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PubMed2005

Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism.

Transcription factors play essential role in the gene regulation in higher organisms, binding to multiple target sequences and regulating multiple genes in a complex manner. In order to decipher the mechanism of gene regulation, it is important to understand the molecular mechanism of protein-DNA recognition. Here we describe a strategy to approach this problem, using various methods in bioinformatics and computational biology. We have used a knowledge-based approach, utilizing rapidly increasing structural data of protein-DNA complexes, to derive empirical potential functions for the specific interactions between bases and amino acids as well as for DNA conformation, from the statistical analyses on the structural data. Then these statistical potentials are used to quantify the specificity of protein-DNA recognition. The quantification of specificity has enabled us to establish the structure-function analysis of transcription factors, such as the effects of binding cooperativity on target recognition. The method is also applied to real genome sequences, predicting potential target sites. We are also using computer simulations of protein-DNA interactions and DNA conformation in order to complement the empirical method. The integration of these approaches together will provide deeper insight into the mechanism of protein-DNA recognition and improve the target prediction of transcription factors.

Binding Sites↗

PubMed1999

Uterine differentiation as a foundation for subsequent fertility.

Uterine differentiation in cattle and sheep begins prenatally, but is completed postnatally. Mechanisms regulating this process are not well defined. However, studies of urogenital tract development in murine systems, particularly those involving tissue recombination and targeted gene mutation, indicate that the ideal uterine organizational programme evolves epigenetically through dynamic cell-cell and cell-matrix interactions that define the microenvironmental context within which gene expression occurs and may ensure adult tissue stability. In the cow and ewe, transient postnatal exposure of the developing uterus to steroids can produce immutable changes in adult uterine tissues that may alter the embryotrophic potential of the uterine environment. Thus, success of steroid-sensitive postnatal events supporting uterine growth and development can dictate the functional potential of the adult uterus. Studies to determine effects of specific steroidal agents on patterns of uterine development during defined neonatal periods, as well as the functional consequences of targeted neonatal steroid exposure in the adult uterus, should enable identification of critical developmental mechanisms and determinants of uterine integrity and function. Extreme adult uterine phenotypes (lesion models) created in cattle and sheep by strategic postnatal steroid exposure hold promise as powerful tools for the study of factors affecting uterine function and the rapid identification of novel uterine genes.

Animals↗

PubMed1985

Somatosensory evoked potentials: monitoring cerebral functions following liver transplantation.

Serial somatosensory evoked potentials (SEPs) were obtained from a patient with Wilson's disease who had had liver transplantation. Correlating with recovery of hepatic encephalopathy and liver functions following the surgery, SEPs showed progressive normalization of peak latencies and waveforms. The data indicate that SEP may be a useful objective method in assessing recovery of cerebral functions following liver transplantation.

Adolescent↗

PubMed1991

Prediction of protein folding from amino acid sequence over discrete conformation spaces.

Predicting the three-dimensional structure of a protein given only its amino acid sequence is a long-standing goal in computational chemistry. In the thermodynamic approach, one needs a potential function of conformation that resembles the free energy of the real protein to the extent that the global minimum of the potential is attained by the native conformation and no other. In practice, this has never been achieved with certainty because even with greatly simplified representations of the polypeptide chain, there are an astronomical number of local minima to examine. If one chooses instead a protein representation with only a large but manageable number of discrete conformations, then the global preference of the potential for the native can be directly verified. Representing a protein as a walk on a two-dimensional square lattice makes it easy to see that simple functions of the interresidue contacts are sufficient to globally favor a given "native" conformation, as long as it is a compact, globular structure. Explicit representation of the solvent is not required. Another more realistic way to confine the conformational search to a finite set is to draw alternative conformations from fragments of larger proteins having known crystal structure. Then it is possible to construct a simple function of interresidue contacts in three dimensions such that only 8 proteins are required to determine the adjustable parameters, and the native conformations of 37 other proteins are correctly preferred over all alternative conformations. The deduced function favors short-range backbone-backbone contacts regardless of residue type and long-range hydrophobic associations. Interactions over long distances, such as electrostatics, are not required.

Amino Acid Sequence↗

PubMed2001

Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability.

The ability to detect and degrade transcripts that lack full coding potential is ubiquitous but non-essential in lower eukaryotes, leaving in question the evolutionary basis for complete maintenance of this function. One hypothesis holds that nonsense-mediated RNA decay (NMD) protects the organism by preventing the translation of truncated peptides with dominant negative or deleterious gain-of-function potential. All organisms studied to date that are competent for NMD express a structural homolog of Saccharomyces cerevisiae Upf1p. We have now explored the consequences of loss of NMD function in vertebrates through targeted disruption of the Rent1 gene in murine embryonic stem cells which encodes a mammalian ortholog of Upf1p. Mice heterozygous for the targeted allele showed no apparent phenotypic abnormalities but homozygosity was never observed, demonstrating that Rent1 is essential for embryonic viability. Homozygous targeted embryos show complete loss of NMD and are viable in the pre-implantation period, but resorb shortly after implantation. Furthermore, Rent1(-/-) blastocysts isolated at 3.5 days post-coitum undergo apoptosis in culture following a brief phase of cellular expansion. These data suggest that NMD is essential for mammalian cellular viability and support a critical role for the pathway in the regulated expression of selected physiologic transcripts.

Animals↗

PubMed2002

The predominantly HEAT-like motif structure of huntingtin and its association and coincident nuclear entry with dorsal, an NF-kB/Rel/dorsal family transcription factor.

BACKGROUND: Huntington's disease (HD) pathogenesis is due to an expanded polyglutamine tract in huntingtin, but the specificity of neuronal loss compared with other polyglutamine disorders also implies a role for the protein's unknown inherent function. Huntingtin is moderately conserved, with 10 HEAT repeats reported in its amino-terminal half. HD orthologues are evident in vertebrates and Drosophila, but not in Saccharomyces cerevisiae, Caenorhabditis elegans or Arabidopsis thaliana, a phylogenetic profile similar to the NF-kB/Rel/dorsal family transcription factors, suggesting a potential functional relationship. RESULTS: We initially tested the potential for a relationship between huntingtin and dorsal by overexpression experiments in Drosophila S2 cells. Drosophila huntingtin complexes via its carboxyl-terminal region with dorsal, and the two enter the nucleus concomitantly, partly in a lipopolysaccharide (LPS)- and Nup88-dependent manner. Similarly, in HeLa cell extracts, human huntingtin co-immunoprecipitates with NF-kB p50 but not with p105. By cross-species comparative analysis, we find that the carboxyl-terminal segment of huntingtin that mediates the association with dorsal possesses numerous HEAT-like sequences related to those in the amino-terminal segment. Thus, Drosophila and vertebrate huntingtins are composed predominantly of 28 to 36 degenerate HEAT-like repeats that span the entire protein. CONCLUSION: Like other HEAT-repeat filled proteins, huntingtin is made up largely of degenerate HEAT-like sequences, suggesting that it may play a scaffolding role in the formation of particular protein-protein complexes. While many proteins have been implicated in complexes with the amino-terminal region of huntingtin, the NF-kB/Rel/dorsal family transcription factors merit further examination as direct or indirect interactors with huntingtin's carboxyl-terminal segment.

Active Transport, Cell Nucleus↗

PubMed2006

Intersphincteric resection in patients with very low rectal cancer: a review of the Japanese experience.

PURPOSE: This study was designed to evaluate the feasibility and oncologic and functional outcomes of intersphincteric resection for very low rectal cancer. METHODS: A feasibility study was performed using 213 specimens from abdominoperineal resections of rectal cancer. Oncologic and functional outcomes were investigated in 228 patients with rectal cancer located <5 cm from the anal verge who underwent intersphincteric resection at seven institutions in Japan between 1995 and 2004. RESULTS: Curative operations were accomplished by intersphincteric resection in 86 percent of patients who underwent abdominoperineal resection. Complete microscopic curative surgery was achieved by intersphincteric resection in 225 of 228 patients. Morbidity was 24 percent, and mortality was 0.4 percent. During the median observation time of 41 months, rate of local recurrence was 5.8 percent at three years, and five-year overall and disease-free survival rates were 91.9 percent and 83.2 percent, respectively. In 181 patients who received stoma closure, 68 percent displayed good continence, and only 7 percent showed worsened continence at 24 months after stoma closure. Patients with total intersphincteric resection displayed significantly worse continence than patients with partial or subtotal resection. CONCLUSIONS: Curability with intersphincteric resection was verified histologically, and acceptable oncologic and functional outcomes were obtained by using these procedures in patients with very low rectal cancer. However, information on potential functional adverse effects after intersphincteric resection should be provided to patients preoperatively.

Adult↗

PubMed2005

Cell-type specific expression of IGF-1R in porcine islet cells.

Insulin-like growth factor-1 (IGF-1) functions as a growth factor regarding physiological regulations of cellular metabolism, regeneration and growth. In pancreas islets their potential function is unclear and only little information is available on occurrence and distribution of the corresponding insulin-like growth factor-1 receptor (IGF-1R) in islet cells. Therefore, we investigated the localization of IGF-1R by immunohistochemical techniques and its possible co-localization with other islet hormones. Further, we applied molecular biology techniques to determine the present of local gene expression of IGF-1R and IGF-1. Immunostaining on serial sections with anti-insulin, anti-glucagon and anti-somatostatin antibodies shows, IGF-1R was selectively expressed in insulin-producing B-cells and additionally more pronounced in somatostatin-containing D-cells, which are located in the periphery of porcine pancreatic islets. Furthermore, the RT-PCR experiment demonstrates clearly that IGF-1 and IGF-1R was expressed together in the porcine pancreas. The high expression of IGF-1R in porcine D-cells indicates that mammalian IGF-1R genes are regulated in a different manner since it was shown that in all other species IGF-1R was expressed in B- and A-cells but not in D-cells.

Animals↗

PubMed2004

Mutational analysis of the nuclease domain of Escherichia coli ribonuclease III. Identification of conserved acidic residues that are important for catalytic function in vitro.

The ribonuclease III superfamily represents a structurally distinct group of double-strand-specific endonucleases with essential roles in RNA maturation, RNA decay, and gene silencing. Bacterial RNase III orthologs exhibit the simplest structures, with an N-terminal nuclease domain and a C-terminal double-stranded RNA-binding domain (dsRBD), and are active as homodimers. The nuclease domain contains conserved acidic amino acids, which in Escherichia coli RNase III are E38, E41, D45, E65, E100, D114, and E117. On the basis of a previously reported crystal structure of the nuclease domain of Aquifex aeolicus RNase III, the E41, D114, and E117 side chains of E. coli RNase III are expected to be coordinated to a divalent metal ion (Mg(2+) or Mn(2+)). It is shown here that the RNase III[E41A] and RNase III[D114A] mutants exhibit catalytic activities in vitro in 10 mM Mg(2+) buffer that are comparable to that of the wild-type enzyme. However, at 1 mM Mg(2+), the activities are significantly lower, which suggests a weakened affinity for metal. While RNase III[E41A] and RNase III[D114A] have K(Mg) values that are approximately 2.8-fold larger than the K(Mg) of RNase III (0.46 mM), the RNase III[E41A/D114A] double mutant has a K(Mg) of 39 mM, suggesting a redundant function for the two side chains. RNase III[E38A], RNase III[E65A], and RNase III[E100A] also require higher Mg(2+) concentrations for optimal activity, with RNase III[E100A] exhibiting the largest K(Mg). RNase III[D45A], RNase III[D45E], and RNase III[D45N] exhibit negligible activities, regardless of the Mg(2+) concentration, indicating a stringent functional requirement for an aspartate side chain. RNase III[D45E] activity is partially rescued by Mn(2+). The potential functions of the conserved acidic residues are discussed in the context of the crystallographic data and proposed catalytic mechanisms.

Alanine↗

PubMed2001

Different responses of masticatory movements after alteration of occlusal guidance related to individual movement pattern.

We hypothesized that the motor response of the masticatory system to peripheral inputs varies according to the functional potential of an individual. The specific aim of the present study was to determine whether individually different types of masticatory patterns, especially with respect to the closing movement pattern, would produce different motor responses to an alteration of occlusal guidance. The inclination of the occlusal guidance was steepened by approximately 10 degrees by attaching a metal overlay to the lingual surface of the maxillary working-side canine. The masticatory movements of 20 young adults were measured using a three-dimensional mandibular movement analysis system before and after the alteration of occlusal guidance. The individual masticatory patterns were divided into two groups based on the closing movement pattern before the alteration of occlusal guidance, i.e. vertical and lateral types. The alteration of occlusal guidance significantly influenced the masticatory closing angle, closing time, occlusal time, the stability of the opening angle and the cycle time in the lateral-type group (n = 9, paired t-test; P < 0;05), while no significant changes were found in the vertical-type group (n = 11). These differences in motor response between the two groups were not found in the overall analysis of all the 20 subjects. We concluded that the oral motor response to the alteration of occlusal guidance depends on the individual masticatory movement pattern. Because the present analysis of subgroups of the subjects revealed motor response findings different from those in the overall analysis of all the 20 subjects, such potential subgroupings should be considered as an attempt to identify a specific effect of peripheral inputs on masticatory function in humans.

Adult↗

PubMed2002

Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria.

Mitochondrial inner membrane carrier proteins are imported into mitochondria from yeast, fungi and mammals by specific machinery, some components of which are distinct from those utilized by other proteins. Import of two different carriers into plant mitochondria showed that one contains a cleavable presequence which was processed during import, while the other imported in a valinomycin-sensitive manner without processing. Mild osmotic shock of mitochondria released intermembrane space (IMS) components and impaired carrier protein import. Adding back the released IMS proteins as a concentrate in the presence of micromolar ZnCl2 stimulated carrier import into IMS-depleted mitochondria, but did not stimulate import of a non-carrier control precursor protein, the alternative oxidase. Anion-exchange separation of IMS components before addition to IMS-depleted mitochondria revealed a correlation between several 9-10 kDa proteins and stimulation of carrier import. MS/MS sequencing of these proteins identified them as plant homologues of the yeast zinc-finger carrier import components Tim9 and Tim10. Stimulation of import was dependent on either Zn2+ or Cd2+ and inhibited by both N-ethylmalamide (NEM) and a divalent cation chelator, consistent with a functional requirement for a zinc finger protein. This represents direct functional evidence for a distinct carrier import pathway in plant mitochondria, and provides a tool for determining the potential function of other IMS proteins associated with protein import.

Biological Transport↗

PubMed1999

Moving lattice kinks and pulses: an inverse method.

We develop a general mapping from given kink or pulse shaped traveling-wave solutions including their velocity to the equations of motion on one-dimensional lattices which support these solutions. We apply this mapping-by definition an inverse method-to acoustic solitons in chains with nonlinear intersite interactions, nonlinear Klein-Gordon chains, reaction-diffusion equations, and discrete nonlinear Schrödinger systems. Potential functions can be found in a unique way provided the pulse shape is reflection symmetric and pulse and kink shapes are at least C2 functions. For kinks we discuss the relation of our results to the problem of a Peierls-Nabarro potential and continuous symmetries. We then generalize our method to higher dimensional lattices for reaction-diffusion systems. We find that increasing also the number of components easily allows for moving solutions.

Journal Article↗

PubMed2004

Freshly isolated rat alveolar type I cells, type II cells, and cultured type II cells have distinct molecular phenotypes.

We used microarray analysis with Affymetrix rat chips to determine gene expression profiles of freshly isolated rat type I (TI) and TII cells and cultured TII cells. Our goals were 1) to describe molecular phenotypic "fingerprints" of TI and TII cells, 2) to gain insight into possible functional differences between the two cell types through differentially expressed genes, 3) to identify genes that might indicate potential functions of TI cells, since so little is known about this cell type, and 4) to ascertain the similarities and differences in gene expression between cultured TII cells and freshly isolated TI cells. For these experiments, we used preparations of isolated TI and TII cells that contained <2% cross-contamination. With a false discovery rate of 1%, 601 genes demonstrated over twofold different expression between TI and TII cells. Those genes with very high levels of differential expression may be useful as markers of cell phenotype and in generating novel hypotheses about functions of TI and TII cells. We found similar numbers of differentially expressed genes between freshly isolated TI or TII cells and cultured TII cells (698, 637 genes) and freshly isolated TI and TII cells (601 genes). Tests of sameness/difference including cluster dendrograms and log/log identity plots indicated major differences between the phenotypes of freshly isolated TI cell and cultured type II cell populations. The latter results suggest that experiments with TII cells cultured under these conditions should be interpreted with caution with respect to biological relevance to TI or TII cells.

Animals↗

PubMed2002

Calcitonin: characterisation and expression in a teleost fish, Fugu rubripes.

The present report describes the structure and expression of the calcitonin gene in Fugu rubripes. It is composed of 4 exons and 3 introns. Splicing of exons 1, 2 and 3 generates the calcitonin pre-proprotein, while splicing of exons 1, 2 and 4 generates calcitonin gene-related protein (CGRP). Exons 1 and 2 encoding the signal sequence and the N-terminal peptide are common in both the gene products and this gene organisation has been conserved in human, rat, chicken and salmon. The gene environment around calcitonin in Fugu has been poorly conserved when compared with human, apart from a small gene cluster. The calcitonin gene in Fugu has a widespread tissue distribution but it is most highly expressed in the brain. The abundance of gene expression in the ultimobranchial gland and the pituitary indicates that these are important sites of production and that the peptide is probably secreted into the circulation and/or acts as a paracrine or autocrine controlling factor. Whilst the function of calcitonin in fish is still largely unknown, the distribution described here suggests that one of the potential functions may be as a neuropeptide.

Amino Acid Sequence↗

PubMed1993

Endogenous Ig production in mu transgenic mice. I. Allelic exclusion at the level of expression.

Our findings indicate that allelic exclusion is maintained in B cells that successfully rearrange and express and endogenous H chain gene, despite carrying a functionally rearranged H chain transgene (17.2.25 mu a). Cloned hybridomas having a functionally rearranged endogenous H chain gene as well as the transgene produce only endogenous gene products. Some of these hybridoma cultures, upon continuous growth, will secrete transgene as well as endogenous gene products. However, the two H chain polypeptides appear to be made by different cells. In each of three cases of such "double producer" lines examined, further subcloning at this time reveals two types of clones: those that secrete only transgene and those that secrete only endogenous H chains. The clones producing transgene product have lost the functionally rearranged endogenous H chain genes, whereas the clones producing endogenous gene products still contain both transgene and endogenous functionally rearranged H chain genes. These results indicate that hybridomas expressing endogenous Ig have transgene copies that are potentially functional but are reversibly silenced by an unknown mechanism and suggest that inhibition of transgene expression may be mediated by endogenous Ig gene expression.

Alleles↗

PubMed1999

Structure-function analysis of the ADAM family of disintegrin-like and metalloproteinase-containing proteins (review).

The ADAMs belong to a disintegrin-like and metalloproteinase-containing protein family that are zinc-dependent metalloproteinases. These proteins share all or some of the following domain structure: a signal peptide, a propeptide, a metalloproteinase, a disintegrin, a cysteine-rich, and an epidermal growth factor (EGF)-like domains, a transmembrane region, and a cytoplasmic tail. ADAMs are widely distributed in many organs, tissues, and cells, such as brain, testis, epididymis, ovary, breast, placenta, liver, heart, lung, bone, and muscle. These proteins are capable of four potential functions: proteolysis, adhesion, fusion, and intracellular signaling. Because the number of ADAM genes has grown rapidly and the biological functions of most members are unclear, this review analyzes the protein structures and functions, their activation and processing, their known and potential activities, and their evolutionary relationships. A sequence alignment of human ADAMs is compiled and their homology and physical data are calculated. The conceivable functions of ADAMs in reproduction, development, and diseases are also discussed.

Amino Acid Sequence↗

PubMed2001

Algorithm for data clustering in pattern recognition problems based on quantum mechanics.

We propose a novel clustering method that is based on physical intuition derived from quantum mechanics. Starting with given data points, we construct a scale-space probability function. Viewing the latter as the lowest eigenstate of a Schrödinger equation, we use simple analytic operations to derive a potential function whose minima determine cluster centers. The method has one parameter, determining the scale over which cluster structures are searched. We demonstrate it on data analyzed in two dimensions (chosen from the eigenvectors of the correlation matrix). The method is applicable in higher dimensions by limiting the evaluation of the Schrödinger potential to the locations of data points.

Journal Article↗

PubMed1999

Activated memory CD4(+) T helper cells repopulate the intestine early following antiretroviral therapy of simian immunodeficiency virus-infected rhesus macaques but exhibit a decreased potential to produce interleukin-2.

Using the simian immunodeficiency virus (SIV)-infected rhesus macaque model, we performed a longitudinal study to determine the effect of antiretroviral therapy on the phenotype and functional potential of CD4(+) T cells repopulating intestinal mucosa in human immunodeficiency virus infection. Severe depletion of CD4(+) and CD4(+) CD8(+) T cells occurred in the intestinal mucosa during primary SIV infection. The majority of these cells were of activated memory phenotype. Phosphonate 9-[2-(phosphomethoxypropyl]adenine (PMPA) treatment led to a moderate suppression of intestinal viral loads and repopulation of intestinal mucosa by predominantly activated memory CD4(+) T-helper cells. This repopulation was independent of the level of viral suppression. Compared to preinfection values, the frequency of naive CD4(+) T cells increased following PMPA therapy, suggesting that new CD4(+) T cells were repopulating the intestinal mucosa. Repopulation by CD4(+) CD8(+) T cells was not observed in either jejunum or colon lamina propria. The majority of CD4(+) T cells repopulating the intestinal mucosa following PMPA therapy were CD29(hi) and CD11ahi. A subset of repopulating intestinal CD4(+) T cells expressed Ki-67 antigen, indicating that local proliferation may play a role in the repopulation process. Although the majority of repopulating CD4(+) T cells in the intestinal mucosa were functionally capable of providing B- and T-cell help, as evidenced by their expression of CD28, these CD4(+) T cells were found to have a reduced capacity to produce interleukin-2 (IL-2) compared to the potential of CD4(+) T cells prior to SIV infection. Persistent viral infection may play a role in suppressing the potential of repopulating CD4(+) T cells to produce IL-2. Hence, successful antiretroviral therapy should aim at complete suppression of viral loads in mucosal lymphoid tissues, such as intestinal mucosa.

Adenine↗