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Results for “functional inference”

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PubMed1998

Gabor spectra for Doppler echocardiography.

Doppler echocardiography on current ultrasonography machines makes use of short-time Fourier spectrograms (STFTs) to display the patterns of blood velocities in the heart chamber. From these sonologists infer the functional parameters, such as valve area, that have pathological significance. After mention of the lacuna in such an STFT display, the Gabor transform and associated Gabor spectrogram evaluation techniques are described. Finally, comparative views of ultrasound machine display with PC-based STFT and Gabor displays for two typical patients are shown, with inferences in support of the proposed Gabor display.

Blood Flow Velocity↗

PubMed2005

Applications of random field theory to electrophysiology.

The analysis of electrophysiological data often produces results that are continuous in one or more dimensions, e.g., time-frequency maps, peri-stimulus time histograms, and cross-correlation functions. Classical inferences made on the ensuing statistical maps must control family wise error (FWE) when searching across the map's dimensions. In this paper, we borrow multiple comparisons procedures, established in neuroimaging, and apply them to electrophysiological data. These procedures use random field theory (RFT) to adjust p-values from statistics that are functions of time and/or frequency. This RFT adjustment for continuous statistical processes plays the same role as a Bonnferonni adjustment in the context of discrete statistical tests. Here, by analysing the time-frequency decompositions of single channel EEG data we show that RFT adjustments can be used in the analysis of electrophysiological data and illustrate the advantages of this method over existing approaches.

Animals↗

PubMed2006

Comparison of protein active site structures for functional annotation of proteins and drug design.

Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.

Adenosine Triphosphate↗

PubMed2002

Bayesian approach to searching for susceptibility genes: Gc2 and EsD1 alleles and multiple sclerosis.

Multiple sclerosis (MS) is one of the most common causes of neurological disability in early adulthood. The current literature is interested in identifying biological or DNA markers associated with genetic susceptibility to MS. The aim of this study is to investigate, by means of Bayesian statistical inference, whether the presence of Gc2 (Gc = group-specific component) and/or EsD1 (EsD = esterase D) alleles affects MS susceptibility. Gc and EsD are two classical genetic markers, being the first a serum protein polymorphism, the latter an isoenzyme polymorphism. The interest of the proposed statistical approach of searching for MS susceptibility genes relies on the analysis of two different functions, one function being inferred from our results on 56 unrelated patients from central Italy affected by MS, the other one from Italian and worldwide epidemiological data. The graphical analysis suggests that MS susceptibility is influenced by both Gc2 and EsD1 alleles; and EsD1 allele is more informative than Gc2. These results point out the advantages of the Bayesian approach in searching for susceptibility genes. Furthermore, the significant association between the considered alleles and the susceptibility to MS suggests possible hypotheses about the pathogenesis of the disease.

Bayes Theorem↗

PubMed1996

New pedal remains of Megaladapis and their functional significance.

New remains of Megaladapis from the caves within the Ankarana Range of northern Madagascar and the cave site of Ankilitelo near Toliara in southwestern Madagascar add considerably to the present sample of pedal remains for this genus. Here we describe and analyze the new pedal material and discuss the function of the Megaladapis foot in terms of positional behavior and substrate use. The northern specimens belong to the M. madagascariensis /M. grandidieri group in terms of size and morphology whereas the new southwestern fossils are assigned to M. madagascariensis. The new specimens demonstrate that the small and intermediate sized M. madagascariensis and M. grandidieri were very similar in anatomy and inferred locomotor function, findings that also support the prior suggestion that they belong to a single widespread subgenus (Megaladapis). The new fossils provide the first examples of many pedal elements and present the first opportunity to analyze the whole pedal complex from associated remains. The foot of Megaladapis is distinctive among primates in numerous features. Intrinsic proportions of the hindlimb indicate that the foot is relatively longer than that of any other primate. The first complete calcanei reveal a large and highly modified hindfoot. The calcaneus is reduced distally, indicating an emphasis on climbing over leaping or quadrupedal walking and running. Proximally, a large, medially directed calcaneal tuberosity suggests both a strong inversion component to plantarflexion and a well-developed abductor mechanism and recalls the calcaneal morphology of the larger lorisines in some respects. Talar shape is consistent with considerable tibial rotation during plantarflexion and dorsiflexion. The subtalar joint is designed to emphasize supination/pronation and medial/lateral rotation over proximodistal translation. The distal tarsals are extremely reduced in length, and they form a high transverse arch and a serial tarsus; this configuration promotes inversion/eversion at the transverse tarsal joint. The phalanges are long and moderately curved, and the hallux is very long, robust, and abducted. Pedal morphology suggests that Megaladapis (subgenus Megaladapis) was well adapted to exploit an arboreal environment.(ABSTRACT TRUNCATED)

Animals↗

PubMed2026

Functional unknomics of the SAR11 clade reveal hidden genetic potential underlying adaptation to bottom-up and top-down pressures.

UNLABELLED: A substantial fraction of the genes in bacteria lack detectable sequence similarity to genes with known functions. These functionally uncharacterized genes-collectively referred to as the "unknome"-represent a largely unexplored genetic repertoire harboring insights into marine bacterial ecology. In this study, we explored the function of the unknome of the SAR11 clade, the most abundant bacterial lineage in the ocean, with a particular focus on genes that provide insight into its ecology. Based on the Clusters of Orthologous Genes and Kyoto Encyclopedia of Genes and Genomes classifications, approximately 56% of SAR11 ortholog groups were classified as members of the unknome. Among the SAR11 unknome, we successfully inferred the functions of 57 ortholog groups that are conserved in the SAR11 clade by protein structure similarity searches and genomic context analyses. These ortholog groups include putative transporter components, supporting the current ecological understanding that the SAR11 clade is specialized in substrate uptake to adapt to oligotrophic marine environments. Furthermore, structural analysis indicated that the DUF2237-containing protein, enriched in marine environments, may interact with purine nucleotide-containing compounds. This may suggest the existence of unique nucleotide utilization mechanisms in marine bacteria. In addition, we identified candidate viral defense systems within the unknome, indicating that diverse defense systems are present in at least one-third of cultured SAR11 strains. The presence of these defense systems, even within streamlined SAR11 genomes, suggests that they confer significant ecological advantages. Our analyses provide insights into the genetic basis of bottom-up processes (adaptation to oligotrophic environments) and top-down processes (antiviral defense strategy) contributing to ecological success. IMPORTANCE: Many microbial genes have no experimentally established function, limiting our ability to explain how microorganisms adapt to their environments. We examined this uncharacterized gene space, or "unknome" in SAR11, the most abundant bacterial clade in the ocean, by integrating evolutionary conservation, genomic context, predicted protein structure, and environmental distribution. This approach enabled us to prioritize components of the SAR11 unknome, including a core unknome conserved across the clade and genes enriched in specific lineages, and to identify several candidates with possible ecological roles in nutrient acquisition and defense against viruses. Our results suggest that the SAR11 unknome contains important clues to the ecological success of SAR11 rather than merely reflecting incomplete annotation or gene-prediction artifacts. Our study highlights the potential value of unknome analysis for identifying ecologically relevant genes in environmental microorganisms.

Pelagibacterales↗

PubMed1992

Computer-assisted three-dimensional reconstruction and simulations of vestibular macular neural connectivities.

The macular neuroepithelium is morphologically organized as a weighted neural network for parallel distributed processing of information. The network is continuous across the striola, where some type II hair cells synapse with calyces containing type I cells with tufts of opposite directional polarities. Whether other hair cell to calyx appositions that lack synapses interact because of intercellular potassium accumulation remains an open question. A functionally important inference of macular organization is that just as arrays of hair cells communicate an entire piece of information to a nerve fiber, so do macular subarrays of nerve fibers (not single units) carry the whole coded message to the brain stem. Moreover, the size of the network subarray can expand or become more limited depending upon the strength and/or duration of the input. It is the functioning of the network and its subarrays that must be understood if we are to learn how maculas carry out their work and adapt to new environments. Simulations of functioning maculas, or subparts, based on precise morphology and known physiology are useful tools to gain insights into macular information processing. The current simulations of afferent collateral electrical activity are a prelude to development of a 3-D model. The simulations demonstrate a relationship between geometry and function, with the diameter of the stem apparently being a major determinant of electrical activity transmitted to the base in the case of collaterals with short stems. Thus, while changes in synaptic number and/or size may be an important adaptive mechanism in an altered g environment, changes in diameter of the stem is another means of altering outflow. Research on the effects of microgravity should be extremely useful in examining the validity of this and other concepts of neural adaptation, since maculas are biological linear accelerometers ideally suited to the task. Maculas are also extremely interesting to study in detail because of the richness of connectivities and submicroscopic organization they present. Many of their features are common with more complex parts of the brain. It seems possible that knowledge of the three-dimensional geometric relationships operative in a functioning macula will contribute much to the understanding of the dynamics underlying more complex behavior. Computerized approaches greatly facilitate this task and provide an objective method of analysis. It is likely that, in the end, simple rules will be found to govern optimal neural architectural organization, even at higher cognitive levels. The architecture only appears complex because we do not yet grasp its meaning.(ABSTRACT TRUNCATED AT 400 WORDS)

Acoustic Maculae↗

PubMed2025

Functional metaproteomics for enzyme discovery.

Discovery of microbial biocatalysts traditionally relied on activity screening of isolated bacterial strains. However, since most microorganisms cannot be cultivated in the lab, such an approach leaves the majority of the microbial enzyme diversity untapped. Metagenomic approaches, in which the DNA from a microbial community is directly isolated and then used either for the creation of an expression library or for sequencing and metagenome annotation have alleviated this shortcoming to an extent, but have their own limitations: the generation of large expression libraries is time-consuming and their screening is costly, while metagenome annotation can infer biocatalytic function only from prior knowledge. We have thus developed a functional metaproteomic approach, which combines the immediacy of traditional activity screening with the comprehensiveness of a meta-omics approach. Briefly, the whole metaproteome of an environmental sample is separated on a 2-D gel, biocatalytically active proteins are visualized in-gel through zymography, and those candidate biocatalysts are then identified through mass spectrometry, searching against a metagenome-derived database obtained from the very same environmental sample. Here we explain the process in detail, with a focus on esterases, and give guidelines on how to develop a functional metaproteomic workflow for enzyme discovery.

Proteomics↗

PubMed1982

Functional differences between rat islets of ventral and dorsal pancreatic origin.

Do functional linkages between islet endocrine cells exist? The effect of differences in frequency and distribution of islet endocrine cells on B cell function was examined in islets from the ventral (ventral islets) and dorsal (dorsal islets) areas of the rat pancreas. Dorsal islets contained 10 times as much glucagon as ventral islets, whereas insulin and total protein contents were similar. Basal rates of insulin secretion and proinsulin biosynthesis were similar in the two types of islet, but, under conditions of glucose stimulation, both insulin secretion and proinsulin biosynthesis were significantly greater in the glucagon-rich dorsal islets. Similarly, glucose utilization rates an ATP levels were greater in dorsal islets. In contrast, the rates of processing of newly synthesized proinsulin were similar in ventral and dorsal islets. That the islet glucagon content may have affected B cell function is inferred from two independent findings. Firstly, basal and glucose-stimulated cyclic AMP contents of glucagon-rich dorsal islets were greater than those of ventral islets. Secondly, in the presence of excess exogenous glucagon (1 microgram/ml), the differences in glucose-induced insulin secretion and proinsulin biosynthesis rates between the two types of islets were eliminated. These results strongly suggest that changes in the relative proportions of the different islet endocrine cells exert marked effects on islet function. In particular, a greater A cell and glucagon content is associated with higher rates of glucose-induced insulin secretion and biosynthesis.

1-Methyl-3-isobutylxanthine↗

PubMed1993

Guanine nucleotide regulatory protein alterations in the Milan hypertensive rat strain.

OBJECTIVE: To examine whether the altered regulation of adenylyl cyclase that has been reported in vascular tissues from spontaneously hypertensive rats is also evident in the Milan hypertensive (MHS) rat strain. DESIGN: The plasma membranes of vascular smooth muscle cells derived from thoracic aortae from adult (60-day-old) MHS and Milan normotensive (MNS) strain rats were studied. METHODS: Guanine nucleotide regulatory protein (G-protein) function was inferred from adenylyl cyclase activity studies, and levels of G-protein subunits were assessed by immunoblotting. beta-Adrenergic receptor number and affinity were measured from the binding of the antagonist [125I]-cyanopindolol. RESULTS: Basal adenylyl cyclase activity was increased significantly in MHS rat cell membranes, and stimulation by 0.1 mmol/l isoproterenol and 0.01 mmol/l prostaglandin E1 was significantly greater in MHS than in MNS rat cell membranes. Forskolin (at 0.1 mmol/l) resulted in a significantly greater stimulatory response in MHS membranes, which was eliminated by 0.01 mol/l NaF. Biphasic effects of GTP on isoproterenol-stimulated membranes demonstrated similar Gi function in MHS and MNS rat cell membranes, although a greater stimulatory GTP response was observed in MHS rat cell membranes. The levels of Gs alpha (both forms), Gi3 alpha and the beta-subunit were reduced in MHS rat cell membranes, whereas the levels of Gi2 alpha and Gq alpha and G11 alpha were unchanged. The number of beta-adrenoceptors was increased significantly in MHS rat cell membranes, whereas receptor affinity for the antagonist was unaltered. CONCLUSIONS: There are differences in adenylyl cyclase stimulatory responses in MHS rat vascular smooth muscle cell membranes. We have found evidence of reduced levels of particular G-protein subunits, altered beta-adrenoceptor-Gs coupling and increased beta-adrenoceptor number.

Adenylyl Cyclases↗

PubMed2003

Runx3 knockouts and stomach cancer.

Gene targeting often results in knockout mice that show several phenotypes, some of which may not directly relate to the intrinsic function of the disrupted gene. Hence, to study the biological function of genes using knockout mice, one must identify the defects that are directly due to the loss of the targeted gene. Runx3 is a transcription factor that regulates lineage-specific gene expression in developmental processes. Recently, two groups produced Runx3 knockout mice. Two comparable defects were identified in both knockout strains, one involved neurogenesis and the other thymopoiesis. In addition, a stomach defect pertaining to gastric cancer was observed in one of the mutant strains, but not in the other. Here, we assess the differences between the two Runx3 mutant strains and discuss further studies that could reconcile these discrepancies. This article highlights the difficulties of inferring gene function through the interpretation of knockout phenotypes.

Animals↗

PubMed2005

Deciphering protein network organization using phylogenetic profile groups.

Phylogenetic profiling is now an effective computational method to detect functional associations between proteins. The method links two proteins in accordance with the similarity of their phyletic distributions across a set of genomes. While pair-wise linkage is useful, it misses correlations in higher order groups: triplets, quadruplets, and so on. Here we assess the probability of observing co-occurrence patterns of 3 binary profiles by chance and show that this probability is asymptotically the same as the mutual information in three profiles. We demonstrate the utility of the probability and the mutual information metrics in detecting overly represented triplets of orthologous proteins which could not be detected using pairwise profiles. These triplets serve as small building blocks, i.e. motifs in protein networks; they allow us to infer the function of uncharacterized members, and facilitate analysis of the local structure and global organization of the protein network. Our method is extendable to N-component clusters, and therefore serves as a general tool for high order protein function annotation.

Amino Acid Motifs↗

PubMed2006

Detection of operons.

Operons are clusters of genes that are transcribed as a single message, and regulated by the same gene expression machinery. They are found primarily in prokaryotic genomes. Because genes in the same operon are likely to have related functions, identification of the operon structure is potentially useful for assigning gene function. We report the development and benchmarking of two different methods for detecting operons, based on an analysis of 42 fully sequenced prokaryotic organisms. The Gene Neighbor method (GNM) utilizes the relatively high conservation of gene order in operons, compared with genes in general. The Gene Gap Method (GGM) makes use of the relatively short gap between genes in operons compared with that otherwise found between adjacent genes. The methods have been benchmarked using KEGG pathway data and RegulonDB Escherichia coli operon data. With optimum parameters, the specificity of the GNM is 93% and the sensitivity is 70%. For the GGM, the specificity is 95% and the sensitivity is 68%. Together, the two methods have a sensitivity of 87.2%, while joint predictions have a sensitivity of 50% and a specificity of 98%. The methods are used to infer possible functions for some hypothetical genes in prokaryotic genomes. The methods have proven a useful addition to structure information in deriving protein function in a structural genomics project.

Computational Biology↗

PubMed1999

Protein fold analysis of the B30.2-like domain.

The B30.2-like domain occurs in some members of a diverse and growing family of proteins containing zinc-binding B-box motifs, whose functions include regulation of cell growth and differentiation. The B30.2-like domain is also found in proteins without the zinc-binding motifs, such as butyrophilin (a transmembrane glycoprotein) and stonustoxin (a secreted cytolytic toxin). Currently, the function for the B30.2-like domain is not clear and the structure of a protein containing this domain has not been solved. The secondary structure prediction methods indicate that the B30.2-like domain consists of fifteen or fewer beta-strands. Fold recognition methods identified different structural topologies for the B30.2-like domains. Secondary structure prediction, deletion and lack of local sequence identity at the C-terminal region for certain members of the family, and packing of known core structures suggest that a structure containing two beta domains is the most probable of these folds. The most C-terminal sequence motif predicted to be a beta-strand in all B30.2-like domains is a potential subdomain boundary based on the sequence-structure alignments. Models of the B30.2-like domains were built based on immunoglobulin-like folds identified by the fold recognition methods to evaluate the possibility of the B30.2 domain adopting known folds and infer putative functional sites. The SPRY domain has been identified as a subdomain within the B30.2-like domain. If the B30.2-like domain is a subclass of the SPRY domain family, then this analysis would suggest that the SPRY domains are members of the immunoglobulin superfamily.

Amino Acid Sequence↗

PubMed2004

Comparative analysis detects dependencies among the 5' splice-site positions.

Human-mouse comparative genomics is an informative tool to assess sequence functionality as inferred from its conservation level. We used this approach to examine dependency among different positions of the 5' splice site. We compiled a data set of 50,493 homologous human-mouse internal exons and analyzed the frequency of changes among different positions of homologous human-mouse 5' splice-site pairs. We found mutual relationships between positions +4 and +5, +5 and +6, -2 and +5, and -1 and +5. We also demonstrated the association between the exonic and the intronic positions of the 5' splice site, in which a stronger interaction of U1 snRNA and the intronic portion of the 5' splice site compensates for weak interaction of U1 snRNA and the exonic portion of the 5' splice site, and vice versa. By using an ex vivo system that mimics the effect of mutation in the 5' splice site leading to familial dysautonomia, we demonstrated that U1 snRNA base-pairing with positions +6 and -1 is the only functional requirement for mRNA splicing of this 5' splice site. Our findings indicate the importance of U1 snRNA base-pairing to the exonic portion of the 5' splice site.

Animals↗

PubMed1985

Plasma concentrations of N-acetylneuraminic acid in severe malnutrition.

In rat studies, circulating concentrations of N-acetylneuraminic acid (NANA) have been shown to be an indicator of NANA concentrations in the brain and functional brain activity, in relation to nutritional state and stimulation. Abnormal behaviour can be improved with exogenous NANA. In the present study, the plasma NANA concentration has been measured in children with severe malnutrition and compared with that in controls. NANA was measured colorimetrically in the plasma of twenty-three severely malnourished children (mean age 11.43 (SD 6.05) months) before and after recovery, and in thirty-four controls (mean age 14.28 (SD 7.32)months). In thirteen of the malnourished children, NANA was measured after infections had been treated with a course of antibiotics. Mean plasma NANA concentration was significantly higher in protein-energy malnutrition (PEM) (2.89 (SD 0.58) mumol/ml; n 23) compared with controls (2.13 (SD 0.37) mumol/ml; n 34, P less than 0.001). The levels remained high in PEM after infections had been treated (2.87 (SD 0.43) mumol/ml, n 13) but returned to control levels at recovery from PEM (2.14 (SD 0.24) mumol/ml). In contrast to the findings in rats, in malnourished children plasma NANA concentrations were not reduced and did not relate directly to nutritional state or, by inference, brain function. These findings do not provide any support for the use of exogenous NANA supplements to improve brain function in humans.

Child, Preschool↗

PubMed1997

The economics of uncomplicated mitral valve surgery.

BACKGROUND AND AIMS OF THE STUDY: Comparisons of mitral valve (MV) replacement and reconstruction have demonstrated lower overall complication rates, better left ventricular (LV) function, and inferred overall lower cost for the latter procedure compared with the former. However, assessment of economic differences between the two procedures in routine cases, without complications, has not been reported. This study retrospectively evaluates the economic impact of uncomplicated MV repair versus replacement. METHODS: As this study seeks only to evaluate economic comparisons between routine cases of mitral repair versus replacement, those patients having concomitant procedures performed (coronary revascularization or other valve procedure) or postoperative complications (i.e. pulmonary failure, wound infections, new-onset atrial fibrillation, return for bleeding, or neurologic sequelae) were excluded from the study. Among patients who underwent uncomplicated MV procedures, 30 were selected at random and reviewed. RESULTS: Variables for MV replacement versus reconstruction included aortic cross-clamp time (112 +/- 54 versus 92 +/- 20 min; p = NS), cardiopulmonary bypass (CPB) time (189 +/- 70 versus 128 +/- 18 min; p < 0.05), total hospital stay (8.3 +/- 1.6 versus 5.6 +/- 1.6 days; p < 0.0001), and total hospital charges ($44,697 +/- 4903 versus $31,337 +/- 4484; p < 0.0001), respectively. CONCLUSIONS: These data suggest that, beyond the recognized benefits of MV reconstruction, namely preservation of LV function and avoidance of long-term anticoagulation, there is an economic advantage to MV reconstruction for patients and payors, even in uncomplicated cases. These differences may become more apparent with longer follow-up and in patients having poor function or combined procedures. This finding reinforces the idea that MV reconstruction is the option of choice for patients with mitral regurgitation.

Cardiac Surgical Procedures↗

PubMed1999

An analysis of the Protein Data Bank in search of temporal and global trends.

MOTIVATION: Biological databases, with their rapidly expanding contents, are indispensable tools in the quest to understand more about biological function. However, a serious user of a database that comprises a large collection of data, collected over a long period, will likely be struck by the inconsistency in reporting individual items of data. This paper takes a critical look at the Protein Data Bank (PDB) to explore the seriousness of the problem in one particular data set and to explore the implications to those actively engaged in comparative analysis of these data. RESULTS: Averaged over the complete corpus, the stereochemical quality of atomic models has, in the past few years, moved towards ideal values. At the same time, there are inconsistencies in how data are reported. Water content is not reported consistently and the percent of data collected when reporting the high-resolution shell varies, detracting from the value of resolution as a yardstick for assessing the quality of a structure. A more detailed analysis of these inconsistencies is hampered by the lack of machine-readable experimental data. To the user of macromolecular structure data, this suggests that structural details beyond the standard quality measures of resolution and R value should be considered when using coordinate sets for further derivation or in inferring biological function. To the curators of the PDB, this suggests the need to capture more of the experimental data associated with the experiment in a way that permits straightforward parsing.

Computational Biology↗