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PubMed2006

The relationship between protein sequences and their gene ontology functions.

BACKGROUND: One main research challenge in the post-genomic era is to understand the relationship between protein sequences and their biological functions. In recent years, several automated annotation systems have been developed for the functional assignment of uncharacterized proteins. The underlying assumption of these systems is that similar sequences imply similar biological functions. However, it has been noted that matching sequences do not always infer similar functions. RESULTS: In this paper, we present the correlation between protein sequences and protein functions for the yeast proteome in the context of gene ontology. A novel measure is introduced to define the overall similarity between two protein sequences. The effects of the level as well as the size of a gene ontology group on the degree of similarity were studied. The similarity distributions at different levels of gene ontology trees are presented. To evaluate the theoretical prediction power of similar sequences, we computed the posterior probability of correct predictions. CONCLUSION: The results indicate that protein pairs of similar biological functions tend to have higher sequence similarity, although the similarity distribution in each functional group is heterogeneous and varies from group to group. We conclude that sequence similarity can serve as a key measure in protein function prediction. However, the resulting annotations must be verified through other means. A method that combines a broader range of measures is more likely to provide more accurate prediction. Our study indicates that the posterior probability of a correct prediction could serve as one of the key measures.

Amino Acid Sequence↗

PubMed1997

Molecular and structural characterization of five novel mutations in the Bruton's tyrosine kinase gene from patients with X-linked agammaglobulinemia.

BACKGROUND: The Btk (Bruton's tyrosine kinase) gene has been shown to be mutated in the human immunodeficiency disease, XLA (X-linked agammaglobulinemia). Btk is a member of the Tec family of cytosolic protein tyrosine kinases with distinct functional domains PH, TH, SH3, SH2, and kinase. Mutations have been observed in each of the Btk subdomains in XLA. We have analyzed the Btk gene in six XLA patients from five unrelated families. MATERIALS AND METHODS: DNA was prepared from the patients peripheral blood. The Btk exons including the junctional sequences were analyzed by single-strand conformation polymorphism (SSCP) followed by direct nucleotide sequencing after PCR-amplification. For structural analysis, the missense mutations were introduced into three-dimensional models of the PH and kinase domains of Btk and the outcome was predicted based on the knowledge of the protein function. RESULTS: Five novel mutations and two novel polymorphisms, all of which resulted from single-base alterations, were identified. Three of the five mutations were in the PH domain and two were in the kinase domain of Btk. Three of these mutations were of the missense type, two of which altered the same codon in the PH domain; the third one was located in the kinase domain. The fourth mutation was a point deletion in the PH domain causing a frameshift followed by premature termination. The fifth mutation was a splice donor-site mutation within the kinase domain which could result in an exon skipping. In four of the five instances, mothers of the patients were shown to be obligate carriers. In one instance, a sibling sister was identified as a heterozygote establishing her as a carrier. CONCLUSIONS: Functional consequences of the mutations causing frameshifts and altered splicing can be inferred directly. Functional consequences of the missense mutations were interpreted by 3-dimensional structural modeling of Btk domains. It is proposed that the two PH domain mutations will interfere with membrane localization while the kinase domain mutation will interfere with the enzymatic function of Btk. This study provides further insight into the role of Btk in XLA.

Adult↗

PubMed2006

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

BACKGROUND: Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. DESCRIPTION: From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. CONCLUSION: Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families.

Animals↗

PubMed1995

Form-function correspondences in children's inference.

Perceptual similarity among concept members has been viewed as inadequate to motivate concept formation. Instead, it has been argued that intuitive beliefs about the world offer more structured motivation for concepts. Our research explores children's beliefs about the relations between perceptually based similarity among things and their predicted behaviors. We focus on form-function correspondences as fundamental components of very young children's belief systems. Groups of 2- and 4-year-old children were asked to choose which of 2 line-drawn animals evidenced a particular "function," a special behavior. Even the youngest children showed sensitivity to form-function correspondences by selecting the animal whose form afforded the particular function. A second study investigated how form-function correspondences affect the relative influences of perceptual similarity and shared labels over patterns of children's inference. Perceptual similarity, if "motivated" by intuitive beliefs about correspondences between form and function, was found to be sufficient basis for inference and a more robust basis than shared labels when children attributed meaningful functions to novel animal forms.

Animals↗

PubMed1994

Mandibular growth and function in Archaeolemur.

Ontogenetic changes in the morphology of the mandibular symphysis are described in Archaeolemur so as to infer the functional significance of symphyseal fusion in this subfossil Malagasy lemur. The first regions of the symphysis to show a more complex morphology were the lower and anterior borders of the joint and, to a lesser extent, the lingual borders of the superior and inferior transverse tori. During growth, these regions became increasingly rugose and encroached upon a centrally located, smooth, "oval" region, which may have been a principal pathway for neurovascular structures communicating with the unfused joint. In subadults, the symphysis was completely fused except for the lingual surface of the inferior transverse torus, where a patent suture and potential space were present between dentaries. Thus, in Archaeolemur there was an age- and size-related pattern of increased symphyseal ossification or fusion that was complete by adulthood. The morphology of the interlocking bony processes and the sequence of ossification in the symphysis suggest that increased dorsoventral shear stress during mastication was the most likely determinant of symphyseal fusion in Archaeolemur. The allometric pattern of greater symphyseal fusion may be linked to the presence of relatively greater dorsoventral shear in adults due to an increased recruitment of balancing-side jaw-muscle force. There is little indication that the symphysis of juvenile Archaeolemur was buttressed to resist forces associated with "wishboning" during mastication or vertical bending during incision. Our observations, as well as those of others, suggest that symphyseal fusion in primates occurs initially as a response to increased dorsoventral shear during mastication. Therefore, wishboning stress might only become a major determinant of symphyseal form and function in those taxa that develop a fused symphysis to counter increased dorsoventral shear.

Animals↗

PubMed2002

A powerful non-homology method for the prediction of operons in prokaryotes.

MOTIVATION: The prediction of the transcription unit organization of genomes is an important clue in the inference of functional relationships of genes, the interpretation and evaluation of transcriptome experiments, and the overall inference of the regulatory networks governing the expression of genes in response to the environment. Though several methods have been devised to predict operons, most need a high characterization of the genome analysed. Log-likelihoods derived from inter-genic distance distributions work surprisingly well to predict operons in Escherichia coli and are available for any genome as soon as the gene sets are predicted. RESULTS: Here we provide evidence that the very same method is applicable to any prokaryotic genome. First, the method has the same efficiency when evaluated using a collection of experimentally known operons of Bacillus subtilis. Second, operons among most if not all prokaryotes seem to have the same tendencies to keep short distances between their genes, the most frequent distances being the overlaps of four and one base pairs. The universality of this structural feature allows us to predict the organization of transcription units in all prokaryotes. Third, predicted operons contain a higher proportion of genes with related phylogenetic profiles and conservation of adjacency than predicted borders of transcription units.

Algorithms↗

PubMed2007

Impaired cardiac autonomic function in women with prior gestational diabetes mellitus.

BACKGROUND: Cardiac autonomic neuropathy is a common dysfunction in manifest diabetes mellitus and is associated with duration of diabetes and/or an inadequate glycaemic control. Heart rate variability (HRV) reflects autonomic heart function. The aim of the present study was to investigate whether in women with prior gestational diabetes (GD; pre-type 2 diabetes) alterations of cardiac autonomic function can be observed after delivery in relation to insulin sensitivity and glycaemic control. MATERIALS AND METHODS: Forty-eight healthy women with prior GD were consecutively admitted to the study. HRV was analysed by both time, as well as frequency, domain methods using 24-h Holter monitoring. In addition, 20 women with normal glucose tolerance during and after pregnancy were investigated as control subjects. All women underwent a frequently sampled intravenous glucose tolerance test (FSIGT) for measurement of insulin sensitivity. RESULTS: Time domain analysis (standard deviation of normal RR intervals; SDNN) showed a reduced HRV in 25 out of the 48 (52%) women with prior GD. Frequency domain analysis revealed that in these 25 subjects both low and high frequency components of power spectral density (reflecting mainly sympathetic respectively parasympathetic activity) were reduced, indicating that sympathetic as well as parasympathetic functional impairment may be assumed. However, a relative predominance of the sympathetic over parasympathetic cardiac function was observed. The impairment of cardiac autonomic function (reduced SDNN) was correlated with HbA1c values and the 2-h blood glucose concentration (oral glucose tolerance test) but not with insulin sensitivity. CONCLUSION: The present results demonstrate that in 52% of the women examined who had prior GD, an impairment of cardiac sympathetic as well as parasympathetic function was present, which related to glycaemic control, but not to insulin sensitivity. This infers that functional autonomic changes could be an early prognostic indicator in pre-type 2 diabetes.

Adult↗

PubMed1990

[Changes in mechanical and functional processes of the lower esophageal sphincter in patients with reflux esophagitis].

The present study was performed to establish eventual inferences of functional and mechanical alterations of the lower esophageal sphincter (LES) in determining reflux esophagitis. The LES basal pressure, the percentual incidence of the incoordinate LES relaxations swallowing-induced, the LES overall and abdominal length, with gastroesophageal reflux disease (GERD), with and without endoscopic evidence of esophagitis, were manometrically evaluated in 117 consecutive patients. In patients with symptomatic GERD, a significant LES pressure reduction, which is inversely related to the severity of the endoscopic mucosal damage, an increased prevalence of the incoordinate LES relaxations swallowing-induced and, only in patients with esophagitis, a significant reduction of the LES overall and abdominal length of the LES, were showed. Two or three alterations of the LES antireflux devices can occur in the same patient, thus increasing the risk of esophagitis.

Adolescent↗

PubMed2002

Using fold recognition to search for useful proteins: Bayesian approach to fold recognition.

The wealth of protein sequence and structure data is greater than ever, thanks to the ongoing Genomics and Structural Genomics projects. The information available through such efforts needs to be analysed by new methods that combine both databases. One important result of genomic sequence analysis is the inference of functional homology among proteins. Until recently sequence similarity comparison was the only method for homologue inference. The new fold recognition approach reviewed in this paper enhances sequence comparison methods by including structural information in the process of protein comparison. This additional information often allows for the detection of similarities that cannot be found by methods that only use sequence information.

Amino Acid Sequence↗

PubMed1990

Next steps in describing aging and disease in longitudinal studies.

Longitudinal studies have contributed much to the understanding of aging. Traditionally, age-specific changes in physiological functioning are inferred from studies in which persons with disease processes believed to be relevant to the function in question are excluded from the results. The main theme of this review is that, in the future, studies of aging must better attempt to capture the interplay between disease and aging processes. A variety of research results, mostly from the Baltimore Longitudinal Study of Aging, are used to support this argument. Topics covered include: the role of longitudinal studies in aging research; the complexity of the aging process; the significance of cohort and secular changes for understanding both aging and disease processes; age changes over the adult life span in the significance of risk factors for disease; and age-related increases in morbidity in a longevous group of men.

Aging↗

PubMed1997

Quantification of cerebral blood flow and partition coefficient using iodine-123-iodoamphetamine.

UNLABELLED: The aim of this study was to develop a simple, noninvasive method for quantifying both regional cerebral blood flow (rCBF) and the partition coefficient (lambda) using N-isopropyl-p[123I]iodoamphetamine and SPECT. METHODS: By employing a two-compartment model (influx, K1: outflux, k2), a new method was introduced that requires two serial SPECT scans at 30 min and 60 min, and a single arterial sample 5 min after tracer injection. The integral of the arterial input function is inferred from the sample by using the correlation obtained from 25 subjects. Two original mathematical functions, phi for K1 and gamma for lambda (= K1/k2), were obtained from the input functions of 12 subjects. The values of K1 and lambda are determined from the two scans and the single arterial sample by using these functions. The values obtained for K1 (= rCBF) and lambda were compared with those obtained by nonlinear least-squares fitting analysis and the 133Xe inhalation SPECT method. RESULTS: K1 and lambda were in good agreement with the values obtained by nonlinear least-squares fitting analysis (r = 0.873 in K1 and r = 0.825 in lambda), and rCBF values were closely correlated with those obtained by the 133Xe method (r = 0.843). CONCLUSION: The proposed method has three advantages: (a) accurate, simultaneous quantification of both rCBF and the partition coefficient; (b) simplicity and noninvasiveness; and (c) a relatively short period (approximately 70 min) for the study.

Amphetamines↗

PubMed2006

Gene evolution and drug discovery.

Mutation and selection are the principle forces governing gene and protein sequence. Mutation is the major source of variation, and selection removes variation. Although many mutations are likely to be neutral with respect to natural selection, much of the extant sequence that is functionally important has experienced selective pressures in the past. By examining the history of DNA sequences, we can infer the functional importance of particular residues and the selective pressures that have influenced their evolution. In this chapter, we review the most interesting approaches for inferring the evolutionary history of DNA and protein sequences and indicate how these analyses can be useful in the drug discovery process.

Animals↗

PubMed2002

Water quality functioning of lowland permeable catchments: inferences from an intensive study of the RIVER KENNEt and upper River Thames.

This paper brings together information on the water quality functioning of the River Kennet and other parts of the upper River Thames in the south east of England. The Kennet represents a groundwater fed riverine environment impacted by agricultural and sewage sources of nutrient pollution. Descriptions of the general water quality of the area, nutrient sources, sinks and within river processes are provided together with biological responses to driving issues of agriculture, sewage treatment and climatic change. Models are developed and applied to assess the key processes involved for a highly dynamic system and to provide initial estimates of the likely responses to environmental change. Furthermore, the economic aspects of pollution control are reviewed, together with legislation issues, which are presented within the context of a landmark case known as the 'Axford Inquiry', the implications of which extend to regional and national dimensions. The paper concludes with a discussion on the present state of knowledge, key issues and future research on the science and management of groundwater fed nutrient impacted riverine systems.

Agriculture↗

PubMed1996

The effect of variance function estimation on nonlinear calibration inference in immunoassay data.

Often with data from immunoassays, the concentration-response relationship is nonlinear and intra-assay response variance is heterogeneous. Estimation of the standard curve is usually based on a nonlinear heteroscedastic regression model for concentration-response, where variance is modeled as a function of mean response and additional variance parameters. This paper discusses calibration inference for immunoassay data which exhibit this nonlinear heteroscedastic mean-variance relationship. An assessment of the effect of variance function estimation in three types of approximate large-sample confidence intervals for unknown concentrations is given by theoretical and empirical investigation and application to two examples. A major finding is that the accuracy of such calibration intervals depends critically on the nature of response variance and the quality with which variance parameters are estimated.

Algorithms↗

PubMed2003

Automatic annotation of protein function based on family identification.

Although genomes are being sequenced at an impressive rate, the information generated tells us little about protein function, which is slow to characterize by traditional methods. Automatic protein function annotation based on computational methods has alleviated this imbalance. The most powerful current approach for inferring the function of new proteins is by studying the annotations of their homologues, since their common origin is assumed to be reflected in their structure and function. Unfortunately, as proteins evolve they acquire new functions, so annotation based on homology must be carried out in the context of orthologues or subfamilies. Evolution adds new complications through domain shuffling: homology (or orthology) frequently corresponds to domains rather than complete proteins. Moreover, the function of a protein may be seen as the result of combining the functions of its domains. Additionally, automatic annotation has to deal with problems related to the annotations in the databases: errors (which are likely to be propagated), inconsistencies, or different degrees of function specification. We describe a method that addresses these difficulties for the annotation of protein function. Sequence relationships are detected and measured to obtain a map of the sequence space, which is searched for differentiated groups of proteins (similar to islands on the map), which are expected to have a common function and correspond to groups of orthologues or subfamilies. This mapmaking is done by applying a clustering algorithm based on Normalized cuts in graphs. The domain problem is addressed in a simple way: pairwise local alignments are analyzed to determine the extent to which they cover the entire sequence lengths of the two proteins. This analysis determines both what homologues are preferred for functional inheritance and the level of confidence of the annotation. To alleviate the problems associated with database annotations, the information on all the homologues that are grouped together with the query protein are taken into account to select the most representative functional descriptors. This method has been applied for the annotation of the genome of Buchnera aphidicola (specific host Baizongia pistaciae). Human inspection of the annotations allowed an estimation of accuracy of 94%; the different kinds of error that may appear when using this approach are described. Results can be accessed at http://www.pdg.cnb.uam.es/funcut.html. The programs are available upon request, although installation in other systems may be complicated.

Algorithms↗

PubMed2003

Functional MR images and scientific inference: reproducibility maps.

Historically, reproducibility has been the sine qua non of experimental findings that are considered to be scientifically useful. Typically, findings from functional magnetic resonance imaging (fMRI) studies are assessed with statistical parametric maps (SPMs) using a p value threshold. However, a smaller p value does not imply that the observed result will be reproducible. In this study, we suggest interpreting SPMs in conjunction with reproducibility evidence. Reproducibility is defined as the extent to which the active status of a voxel remains the same across replicates conducted under the same conditions. We propose a methodology for assessing reproducibility in functional MR images without conducting separate experiments. Our procedures include the empirical Bayes method for estimating effects due to experimental stimuli, the threshold optimization procedure for assigning voxels to the active status, and the construction of reproducibility maps. In an empirical example, we implemented the proposed methodology to construct reproducibility maps based on data from the study by Ishai et al. (2000). The original experiments involved 12 human subjects and investigated brain regions most responsive to visual presentation of 3 categories of objects: faces, houses, and chairs. The brain regions identified included occipital, temporal, and fusiform gyri. Using our reproducibility analysis, we found that subjects in one of the experiments exercised at least 2 mechanisms in responding to visual objects when performing alternately matching and passive tasks. One gave activation maps closer to those reported in Ishai et al., and the other had related regions in the precuneus and posterior cingulate. The patterns of activated regions are reproducible for at least 4 out of 6 subjects involved in the experiment. Empirical application of the proposed methodology suggests that human brains exhibit different strategies to accomplish experimental tasks when responding to stimuli. It is important to correlate activations to subjects' behavior such as reaction time and response accuracy. Also, the latency between the stimulus presentation and the peak of the hemodynamic response function varies considerably among individual subjects according to types of stimuli and experimental tasks. These variations per se also deserve scientific inquiries. We conclude by discussing research directions relevant to reproducibility evidence in fMRI.

Brain↗

PubMed2001

The sequence and antiapoptotic functional domains of the human cytomegalovirus UL37 exon 1 immediate early protein are conserved in multiple primary strains.

The human cytomegalovirus UL37 exon 1 gene encodes the immediate early protein pUL37x1 that has antiapoptotic and regulatory activities. Deletion mutagenesis analysis of the open reading frame of UL37x1 identified two domains that are necessary and sufficient for its antiapoptotic activity. These domains are confined within the segments between amino acids 5 to 34, and 118 to 147, respectively. The first domain provides the targeting of the protein to mitochondria. Direct PCR sequencing of UL37 exon 1 amplified from 26 primary strains of human cytomegalovirus demonstrated that the promoter, polyadenylation signal, and the two segments of pUL37x1 required for its antiapoptotic function were invariant in all sequenced strains and identical to those in AD169 pUL37x1. In total, UL37 exon 1 varies between 0.0 and 1.6% at the nucleotide level from strain AD169. Only 11 amino acids were found to vary in one or more viral strains, and these variations occurred only in the domains of pUL37x1 dispensable for its antiapoptotic function. We infer from this remarkable conservation of pUL37x1 in primary strains that this protein and, probably, its antiapoptotic function are required for productive replication of human cytomegalovirus in humans.

Amino Acid Sequence↗

PubMed1997

Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila.

Drosophila alcohol dehydrogenase (Adh) is highly conserved in size, organization, and amino acid sequence. Adh-psi was hypothesized to be a pseudogene derived from an Adh duplication in the repleta group of Drosophila; however, several results from molecular analyses of this gene conflict with currently held notions of molecular evolution. Perhaps the most difficult observations to reconcile with the pseudogene hypothesis are that the hypothetical replacement sites of Adh-psi evolve only slightly more quickly than replacement sites of closely related, functional Adh genes, and that the replacement sites of the pseudogenes evolve considerably more slowly than neighboring silent sites. The data have been presented as a paradox that challenges our understanding of the mechanisms underlying DNA sequence divergence. Here I show that Adh-psi is actually a new, functional gene recently descended from an Adh duplication. This descendant recruited approximately 60 new N-terminal amino acids, is considerably more basic than ADH, and is evolving at a faster rate than Adh. Furthermore, though the descendant is clearly functional, as inferred from molecular evolution and population genetic data, it retains no obvious ADH activity. This probably reflects functional divergence from its Adh ancestor.

Alcohol Dehydrogenase↗