Misleading local sequence alignments: implications for comparative protein modelling

Although it is well known that significant sequence similarity between proteins is reflected at the structural level, it is commonly assumed that any misaligned regions, as judged by the correct structure based alignment, are those where the local sequence identity is lower than the global. Recent studies have shown that this is not always the case and there can exist short stretches of high local identity which is not reflected in the structure based alignment. An analysis is presented of 290 pairs of homologous proteins with a view to quantifying the occurrence of these misleading local sequence alignments (MLSAs). It is found that such MLSAs are likely if the global sequence identity is less than 40% and can occur even when it is greater than 60%. The results have implications for automated homology modelling and also for the inference of function made by comparison.     

In unison: regularization of protein secondary structure predictions that makes use of multiple sequence alignments

We present a method whose purpose is to post-process the fuzzy results of secondary structure prediction methods that use multiple sequence alignments, in order to obtain 'realistic' secondary structures, i.e., secondary structure elements whose length is greater than or equal to some predefined minimum length. This regularization helps with interpretation of the secondary structure prediction.     

CINEMA--a novel colour INteractive editor for multiple alignments

CINEMA is a new editor for manipulating and generating multiple sequence alignments. The program provides both an interface to existing databases of alignments on the Internet and a tool for constructing and modifying alignments locally. It is written in Java, so executable code will run on most major desktop platforms without modification. The implementation is highly flexible, so the applet can be easily customised with additional functions; and the object classes are reusable, promoting rapid development of program extensions. Formerly, such extended functionality might have been provided via browser plug-ins, which have to be downloaded and installed on every client before loading data. Now, for the first time, an applet is available that allows interactive client-side processing of an alignment, which can then be stored or processed automatically on the server. The program is embedded in a comprehensive help file and is accessible both as a stand-alone tool on UCL's Bioinformatics Server; http:/(/)www.biochem.ucl.ac.uk/bsm/dbbrowser+ ++/CINEMA2.02/, and as an integral part of the PRINTS protein fingerprint database. Exploitation of such novel technologies revolutionises the way users may interact with public databases in the future: bioinformatics centres need not simply provide data, but are now able to offer the means by which information is visualised and manipulated, without the requirement for users to install software.     

Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments

The feasibility of predicting the global fold of small proteins by incorporating predicted secondary and tertiary restraints into ab initio folding simulations has been demonstrated on a test set comprised of 20 non-homologous proteins, of which one was a blind prediction of target 42 in the recent CASP2 contest. These proteins contain from 37 to 100 residues and represent all secondary structural classes and a representative variety of global topologies. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Predicted tertiary restraints are derived from multiple sequence alignments via a two-step process. First, seed side-chain contacts are identified from correlated mutation analysis, and then a threading-based algorithm is used to expand the number of these seed contacts. A lattice-based reduced protein model and a folding algorithm designed to incorporate these predicted restraints is described. Depending upon fold complexity, it is possible to assemble native-like topologies whose coordinate root-mean-square deviation from native is between 3.0 A and 6.5 A. The requisite level of accuracy in side-chain contact map prediction can be roughly 25% on average, provided that about 60% of the contact predictions are correct within +/-1 residue and 95% of the predictions are correct within +/-4 residues. Precision in tertiary contact prediction is more critical than absolute accuracy. Furthermore, only a subset of the tertiary contacts, on the order of 25% of the total, is sufficient for successful topology assembly. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm holds considerable promise for the prediction of the global topology of small proteins.     

Evolution of the cytochrome P450 superfamily: sequence alignments and pharmacogenetics

The evolution of the cytochrome P450 (CYP) superfamily is described, with particular reference to major events in the development of biological forms during geological time. It is noted that the currently accepted timescale for the elaboration of the P450 phylogenetic tree exhibits close parallels with the evolution of terrestrial biota. Indeed, the present human P450 complement of xenobiotic-metabolizing enzymes may have originated from coevolutionary 'warfare' between plants and animals during the Devonian period about 400 million years ago. A number of key correspondences between the evolution of P450 system and the course of biological development over time, point to a mechanistic molecular biology of evolution which is consistent with a steady increase in atmospheric oxygenation beginning over 2000 million years ago, whereas dietary changes during more recent geological time may provide one possible explanation for certain species differences in metabolism. Alignment between P450 protein sequences within the same family or subfamily, together with across-family comparisons, aid the rationalization of drug metabolism specificities for different P450 isoforms, and can assist in an understanding of genetic polymorphisms in P450-mediated oxidations at the molecular level. Moreover, the variation in P450 regulatory mechanisms and inducibilities between different mammalian species are likely to have important implications for current procedures of chemical safety evaluation, which rely on pure genetic strains of laboratory bred rodents for the testing of compounds destined for human exposure.     

Identification of potential ferric binding residues in the iron-binding protein of pathogenic Neisseria meningitidis through structure-based multiple sequence alignments

Toxic effects of hyperglycemia-induced advanced glycosylated end products (AGEs) may explain some vasculopathic complications of diabetes. Aminoguanidine, a known inhibitor of AGE formation, was administered by gavage to Sprague-Dawley streptozotocin-induced diabetic rats made azotemic by surgical reduction of renal mass. All rats became hyperglycemic. Renal ablation caused renal insufficiency, as evidenced by markedly reduced endogenous creatinine clearances at days 7 and 14. Aminoguanidine-treated rats had significantly (P < 0.04) superior survival to that of untreated azotemic diabetic rats. We infer from the extended life in a rat model of uremia in diabetic nephropathy that aminoguanidine may prove beneficial in human diabetes.     

Akathisia diagnosis: an objective test

In summary, we have attempted, in planning the Diploma Nursing Program at Okanagan College, to retain the positive aspects of existent hospital and college programs, while at the same time developing some unique features: a health promotion focus, a comprehensive curriculum framework and a cooperative education design. As yet, in this first year the program, it is too early to predict outcomes, but we anticipate that our students will be better equipped to deal with the reality of a work situation.     

Heat shock protein 70 family: multiple sequence comparisons, function, and evolution

The heat shock protein 70 kDa sequences (HSP70) are of great importance as molecular chaperones in protein folding and transport. They are abundant under conditions of cellular stress. They are highly conserved in all domains of life: Archaea, eubacteria, eukaryotes, and organelles (mitochondria, chloroplasts). A multiple alignment of a large collection of these sequences was obtained employing our symmetric-iterative ITERALIGN program (Brocchieri and Karlin 1998). Assessments of conservation are interpreted in evolutionary terms and with respect to functional implications. Many archaeal sequences (methanogens and halophiles) tend to align best with the Gram-positive sequences. These two groups also miss a signature segment [about 25 amino acids (aa) long] present in all other HSP70 species (Gupta and Golding 1993). We observed a second signature sequence of about 4 aa absent from all eukaryotic homologues, significantly aligned in all prokaryotic sequences. Consensus sequences were developed for eight groups [Archaea, Gram-positive, proteobacterial Gram-negative, singular bacteria, mitochondria, plastids, eukaryotic endoplasmic reticulum (ER) isoforms, eukaryotic cytoplasmic isoforms]. All group consensus comparisons tend to summarize better the alignments than do the individual sequence comparisons. The global individual consensus "matches" 87% with the consensus of consensuses sequence. A functional analysis of the global consensus identifies a (new) highly significant mixed charge cluster proximal to the carboxyl terminus of the sequence highlighting the hypercharge run EEDKKRRER (one-letter aa code used). The individual Archaea and Gram-positive sequences contain a corresponding significant mixed charge cluster in the location of the charge cluster of the consensus sequence. In contrast, the four Gram-negative proteobacterial sequences of the alignment do not have a charge cluster (even at the 5% significance level). All eukaryotic HSP70 sequences have the analogous charge cluster. Strikingly, several of the eukaryotic isoforms show multiple mixed charged clusters. These clusters were interpreted with supporting data related to HSP70 activity in facilitating chaperone, transport, and secretion function. We observed that the consensus contains only a single tryptophan residue and a single conserved cysteine. This is interpreted with respect to the target rule for disaggregating misfolded proteins. The mitochondrial HSP70 connections to bacterial HSP70 are analyzed, suggesting a polyphyletic split of Trypanosoma and Leishmania protist mitochondrial (Mt) homologues separated from Mt-animal/fungal/plant homologues. Moreover, the HSP70 sequences from the amitochondrial Entamoeba histolytica and Trichomonas vaginalis species were analyzed. The E. histolytica HSP70 is most similar to the higher eukaryotic cytoplasmic sequences, with significantly weaker alignments to ER sequences and much diminished matching to all eubacterial, mitochondrial, and chloroplast sequences. This appears to be at variance with the hypothesis that E. histolytica rather recently lost its mitochondrial organelle. T. vaginalis contains two HSP70 sequences, one Mt-like and the second similar to eukaryotic cytoplasmic sequences suggesting two diverse origins.     

New flexible approaches for multiple sequence alignment

The multiple sequence alignment problem is applicable and important in various fields in molecular biology such as the prediction of three-dimensional structures of proteins and the inference of phylogenetic trees. However, the optimal alignment based on the scoring criterion is not always biologically the most significant alignment. We here propose two flexible and efficient approaches to solve this problem. One approach is to provide many suboptimal alignments as alternatives for the optimal one. It has been considered almost impossible to investigate such suboptimal alignments of more than two sequences because of the enormous size of the problem. We propose techniques for enumeration of suboptimal alignments using the Eppstein algorithm. We also discuss what kind of suboptimal alignment is unnecessary to enumerate and propose an efficient enumeration algorithm to enumerate only necessary alignments. The other approach is parametric analysis. The obtained optimal solution with fixed parameters such as gap penalties is not always the biologically best alignment. Thus, it is required to vary parameters and check how the optimal alignments change. The way to vary parameters has been studied well on the problem of two sequences, but not on the multiple alignment problem because of the difficulty of computing the optimal solution. We propose techniques for this parametric multiple alignment problem and examine the features of alignments obtained by various parametric analyses. For both approaches, this paper performs experiments on various groups of actual protein sequences and examines the efficiency of these algorithms and properties of sequence groups.     

A genetic algorithm for multiple molecular sequence alignment

MOTIVATION: Multiple molecular sequence alignment is among the most important and most challenging tasks in computational biology. The currently used alignment techniques are characterized by great computational complexity, which prevents their wider use. This research is aimed at developing a new technique for efficient multiple sequence alignment. APPROACH: The new method is based on genetic algorithms. Genetic algorithms are stochastic approaches for efficient and robust searching. By converting biomolecular sequence alignment into a problem of searching for optimal or near-optimal points in an 'alignment space', a genetic algorithm can be used to find good alignments very efficiently. RESULTS: Experiments on real data sets have shown that the average computing time of this technique may be two or three orders lower than that of a technique based on pairwise dynamic programming, while the alignment qualities are very similar. AVAILABILITY: A C program on UNIX has been written to implement the technique. It is available on request from the authors.     

An approach to an objective criterion for research managers.

Traditional clinical rating practices for evaluating research-manager performance are mainly subjective and fail to objectively quantify performance. This research shows that quantification is possible using operation-research techniques for group-centered evaluation. The technique was tested by evaluating manager performance in 4 dissimilar departments averaging 19 professional men each. An upper-management executive supplied comparative clinical ratings. A mathematical model provided a framework permitting objective study of each department's contribution in relation to company goals. The technique has exceptional analytical qualities and permits convenient quantification of research-manager performance. The results suggest that the validity of the clinical, subjective approach to management evaluation should be questioned. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

SMAS rhytidectomy versus deep plane rhytidectomy: an objective comparison

Although there are a multitude of techniques currently used for performing face lifts, there is no general agreement as to which, if any, of these techniques is most effective. There may never be a definitive answer to this issue because of the highly subjective nature of aesthetics, variability among surgeons, differences in patient anatomy, and specific patient desires. In an attempt to evaluate face lift techniques objectively, this study compares the rate of patients undergoing a tuck procedure after traditional SMAS (superficial musculoaponeurotic system) rhytidectomy to that of patients after deep plane rhytidectomy. A retrospective chart review was performed on all patients who underwent a tuck procedure following a face lift by the senior author (Kamer) between July of 1990 and January of 1997. There were 634 patients who electively underwent either a SMAS or deep plane type of rhytidectomy during the 6.5-year period; 48 patients subsequently underwent tuck operations, and adequate information was available on 44 patients. Of these, 43 were women and the average age was 57 years. The overall tuck rate from July of 1990 to January of 1997 was 7.5 percent. The tuck rate following SMAS rhytidectomy was 11.4 percent, and that following deep plane rhytidectomy was 3.3 percent. Therefore, a tuck was required 71 percent less frequently after a deep plane lift than after a SMAS lift. This was found to be a statistically significant difference with a p value of .0001 (Fisher's exact test, 2-tail). If the assumption is made that the need for a tuck procedure implies a less than optimal face lift, then the data of this study suggest that the deep plane technique is more effective than the SMAS technique.     

Pulsus paradoxus: an objective measure of severity in croup

We used a noninvasive monitor of arterial pressure to determine the utility of pulsus paradoxus (PP) as an objective severity measure in croup. We performed a prospective, blinded comparison of PP in children with croup versus healthy control subjects, analyzed the relationship between PP and Westley croup score (WCS), and observed the effect of racemic epinephrine (RE) on PP and WCS in a subgroup of patients with severe croup. The PP and WCS were measured at presentation and in severe patients after treatment with RE. Mean PP was 6.1 +/- 1.8 (SD) mm Hg (n = 29) in control subjects compared with a mean of 17.8 +/- 11.2 (SD) mm Hg (n = 28) in patients with croup (p < 0.00001). There was significant concordance between baseline WCS and PP (Spearman's rho: 0.68; p = 0.0001). The mean decrease in PP after RE was 7.5 +/- 11.8 (SD) mm Hg (p = 0.05; n = 12). The magnitude of decrease in PP after RE has significant concordance with the concurrent decrease in WCS (Spearman's rho: 0.73; p < 0.007). PP is elevated in children with croup, and the magnitude of elevation correlates with severity as measured by the WCS. PP may have utility as a research tool to objectively measure the severity of upper airway obstruction in croup.     

Surgical training: an objective assessment of recent changes for a single health board

The reduction in doctors' hours and the introduction of specialist training have reduced general surgical training by 60%. This study assessed the implications for a single health board. A questionnaire listing 13 representative operations was sent to 44 trainees and 52 trainers to determine the number of operations a trainee should perform. The total number of operations required for training was compared against the total actually performed across the health board. Operating times for five representative operations were audited prospectively. Trainers and trainees recommended a similar and conservative number of operations. The total number of operations available for training (4913) was 38% less than the number recommended (7946). Trainees required 50-75% more operating time than consultants. To increase the proportion of operations undertaken by trainees from the current 30% to 70% would require an extra 270 theatre days (of pounds 1.3m) yearly. The minimum number of operations required for training must be defined and the proportion of supervised operations undertaken by trainees substantially increased. Service and financial implications will have to be addressed. Action is needed urgently, as the first trainees will become consultants in less than five years.     

Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments

A number of methods exist for the prediction of protein secondary structure from primary sequence. One method identifies variable charged and conserved hydrophobic residues within large multiple alignments as a means of indicating outside and inside sites respectively in the protein structure. These sites are then manually fitted to secondary structure templates to generate a secondary structure prediction. Using the existing theoretical bases of this method, we present an algorithm (STAMA) which automatically carries out the initial variation/conservation analysis of the alignment. We also test the accuracy of complete predictions carried out by manual fitting of the STAMA-derived assignments to structure templates, using five large multiple alignments each including a protein of known structure. The method was found on average to predict only 57% of residues in the correct secondary structure, and was only as accurate as predictions carried out using the established and automated method of Garnier, Osguthorpe and Robson (1978) applied to a single sequence. When used in conjunction with other secondary structure prediction methods, however, the resulting consensus predictions were found to be very accurate, with 78% of the elements (alpha helices or beta strands) for which a consensus could be obtained being predicted correctly. The algorithm presented here, plus the assessment of the accuracy of prediction generated by this method, should enable this predictive approach to receive informed general use.     

HOMSTRAD: a database of protein structure alignments for homologous families

We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X-ray analysis and accuracy of the structure. For each family, the database provides a structure-based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www-cryst.bioc.cam. ac.uk/-homstrad/, with search facilities and links to other databases.     

Eradication of Helicobacter pylori: an objective assessment of current therapies

The purpose of the present review was to determine objectively the optimal treatment for the eradication of H. pylori amongst the currently used regimens. A comprehensive literature search provided a data-base relating to the following treatments: dual therapy with an anti-secretory drug plus either amoxycillin or clarithromycin; standard triple therapy, with or without additional anti-secretory drugs; proton pump inhibitor triple therapy; and H2-receptor antagonist triple therapy. Emphasis was placed on intention-to-treat analyses of eradication rates using all of the available evidence. The criteria used to select the optimal treatment were efficacy (eradication rates), frequency of side-effects, simplicity of the regimen (number of tablets per day and duration of treatment) and cost. The analysis showed that proton pump inhibitor triple therapy (that is, a proton pump inhibitor plus any two of amoxycillin, clarithromycin or a nitroimidazole) was the preferred treatment for the eradication of H. pylori. In particular, the 1-week, low-dose regimen with omeprazole plus clarithromycin plus tinidazole produced the highest eradication rates (> 90%) with the lowest frequency of side-effects and at only modest cost.