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PubMed2003

Structural modeling of ataxin-3 reveals distant homology to adaptins.

Spinocerebellar ataxia type 3 (SCA3) is a polyglutamine disorder caused by a CAG repeat expansion in the coding region of a gene encoding ataxin-3, a protein of yet unknown function. Based on a comprehensive computational analysis, we propose a structural model and structure-based functions for ataxin-3. Our predictive strategy comprises the compilation of multiple sequence and structure alignments of carefully selected proteins related to ataxin-3. These alignments are consistent with additional information on sequence motifs, secondary structure, and domain architectures. The application of complementary methods revealed the homology of ataxin-3 to ENTH and VHS domain proteins involved in membrane trafficking and regulatory adaptor functions. We modeled the structure of ataxin-3 using the adaptin AP180 as a template and assessed the reliability of the model by comparison with known sequence and structural features. We could further infer potential functions of ataxin-3 in agreement with known experimental data. Our database searches also identified an as yet uncharacterized family of proteins, which we named josephins because of their pronounced homology to the Josephin domain of ataxin-3.

Adaptor Protein Complex gamma Subunits↗

PubMed2003

Overview of structural genomics: from structure to function.

The unprecedented increase in the number of new protein sequences arising from genomics and proteomics highlights directly the need for methods to rapidly and reliably determine the molecular and cellular functions of these proteins. One such approach, structural genomics, aims to delineate the total repertoire of protein folds, thereby providing three-dimensional portraits for all proteins in a living organism and to infer molecular functions of the proteins. The goal of obtaining protein structures on a genomic scale has motivated the development of high-throughput technologies for macromolecular structure determination, which have begun to produce structures at a greater rate than previously possible. These new structures have revealed many unexpected functional and evolution relationships that were hidden at the sequence level.

Amino Acid Sequence↗

PubMed2004

The iProClass integrated database for protein functional analysis.

Increasingly, scientists have begun to tackle gene functions and other complex regulatory processes by studying organisms at the global scales for various levels of biological organization, ranging from genomes to metabolomes and physiomes. Meanwhile, new bioinformatics methods have been developed for inferring protein function using associative analysis of functional properties to complement the traditional sequence homology-based methods. To fully exploit the value of the high-throughput system biology data and to facilitate protein functional studies requires bioinformatics infrastructures that support both data integration and associative analysis. The iProClass database, designed to serve as a framework for data integration in a distributed networking environment, provides comprehensive descriptions of all proteins, with rich links to over 50 databases of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy. In particular, the database is organized with PIRSF family classification and maps to other family, function, and structure classification schemes. Coupled with the underlying taxonomic information for complete genomes, the iProClass system (http://pir.georgetown.edu/iproclass/) supports associative studies of protein family, domain, function, and structure. A case study of the phosphoglycerate mutases illustrates a systematic approach for protein family and phylogenetic analysis. Such studies may serve as a basis for further analysis of protein functional evolution, and its relationship to the co-evolution of metabolic pathways, cellular networks, and organisms.

Amino Acid Sequence↗

PubMed2001

Illuminating the human genome.

The identification and analysis of novel genes and their encoded protein products remains a vigorous area of research in biology today. Worldwide genomic and cDNA sequencing projects are now identifying new molecules every day and the need for methodologies to functionally characterise these proteins has never been greater. The distinct compartmental arrangement of eukaryotic cells helps define the processes which occur within or in proximity to these membranes, and as such provides one means of inferring protein function. We describe here some of the methods recently reported in the literature, which use the subcellular localisation of proteins as a first step towards their further characterisation.

Cytological Techniques↗

PubMed2025

FUSE-PhyloTree: linking functions and sequence conservation modules of a protein family through phylogenomic analysis.

SUMMARY: FUSE-PhyloTree is a phylogenomic analysis software for identifying local sequence conservation associated with the different functions of a multi-functional (e.g. paralogous or multi-domain) protein family. FUSE-PhyloTree introduces an original approach that combines advanced sequence analysis with phylogenetic methods. First, local sequence conservation modules within the family are identified using partial local multiple sequence alignment. Next, the evolution of the detected modules and known protein functions is inferred within the family's phylogenetic tree using three-level phylogenetic reconciliation and ancestral state reconstruction. As a result, FUSE-PhyloTree provides a gene tree annotated with both predicted sequence modules and ancestral gene functions, enabling the association of functions with specific sequence regions based on their co-emergence. AVAILABILITY AND IMPLEMENTATION: FUSE-PhyloTree is provided as Docker and Singularity images including all the required software tools. Images, source code, test data, and documentation are available at https://github.com/OcMalde/fuse-phylotree and https://zenodo.org/records/15855068.

Phylogeny↗

PubMed1997

The topology of perceptive functions as a corollary of the theorem of existence in closed spaces.

The capability for a system of perceiving both outer objects and an inner self are two fundamental features of abstract mathematical objects endowed with the properties of topologically closed sets. Such structures exist upon intersection of topological spaces owning different dimensions. Then, the theorem of Jordan-Veblen provides their capability of being observable, while the theorems of Brouwer and of Banach-Caccioppoli provide two kinds of fixed points which account for the properties of so-called right and left brain functions. Fixed points account for the biological 'self', and the system provides theoretical justification for the existence of brain structure/function relationships, including memory, emotion, and respective characteristics of right and left hemispheres. Hence, an abstract topological reasoning based on set properties, provides evidence that the observer's function directly infers from the phenomenon of existence and that it belongs to the same mathematical system as the property of being observable. Order relations are raised from equivalence relations by Poincaré groups, upon mappings on the sets of functions and related homotopic transformations in sequences of intersections. Therefore, time is a construction of abstract brain functions, and a living organism just fills the system with appropriate molecular structures.

Biological Evolution↗

PubMed1992

Functional domains of aromatase cytochrome P450 inferred from comparative analyses of amino acid sequences and substantiated by site-directed mutagenesis experiments.

Several functional domains, especially the active site regions, in aromatase cytochrome P450 were inferred by alignment of amino acid sequences of the enzyme from five species, human, rat, mouse, chicken, and trout, and that of Pseudomonas putida cytochrome P450cam, whose x-ray structure has been determined (Poulos, T.L., Finzel, B.C., and Howard, A.J. (1987) J. Mol. Biol. 195, 687-700). The predicted functions of these domains have been evaluated by site-directed mutagenesis. Eighteen mutants, including seven new mutants, have been generated in this laboratory. The seven newly prepared mutants are Q123E, Q123H, T310S, T310C, R365K, R365A, and N delta 20 (a mutant without the first 20 amino acids). The preparation and characterization of these new mutants are described. The structural model described in this paper should be very useful for future structure-function studies of aromatase by site-directed mutagenesis.

Amino Acid Sequence↗

PubMed2000

Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.

We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022 (40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and members of the lambdoid or lambda-like group of phages. We provide a comparative analysis of these sequences with each other and with two previously determined lambdoid family genome sequences, those of E. coli phage lambda and Salmonella typhimurium phage P22. The comparisons confirm that these phages are genetic mosaics, with mosaic segments separated by sharp transitions in the sequence. The mosaicism provides clear evidence that horizontal exchange of genetic material is a major component of evolution for these viruses. The data suggest a model for evolution in which diversity is generated by a combination of illegitimate and homologous recombination and mutational drift, and selection for function produces a population in which most of the surviving mosaic boundaries are located at gene boundaries or, in some cases, at protein domain boundaries within genes. Comparisons of these genomes highlight a number of differences that allow plausible inferences of specific evolutionary scenarios for some parts of the genome. The comparative analysis also allows some inferences about function of genes or other genetic elements. We give examples for the generalized recombination genes of HK97, HK022 and P22, and for a putative headtail adaptor protein of HK97 and HK022. We also use the comparative approach to identify a new class of genetic elements, the morons, which consist of a protein-coding region flanked by a putative delta 70 promoter and a putative factor-independent transcription terminator, all located between two genes that may be adjacent in a different phage. We argue that morons are autonomous genetic modules that are expressed from the repressed prophage. Sequence composition of the morons implies that they have entered the phages' genomes by horizontal transfer in relatively recent evolutionary time.

Amino Acid Sequence↗

PubMed1997

Genome structure of the Lactobacillus temperate phage phi g1e: the whole genome sequence and the putative promoter/repressor system.

The complete genome sequence of a Lactobacillus temperate phage phi g1e was established. The double-stranded DNA is composed of 42,259 bp, and encodes for sixty-two possible open reading frames (ORF) as well as several potential regulatory sequences. Based on comparative analysis with other related proteins of the Lactobacillus and Lactococcus phages as well as the Escherichia coli phages (such as lambda), functions were putatively assigned to several phi g1e ORFs: cng and cpg (encoding for repressors), hel (helicase), ntp (NTPase), and several ORFs (e.g., minor capsid proteins). An about 1000-bp DNA region of phi g1e containing cpg and cng was inferred to function as a promoter/repressor system for the phi g1e lysogenic and lytic pathway.

Amino Acid Sequence↗

PubMed2005

The hominoid proximal radius: re-interpreting locomotor behaviors in early hominins.

Studies of fossil hominins are traditionally taxonomically narrow and often exclude comparisons with hylobatids. Hence, results of functional analyses of postcrania, interpreted as indicating that early hominins are "African-ape-like" in their postcranial skeletons and positional behaviors, may reflect an artifact of inadequate taxonomic and morphological breadth of the comparative sample. To address this problem and better understand early hominin positional behaviors, this study included hylobatids in a comparative analysis, focusing on the hominoid elbow joint. Specifically, morphometric variables of the proximal radius were derived from measurements from a sample of all genera of extant hominoids and casts of extinct hominin species. Univariate and multivariate analyses were performed on these data. Results show that early hominins are morphologically diverse and are not, as a group, similar to any one extant group. Instead, the fossils resemble Pan, Gorilla, and Hylobates, and are not like modern Homo sapiens or Pongo. This suggests that the morphology of Hylobates may reflect a morphotype for all later hominoids, thus complicating the functional interpretations of fossil hominins. The implications of these results are that the proximal radius is not a sensitive indicator of locomotor behavior among hominoids since the morphology in hylobatids and Gorilla and Pan is similar despite widely varying positional repertoires. Furthermore, inferences of function from form in extinct hominins can be drastically affected by the comparative outgroup selection. A re-evaluation of the functional morphology of the proximal radius in early hominins is addressed.

Animals↗

PubMed1984

A functional map of the nopaline synthase promoter.

This paper describes the first functional map of a promoter expressed from the plant chromosome. We have constructed a series of overlapping deletion mutants within the region upstream of the Ti-plasmid encoded nopaline synthase (nos) gene. By monitoring nos expression in tumour tissue we have inferred a functional map of the nos promoter. The maximum length of sequence upstream of the transcription initiation point required to express wild type levels of nopaline synthase is 88 bp. Within this region, the "CAAT" box is essential for maximal activity; deletion of this sequence reduced apparent nos expression by over 80%. Presence of an intact or partial "TATA" box in the absence of the "CAAT" box supports a barely detectable level of nopaline synthase. Removal of all sequences upstream of the nos coding sequence results in no detectable activity.

Amino Acid Oxidoreductases↗

PubMed2006

Bayesian inference of hemodynamic changes in functional arterial spin labeling data.

The study of brain function using MRI relies on acquisition techniques that are sensitive to different aspects of the hemodynamic response contiguous to areas of neuronal activity. For this purpose different contrasts such as arterial spin labeling (ASL) and blood oxygenation level dependent (BOLD) functional MRI techniques have been developed to investigate cerebral blood flow (CBF) and blood oxygenation, respectively. Analysis of such data typically proceeds by separate, linear modeling of the appropriate CBF or BOLD time courses. In this work an approach is developed that provides simultaneous inference on hemodynamic changes via a nonlinear physiological model of ASL data acquired at multiple echo times. Importantly, this includes a significant contribution by changes in the static magnetization, M, to the ASL signal. Inference is carried out in a Bayesian framework. This is able to extract, from dual-echo ASL data, probabilistic estimates of percentage changes of CBF, R(2) (*), and the static magnetization, M. This approach provides increased sensitivity in inferring CBF changes and reduced contamination in inferring BOLD changes when compared with general linear model approaches on single-echo ASL data. We also consider how the static magnetization, M, might be related to changes in CBV by assuming the same mechanism for water exchange as in vascular space occupancy.

Bayes Theorem↗

PubMed2026

Zea mays Drought-Overly Sensitive1/TUBA4 Is Wilty3, and Transcriptome Co-Expression Analysis of Shoot Meristem Mutant Tissues Reveals Wilty2/TUB6:Wi3 Interactions Associated With Stem Vascular Bundle Development.

Plant vasculature is essential for the transport of water, nutrients, and signaling molecules across organs, while also providing critical mechanical support for growth and development. Disruptions in vascular bundle formation can therefore lead to severe physiological and developmental defects. In maize, ethyl methanesulfonate (EMS)-induced dominant nonallelic Wilty mutants exhibit a pronounced wilting phenotype even under well-watered conditions, indicating underlying defects in vascular function. In this study, we characterized the Wi3 mutant, identified as ZmDrought-Overly-Sensitive1/DOS1, and compared it with the previously described Wi2 mutant to uncover shared mechanisms underlying their phenotypes. We provide evidence, by bulk segregant resequencing linkage disequilibrium of SNPs adjacent to the causal Wilty SNPs in respective ß- and α-tubulin genes, for the personal communication from Gerry Neuffer that Wi2/ß-tub6 provenance is from ACR-related stock, whereas Wi3/α-tub4 allele is from Mo17, not B73 as claimed by the authors who cloned Dos1. Histochemical staining and Fourier-transform infrared (FTIR) spectroscopy of vascular bundles in Wi3 indicated apparent alterations in cellulose and lignin content consistent with those observed in Wi2. Transcriptome analysis of shoot meristems further indicated that similar sets of genes and pathways are differentially expressed in both mutants, suggesting convergence on common biological pathways. Using bulk-segregant whole-genome resequencing, we identified alpha-tubulin4 (TUA4) as the causal gene in Wi3 (ZmDOS1), harboring a C-to-T substitution within the N-terminal GTPase-binding domain. This mutation results in a glutamic acid196-to-lysine substitution. Given that α- and β-tubulin subunits heterodimerize, and in many plants and animal mutant alleles are dominant-negative gains-of-function, we infer Wi2, Wi3, and likely Wi4, based on very similar FTIR biophysical difference spectra, may act as effectors of vascular bundle cell wall deposition, potentially involving vesicle trafficking as recently shown for asymmetric cell divisions in maize stomatal development. Together, these findings highlight the functional interdependence of tubulin subunits and provide a plausible mechanistic framework for the striking biophysical, transcriptomic, and phenotypic similarities observed between Wi2, Wi3/ZmDOS1, and Wi4 mutants.

bulk segregant analysis↗

PubMed2005

Protein function prediction using the Protein Link EXplorer (PLEX).

UNLABELLED: We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways. AVAILABILITY: http://bioinformatics.icmb.utexas.edu/plex

Algorithms↗

PubMed1987

Current activation by membrane hyperpolarization in the slowly adapting lobster stretch receptor neurone.

1. A polarization-induced membrane current, IQ, was investigated in the slowly adapting lobster stretch receptor neurone using conventional electrophysiological techniques including intracellular ion measurements. 2. The current was readily blocked by Cs+ in a voltage-dependent manner, but proved to be unaffected by tetrodotoxin, tetraethylammonium and 4-aminopyridine. 3. From an analysis of the ionic basis of IQ, it appeared that the current is carried by both Na+ and K+ through a membrane channel whose permeability for K+ is about six times larger than that for Na+ in a normal ionic environment. In the presence of reduced external Na+ concentration the Q-channel increases its permeability for both Na+ and K+, but more so for Na+ than for K+. 4. Kinetically, IQ was found to be characterized by a steep sigmoidal relationship between membrane voltage and steady-state current activation, and by a bell-shaped relationship between membrane voltage and the time constant of the exponential phase of current activation or deactivation. A significant feature of the latter relationship is a tendency to level off at finite time-constant values in both strongly hyperpolarizing and strongly depolarizing voltage regions. 5. From the experiments a mathematical IQ model was inferred. This model was based on constant-field and channel-gating kinetics involving a voltage-dependent reaction step in series with a voltage-independent reaction step. The model was found to successfully reproduce IQ behaviour in the living preparation. 6. Functionally, the activation of IQ was found to play a role in setting the cell's resting polarization and membrane excitability. This function was inferred from experiments on unimpaled cells in which it was possible to demonstrate some overlap between the voltage ranges of IQ activation and impulse initiation. In addition, in impaled cells the activation of IQ was found to cause some shortening of post-tetanic membrane hyperpolarization and to accelerate, thereby, the post-tetanic restoration of membrane excitability to control levels.

Action Potentials↗

PubMed1977

Fine structure of noradrenaline containing nerve fibers in the median eminence of female rat demonstrated by in situ fixation of potassium permanganate.

Fine structure of noradrenaline (NA) terminals in the internal layer of the median eminence (ME) was elucidated by in situ fixation of potassium permanganate. The NA terminals in ME contained relatively large cored vesicles (about 1000 A) together with a large number of small core vesicle (400-600 A). The most dominant feature that NA terminals show is the closed contact with ependymal cells and their processes. In the bulging abutting on the contact membrane, some of core vesicles fused or touched the membrane appearing to release the content into intercellular space or take up NA from the space. This finding shows that the NA terminals abutting on the ependymal cells and their processes have a close contact with them and give an important influence on regulation of ependymal function. Our present study further revealed that the NA terminals also had a close contact not only with the axon terminals in which ordinary spherical non-cored vesicles were exclusively present but also with the axonal fibers of neurosecretary system. These findings would infer complicated function of NA in ME.

Animals↗

PubMedDate not supplied

Clinical method to estimate time of origin and maximum volume of malignant tumors.

The purpose of this study is to investigate a method to obtain the magnitude of growth parameters in the Gompertzian function growth model and to extrapolate this function forwards and backwards by applying the parameters. Non exponential linearity of malignant tumors has been reported and experimental and clinical evidence of growth limitation even in malignant tissues has also been detected. In clinical practices the conventional exponential growth model is often insufficient. So we applied the Gompertzian function to infer growth patterns using the parameters obtained from breast carcinoma skin metastases and from leiomyosarcoma lung metastases. We found that breast carcinoma grows faster but its growth rate retards more quickly, whereas the leiomyosarcoma grows slowly but its growth rate hardly regresses. Interesting results are obtained extrapolating this function forwards and backwards using the parameters. As a consequence the retardation factor becomes more important than the growth rate.

Animals↗

PubMedDate not supplied

Pure multiple RNA secondary structure alignments: a progressive profile approach.

In functional, noncoding RNA, structure is often essential to function. While the full 3D structure is very difficult to determine, the 2D structure of an RNA molecule gives good clues to its 3D structure, and for molecules of moderate length, it can be predicted with good reliability. Structure comparison is, in analogy to sequence comparison, the essential technique to infer related function. We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence similarity is not required. We give a systematic generalization of the profile alignment method from strings to trees and forests. We introduce a tree profile representation of RNA secondary structure alignments which allows reasonable scoring in structure comparison. Besides the technical aspects, an RNA profile is a useful data structure to represent multiple structures of RNA sequences. Moreover, we propose a visualization of RNA consensus structures that is enriched by the full sequence information.

5' Untranslated Regions↗