERFAMILY database in 2004: additions and improvements

The SUPERFAMILY database provides structural assignments to protein sequences and a framework for analysis of the results. At the core of the database is a library of profile Hidden Markov Models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent an entire superfamily. We have applied the library to predicted proteins from all completely sequenced genomes (currently 154), the Swiss-Prot and TrEMBL databases and other sequence collections. Close to 60% of all proteins have at least one match, and one half of all residues are covered by assignments. All models and full results are available for download and online browsing at http://supfam.org. Users can study the distribution of their superfamily of interest across all completely sequenced genomes, investigate with which other superfamilies it combines and retrieve proteins in which it occurs. Alternatively, concentrating on a particular genome as a whole, it is possible first, to find out its superfamily composition, and secondly, to compare it with that of other genomes to detect superfamilies that are over- or under-represented. In addition, the webserver provides the following standard services: sequence search; keyword search for genomes, superfamilies and sequence identifiers; and multiple alignment of genomic, PDB and custom sequences.

Flavor decomposition of the sea-quark helicity distributions in the nucleon from semiinclusive deep inelastic scattering

Double-spin asymmetries of semiinclusive cross sections for the production of identified pions and kaons have been measured in deep inelastic scattering of polarized positrons on a polarized deuterium target. Five helicity distributions including those for three sea quark flavors were extracted from these data together with reanalyzed previous data for identified pions from a hydrogen target. These distributions are consistent with zero for all three sea flavors. A recently predicted flavor asymmetry in the polarization of the light quark sea appears to be disfavored by the data.

Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum

The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical map, we devised a novel and general strategy, enabling accurate placement of clones regardless of clone artefacts. Analysis reveals a compact genome, unusually rich in membrane proteins. As in Plasmodium falciparum, the mean size of the predicted proteins is larger than that in other sequenced eukaryotes. We find several predicted proteins of interest as potential therapeutic targets, including one exhibiting similarity to the chloroquine resistance protein of Plasmodium. Coding sequence analysis argues against the conventional phylogenetic position of Cryptosporidium and supports an earlier suggestion that this genus arose from an early branching within the Apicomplexa. In agreement with this, we find no significant synteny and surprisingly little protein similarity with Plasmodium. Finally, we find two unusual and abundant repeats throughout the genome. Among sequenced genomes, one motif is abundant only in C. parvum, whereas the other is shared with (but has previously gone unnoticed in) all known genomes of the Coccidia and Haemosporida. These motifs appear to be unique in their structure, distribution and sequences.

Evolution of the protein repertoire

Most proteins have been formed by gene duplication, recombination, and divergence. Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes.

Implications of nondifferential misclassification on estimates of attributable risk

OBJECTIVES

Only the effects of isolated nondifferential misclassification of exposure or disease on the estimates of attributable risk have been discussed in the literature. The aim of this paper is to broaden the spectrum of scenarios for which implications of misclassification are available.

METHODS

For this purpose, a matrix-based approach allowing a comprehensive, unified analysis of various structures of misclassification is introduced. The relative bias or--in the situation of covariate misclassification--the relative adjustment are presented for the different misclassification scenarios.

RESULTS

Under nondifferential misclassification of exposure or disease, the attributable risk is biased towards the null with the only exception of perfect sensitivity of exposure classification or perfect specificity of disease classification both leading to an unbiased attributable risk. From these two marginal effects, the consequences of simultaneous nondifferential independent misclassification of exposure and disease on the attributable risk are derived in the matrix-based approach. Misclassification of a dichotomous covariate leads to partial adjustment.

CONCLUSIONS

To a large extent, the results for the attributable risk are in accordance with the well-known results for the relative risk. The algebraic differences between the two risk measures, however, make it necessary to repeat the methodological considerations for the attributable risk.

Identification and characterization of a novel murine multigene family containing a PHD-finger-like motif

The genes Phf5a and Phf5b-ps are the first two members of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger genes. The Phf5 gene family contains an active locus on mouse chromosome 15, region E and several processed pseudogenes on different chromosomes. The active locus, Phf5a, is expressed ubiquitously in pre- and postnatal murine tissues and encodes a protein of 110 amino acids. The protein is localized in the nucleus in a non-homogenous pattern as the nucleolar subcompartment is almost free of Phf5a. The molecular and biological functions of Phf5a are unknown up-to-date, but the systematic deletion of its yeast homolog is lethal, pointing out that the protein is required for cell viability. Interpretation of our data and review of the literature suggest both basic and essential cellular functions of the Phf5a protein, possibly acting as a chromatin-associated protein.

Hepatic tissue engineering on 3-dimensional biodegradable polymers within a pulsatile flow bioreactor

BACKGROUND

An optimal method for hepatocyte transplantation is not yet determined. With the principles of tissue engineering in vitro conditioning of hepatocytes on biodegradable polymer in a flow bioreactor before implantation forming spheroids may achieve increased cell mass and function to replace lost organ function in vivo.

METHODS

Biodegradable poly-L-lactic (PLLA) polymer discs were seeded with rat hepatocytes in a concentration of 10 x 10(6) cells per ml and exposed to a medium flow of 24 ml/min for 1, 2, 4 and 6 days. The number and diameter of spheroidal aggregates was measured by phase-contrast microscopy. H&E histology was performed. Albumin production as hepatocyte specific function was determined by ELISA.

RESULTS

Spheroids of viable hepatocytes of 50-200 microm in diameter were formed. Both the number and diameter of the spheroids increased during the first 2 days and then remained constant until day 6. Albumin production was maintained throughout the culture period.

CONCLUSION

Short (2- 3 days) pre-transplant conditioning of hepatocytes in a flow bioreactor on biodegradable PLLA resulted in formation of spheroids with a liver-like morphology and preserved specific metabolic function. Tissue engineered hepatocyte spheroids on polymer may represent a functionally active and easy transplantable neotissue and may serve as an in vivo substitute for lost liver function.

Partitioning methods for multifactorial risk attribution

The epidemiological problem of risk attribution in the framework of multiple exposures has been the subject of intensive research activities in the last decade. In particular, partitioning methods have been developed to define new multidimensional measures of attributable risk putting the task of quantifying a proportion of disease events in a population that can be ascribed to the adverse health effects of certain risk factors into a multifactorial perspective. The parameters generalize the concept of attributable risk to different multifactorial frameworks in which multiple exposures might be arranged in hierarchically ordered classes or in equally ranking groups. Partitioning methods are reviewed and differences between the multifactorial variants of attributable risk are illustrated by a component causes model.

Prevention of cisplatin-induced emesis by the oral neurokinin-1 antagonist, MK-869, in combination with granisetron and dexamethasone or with dexamethasone alone

PURPOSE

The NK1-receptor antagonist MK-869 (L-754,030) has demonstrated antiemetic activity in humans receiving chemotherapy. Objectives of the present trial included the first assessment of oral MK-869 plus dexamethasone compared with a 5HT(3) antagonist plus dexamethasone for prevention of acute and delayed emesis after high-dose cisplatin. Furthermore, the study sought to confirm that addition of MK-869 to a 5HT(3) antagonist plus dexamethasone was more effective than just the 5HT(3) antagonist plus dexamethasone for prevention of acute and delayed emesis.

METHODS

This multicenter, double-blind, parallel-group trial in 351 cisplatin-naïve patients evaluated prevention of acute (0 to 24 hours) and delayed emesis (primary efficacy parameter; days 2 to 5) after cisplatin (> or =70 mg/m(2)). Patients were randomized to four groups (I to IV) (n = number randomized; number evaluable): granisetron (10 microg/kg intravenously) pre-cisplatin followed by placebo on days 2 to 5 (group I) (n = 90; 90); granisetron and MK-869 (400 mg PO [by mouth]) pre-cisplatin, followed by MK-869 (300 mg PO) on days 2 to 5 (group II) (n = 86; 84); MK-869 (400 mg PO) the evening before and pre-cisplatin, followed by MK-869 (300 mg PO) on days 2 to 5 (group III) (n = 89; 88); or MK-869 (400 mg PO) pre-cisplatin, followed by MK-869 (300 mg PO) on days 2 to 5 (group IV) (n = 86; 84). All patients also received dexamethasone (20 mg PO) before cisplatin. Additional medication was available to treat emesis or nausea at any time.

RESULTS

In the acute period, 57%, 80%, 46%, and 43% of patients were without emesis in groups I, II, III, and IV, respectively (P <.01 for group II v group I). In the delayed period, the proportion of patients without emesis in groups I, II, III, and IV was 29%, 63%, 51%, and 57%, respectively (P <.01 for groups II, III, and IV v group I). The distribution of nausea scores in the delayed period was lower when comparing group II with group I (P <.05 for days 1 to 5 and days 2 to 5). One serious adverse event (dizziness) was rated as possibly related to MK-869.

CONCLUSION

Once daily oral administration of MK-869 was effective in reducing delayed emesis and nausea after high-dose cisplatin. However, the combination of the 5HT3 antagonist plus dexamethasone was numerically superior to MK-869 plus dexamethasone in reducing acute emesis. Confirming and extending previous findings, the triple combination of a 5HT(3) antagonist, MK-869, and dexamethasone provided the best control of acute emesis.

Thyroid function, thyroid immunoglobulin status, and urinary iodine excretion after enteral contrast-agent administration by endoscopic retrograde cholangiopancreatography

BACKGROUND AND STUDY AIMS

The aim of this study was to examine the occurrence of clinically relevant changes in thyroid function after enteral administration of contrast agent by endoscopic retrograde cholangiopancreatography (ERCP).

PATIENTS AND METHODS

In this study 70 patients without a history of thyroid disease who had not recently undergone thyroid-specific or thyroid-influencing therapy were examined. Patients were examined on two or three occasions using a standardized questionnaire regarding symptoms of hypothyroidism and hyperthyroidism. The parameters of thyroid function (TT3, TT4, FT4, thyroid-stimulating hormone (TSH)) and urinary iodine excretion were measured on day 0 and on day 21 post-ERCP, and in 23 patients additionally on day 42 post-ERCP. Based on ultrasonographic results, four groups differing in thyroid morphology were distinguished.

RESULTS

The data show that an average amount of only 4.7 g of enterally applied iodine is associated with a lasting decrease of TSH, especially in patients with enlarged organs with nodular transformation. As far as TT3 is concerned, there was a significant increase in all patient groups; regarding FT4 we only observed a marked increase in the group with enlarged, nodular thyroid glands. There was a notable increase in urinary iodine excretion on day 21, and a further increase on day 42 post-ERCP. Clinical symptoms of hyperthyroidism did not occur.

CONCLUSIONS

We conclude that before administration of iodine-containing contrast agent for ERCP in patients without a history of thyroid disease, thyroid ultrasonographic examination, rather than TSH measurements, should be performed, in order to identify patients already at risk for hyperthyroidism before diagnostic enteral contrast-medium application.

First-line, single-agent Herceptin(R) (trastuzumab) in metastatic breast cancer. a preliminary report

Following confirmation of the appropriate dosage, safety and potential efficacy of Herceptin(R) (trastuzumab) in small-scale phase I and II trials involving patients with refractory disease, a large trial was conducted in 222 patients with breast cancer who had relapsed after one or two chemotherapy regimens for their metastatic disease. The results showed a positive and durable overall response rate (15% according to a response evaluation committee (REC) assessment) using trastuzumab monotherapy (initial dose 4 mg/kg intravenously (i.v.) followed by 2 mg/kg i.v. weekly). In another recently completed phase II trial, 113 patients were randomised to two dose levels (initial dose of 4 mg/kg i.v. dose followed by 2 mg/kg i.v. weekly, or initial dose of 8 mg/kg followed by 4 mg/kg i.v. weekly) of single-agent trastuzumab as first-line therapy for metastatic disease. The preliminary overall response rate was 23% based on investigator assessment, and tolerability was excellent as in previous trials; efficacy was similar in both dose groups, but the side-effects tended to be more frequent in the higher dose group. The preferred dosage is therefore the same as that currently recommended, i.e. an initial dose of 4 mg/kg i.v. followed by 2 mg/kg weekly i.v. until disease progression.

[Significance of care for children and adolescents victims of domestic violence]

This is a phenomenological and hermeneutic study. Its objective is to reveal the meaning of "care" for children and adolescents who have suffered domestic violence. The investigation was carried out in two casas-lares (orphanage houses) in Florianópolis. These houses functioned as temporary shelters for either girls or boys who had suffered some kind of violence in their homes. The descriptions obtained through the answers and drawings of eighteen children and adolescents enabled us to characterize "care" as a way of promoting life, expressing oneself, relating to the environment, denying past experiences and resisting in order to survive.

First-line, single-agent Herceptin(trastuzumab) in metastatic breast cancer: a preliminary report

Following confirmation of the appropriate dosage, safety and potential efficacy of Herceptin(trastuzumab) in small-scale phase I and II trials involving patients with refractory disease, a large trial was conducted in 222 patients with breast cancer who had relapsed after one or two chemotherapy regimens for their metastatic disease. The results showed a positive and durable overall response rate (15% according to a response evaluation committee (REC) assessment) using trastuzumab monotherapy (initial dose 4 mg/kg intravenously (i.v.) followed by 2 mg/kg i.v. weekly). In another recently completed phase II trial, 113 patients were randomised to two dose levels (initial dose of 4 mg/kg i.v. dose followed by 2 mg/kg i.v. weekly, or initial dose of 8 mg/kg followed by 4 mg/kg i.v. weekly) of single-agent trastuzumab as first-line therapy for metastatic disease. The preliminary overall response rate was 23% based on investigator assessment, and tolerability was excellent as in previous trials; efficacy was similar in both dose groups, but the side-effects tended to be more frequent in the higher dose group. The preferred dosage is therefore the same as that currently recommended, i.e. an initial dose of 4 mg/kg i.v. followed by 2 mg/kg weekly i.v. until disease progression.

Regulation of prostaglandin endoperoxide H synthase-2 induction by dioxin in rat hepatocytes: possible c-Src-mediated pathway

The tumor promoter 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is known to increase the expression of prostaglandin endoperoxide H synthase (PGHS)-2. This study focused on the regulatory mechanism of TCDD-mediated transcriptional activation of PGHS-2. Treatment of rat hepatocytes with TCDD led to a dose-dependent induction of PGHS-2 mRNA levels associated with an increased synthesis of prostaglandin E(2), whereas expression of PGHS-1 was not affected. In vitro experiments with c-Src inhibitors, such as herbimycin A and geldanamycin, and in vivo studies with c-Src-deficient mice indicated that up-regulation of PGHS-2 but not the cytochrome P450 gene CYP1A1 by TCDD is mediated via a c-Src-dependent pathway. Transient transfection studies with different reporter constructs of the murine PGHS-2 promoter mutated in the xenobiotic-responsive element (XRE) or CCAAT/enhancer binding protein (C/EBP) element revealed that a C/EBP-binding site is an important regulatory cis-acting factor for trans-activation of the PGHS-2 gene by TCDD. Consistent with transfection studies, gel mobility shift assays showed that TCDD led to an enhanced DNA-binding activity of C/EBP beta transcription factor. The experimental data presented in this article reveal a XRE-independent and c-Src-mediated activation of the PGHS-2 gene by TCDD through the C/EBP response element located in its promoter region.

Prostaglandin H synthases and their importance in chemical toxicity

The metabolism of a xenobiotic is an important stage resulting in its toxification (bioactivation) or detoxification. The most common reaction is the oxidation catalyzed by the cytochrome P450 (CYP) enzyme system. An alternate enzyme for chemical oxidation is the prostaglandin H synthase (PGHS) also known as cyclooxygenase (COX). The PGHS is the initial enzyme in arachidonate metabolism and formation of prostanoids such as prostaglandins (PG), prostacyclins, and thromboxanes. However, 25 years ago it was found that during the reduction of the endogenous substrate, hydroperoxy-endoperoxide (PGG2) to hydroxy-endoperoxide (PGH2), the PGHS enzyme is capable to "co-oxidize" chemicals. In this reaction, a broad spectrum of chemicals can serve as electron donors such as phenolic compounds, aromatic amines, and polycyclic aromatic hydrocarbons. In contrast to numerous CYP enzymes in liver, the PGI is an alternate enzyme for xenobiotic metabolism in extrahepatic tissues. In respect of tissue distribution, PGHS can play an essential role in the bioactivation of e.g. procarcinogenic chemicals in certain target tissues that possess low CYP monooxygenase activity. Two PGHS isozymes have been identified: PGHS-1 and PGHS-2, which have very similar kinetic properties, but differ in regard to expression and regulation. In recent studies it was shown that not only endogenous stimuli but also drugs and environmental chemicals can activate PGHS-2 expression. Therefore the PGHS enzymes provide two interesting aspects for pharmacology and toxicology: a) the co-oxidation of chemicals and b) the altered synthesis of prostanoids after exposure to certain xenobiotics which can be essential for their ultimate toxicity.