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PubMedDate not supplied

Client-server, distributed database strategies in a health-care record system for a homeless population.

OBJECTIVE: To design and develop a computer-based health-care record system to address the needs of the patients and providers of a homeless population. DESIGN: A computer-based health-care record system being developed for Boston's Healthcare for the Homeless Program (BHCHP) uses client-server technology and distributed database strategies to provide a common medical record for this transient population. The differing information requirements of physicians, nurses, and social workers are specifically addressed in the graphic application interface to facilitate an integrated approach to health care. This computer-based record system is designed for remote and portable use to integrate smoothly into the daily practice of providers of care to the homeless. The system uses remote networking technology and regular phone lines to support multiple concurrent users at remote sites of care. RESULTS: A stand-alone, pilot system is in operation at the BHCHP medical respite unit. Information on 129 patient encounters from 37 unique sites has been entered. A full client-server system has been designed. Benchmarks show that while the relative performance of a communication link based upon a phone line is 0.07 to 0.15 that of a local area network, optimization permits adequate response. CONCLUSION: Medical records access in a transient population poses special problems. Use of client-server and distributed database strategies can provide a technical foundation that provides a secure, reliable, and accessible computer-based medical record in this environment.

Boston↗

PubMed2006

ProtRepeatsDB: a database of amino acid repeats in genomes.

BACKGROUND: Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. DESCRIPTION: ProtRepeatsDB (v1.2) consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO) annotation IDs and regular expressions (REGEXP) describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. CONCLUSION: ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific repeat markers, interspecies variations and polymorphism.

Amino Acid Sequence↗

PubMed2005

Natural killer cells in pregnancy and recurrent pregnancy loss: endocrine and immunologic perspectives.

The endocrine system and the immune system interact closely during implantation and maintenance of pregnancy. One of the most striking examples of this communication is at the level of the decidua (endometrium of pregnancy). Here, under the influence of sex steroids, there is a dramatic increase of a unique population of lymphocytes, the uterine natural killer (uNK) cells, in early pregnancy. These cells derive predominantly from a subset of peripheral blood NK cells, which under hormonal influence gets recruited to the uterus. In mice, uNK cells play an important role in the development of placental vasculature. The role of these cells in human pregnancy is still not definitively established; however, they are believed to promote placental and trophoblast growth and provide immunomodulation at the maternal-fetal interface. In contrast to their presumptive role in the maintenance of a healthy pregnancy, uNK cells and peripheral NK cells are dysregulated in unexplained recurrent pregnancy loss. Herein, we review NK cell populations, their changes in number and function in altered endocrine environments during the menstrual cycle and pregnancy, the current data on their potential role in unexplained recurrent pregnancy loss, and mechanisms for potential therapies targeted to NK cell function for this enigmatic disorder.

Abortion, Habitual↗

PubMed2005

Crystal structure and functional analysis of DEAD-box protein Dhh1p.

The control of mRNA translation and degradation are critical for proper gene expression. A key regulator of both translation and degradation is Dhh1p, which is a DEAD-box protein, and functions both to repress translation and enhance decapping. We describe the crystal structure of the N- and C-terminal truncated Dhh1p (tDhh1p) determined at 2.1 A resolution. This reveals that, like other DEAD-box proteins, tDhh1p contains two RecA-like domains, although with a unique arrangement. In contrast to eIF4A and mjDEAD, in which no motif interactions exist, in Dhh1p, motif V interacts with motif I and the Q-motif, thereby linking the two domains together. Electrostatic potential mapping combined with mutagenesis reveals that motifs I, V, and VI are involved in RNA binding. In addition, trypsin digestion of tDhh1p suggests that ATP binding enhances an RNA-induced conformational change. Interestingly, some mutations located in the conserved motifs and at the interface between the two Dhh1 domains confer dominant negative phenotypes in vivo and disrupt the conformational switch in vitro. This suggests that this conformational change is required in Dhh1 function and identifies key residues involved in that transition.

Amino Acid Sequence↗

PubMed2006

A large T cell invagination with CD2 enrichment resets receptor engagement in the immunological synapse.

T cell activation is driven by the TCR and complemented by costimulation. We have studied the dynamics of ligand-engagement of the costimulatory receptor CD2 in T cell/APC couples. Thousands of ligand-engaged CD2 molecules were included in a large T cell invagination at the center of the cellular interface within 1 min of cell couple formation. The structure and regulation of this invagination shared numerous features with phagocytosis and macropinocytosis. Three observations further characterize the invagination and the inclusion of CD2: 1) numerous ligand-engaged receptors were enriched in and internalized through the T cell invagination, none as prominently as CD2; 2) dissolution of the T cell invagination and CD2 engagement were required for effective proximal T cell signaling; and 3) the T cell invagination was uniquely sensitive to the affinity of the TCR for peptide-MHC. Based on this characterization, we speculate that the T cell invagination, aided by CD2 enrichment, internalizes parts of the TCR signaling machinery to reset T cell signaling upon agonist-mediated, stable APC contact.

Actins↗

PubMedDate not supplied

Effects of a multimedia project on users' knowledge about normal forgetting and serious memory loss.

OBJECTIVE: The aim of the project was to develop and evaluate the effectiveness of a CD-ROM-based multimedia program as a tool to increase user's knowledge about the differences between "normal" forgetfulness and more serious memory loss associated with Alzheimer's disease. DESIGN AND MEASUREMENTS: The research was a controlled randomized study conducted with 113 adults who were recruited from the community and who expressed a concern about memory loss in a family member. The intervention group (n=56) viewed a module entitled "Forgetfulness: What's Normal and What's Not" on a laptop computer in their homes; the control group (n=57) did not. Both groups completed a 25-item knowledge-about-memory-loss test (primary outcome) and a sociodemographic and technology usage questionnaire; the intervention group also completed a CD-ROM user's evaluation. RESULTS: The mean (SD) number of correct responses to the knowledge test was 14.2 (4.5) for controls and 19.7 (3.1) for intervention participants. This highly significant difference (p<0.001) corresponds to a very large effect size. The program was most effective for participants with a lower level of self-reported prior knowledge about memory loss and Alzheimer's disease (p=0.02). Viewers were very satisfied with the program and felt that it was easy to use and understand. They particularly valued having personal access to a confidential source that permitted them to become informed about memory loss without public disclosure. CONCLUSION: This multimedia CD-ROM technology program provides an efficient and effective means of teaching older adults about memory loss and ways to distinguish benign from serious memory loss. It uniquely balances public community outreach education and personal privacy.

Aged↗

PubMed2001

The production of elevated flight force compromises manoeuvrability in the fruit fly Drosophila melanogaster.

In this study, we have investigated how enhanced total flight force production compromises steering performance in tethered flying fruit flies, Drosophila melanogaster. The animals were flown in a closed-loop virtual-reality flight arena in which they modulated total flight force production in response to vertically oscillating visual patterns. By simultaneously measuring stroke amplitude and stroke frequency, we recorded the ability of each fly to modulate its wing kinematics at different levels of aerodynamic force production. At a flight force that exactly compensates body weight, the temporal deviations with which fruit flies vary their stroke amplitude and frequency are approximately 2.7 degrees and 4.8 Hz of their mean value, respectively. This variance in wing kinematics decreases with increasing flight force production, and at maximum force production fruit flies are restricted to a unique combination of stroke amplitude, stroke frequency and mean force coefficient. This collapse in the kinematic envelope during peak force production could greatly attenuate the manoeuvrability and stability of animals in free flight.

Animals↗

PubMed1998

The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex.

The tertiary structure of Jel42 Fab fragment complexed with HPr, a phosphocarrier protein of the phosphoenolpyruvate:sugar phosphotransferase system of Escherichia coli, has been determined at 2.5 A resolution. X-ray diffraction from a larger crystal provided 22,067 unique reflections as compared to 14,763 unique reflections (2.8 A resolution), which were obtained previously from a smaller crystal. The higher resolution allowed for more precise location of amino acid side-chains and for the location of well-ordered water molecules. Five more residues in the Fab fragment are found to be involved in binding HPr and two additional residues are identified as part of the epitope, bringing the totals to 24 and 16, respectively. At least nine water molecules are found at the interface between the two proteins, and these mediate hydrogen bonding interactions between the Fab fragment and HPr. Three additional hydrogen bonds have been identified (bringing the total to ten) and one salt-bridge occurs between LysL50 of the L2 complementarity-determining region (CDR) and GluP66 of HPr. This salt-bridge is the only interaction between HPr and CDRL2; thus all six CDRs are involved in binding. Inspection and empirical energy minimization of mutant HPrs in the complex indicate that, in some cases in the binding interaction, water molecules may compensate for residue alterations. Binding to the mutant SerP64Tyr HPr may require a movement of the HPr main chain. The active centre region of HPr, which is not involved in binding the antibody, and which was not resolved in the 2.8 A resolution structure of the complex, was determined. This active centre determined at pH 5.8, which is completely free of intermolecular contacts due to crystal packing, shows a potential hydrogen bond between the AsnP12 OD1 atom and the HisP15 NE2 atom, and no involvement of the C terminus with HisP15. The HisP15 ND1 atom is the site of phosphorylation in HPr. Although a specific amino acid at residue 12 is not conserved in HPr molecules from all species, a hydrogen bond between the side-chains of residue 12 and HisP15 may be a conserved feature of the active centres.

Antigen-Antibody Complex↗

PubMed2006

Intravascular palpography for vulnerable plaque assessment.

Palpography assesses the local mechanical properties of tissue using the deformation caused by the intraluminal pressure. The technique was validated in vitro using diseased human coronary and femoral arteries. Especially between fibrous and fatty tissue, a highly significant difference in strain (p = 0.0012) was found. Additionally, the predictive value to identify the vulnerable plaque was investigated. A high-strain region at the lumen vessel wall boundary has 88% sensitivity and 89% specificity for identifying these plaques. In vivo, the technique is validated in an atherosclerotic Yucatan minipig animal model. This study also revealed higher strain values in fatty than in fibrous plaques (p < 0.001). The presence of a high-strain region at the lumen-plaque interface has a high predictive value to identify macrophages. Patient studies revealed high strain values (1% to 2%) in noncalcified plaques. Calcified material showed low strain values (0% to 0.2%). With the development of three-dimensional palpography, identification of weak spots over the full length of a coronary artery becomes available. Patients with myocardial infarction or unstable angina have more high-strain spots in their coronary arteries than patients with stable angina. In conclusion, intravascular palpography is a unique tool to assess lesion composition and vulnerability. Three-dimensional palpography provides a technique that may develop into a clinically available tool for decision making to treat hemodynamically nonsignificant lesions by identifying vulnerable plaques. The clinical utility of this technique is yet to be determined, and more investigation is needed.

Animals↗

PubMed2005

Crystal structure of a secreted insect ferritin reveals a symmetrical arrangement of heavy and light chains.

Ferritins are iron storage proteins made of 24 subunits forming a hollow spherical shell. Vertebrate ferritins contain varying ratios of heavy (H) and light (L) chains; however, known ferritin structures include only one type of chain and have octahedral symmetry. Here, we report the 1.9A structure of a secreted insect ferritin from Trichoplusia ni, which reveals equal numbers of H and L chains arranged with tetrahedral symmetry. The H/L-chain interface includes complementary features responsible for ordered assembly of the subunits. The H chain contains a ferroxidase active site resembling that of vertebrate H chains with an endogenous, bound iron atom. The L chain lacks the residues that form a putative iron core nucleation site in vertebrate L chains. Instead, a possible nucleation site is observed at the L chain 3-fold pore. The structure also reveals inter- and intrasubunit disulfide bonds, mostly in the extended N-terminal regions unique to insect ferritins. The symmetrical arrangement of H and L chains and the disulfide crosslinks reflect adaptations of insect ferritin to its role as a secreted protein.

Amino Acid Sequence↗

PubMed2005

The SIMRI project: a versatile and interactive MRI simulator.

This paper gives an overview of SIMRI, a new 3D MRI simulator based on the Bloch equation. This simulator proposes an efficient management of the T2* effect, and in a unique simulator integrates most of the simulation features that are offered in different simulators. It takes into account the main static field value and enables realistic simulations of the chemical shift artifact, including off-resonance phenomena. It also simulates the artifacts linked to the static field inhomogeneity like those induced by susceptibility variation within an object. It is implemented in the C language and the MRI sequence programming is done using high level C functions with a simple programming interface. To manage large simulations, the magnetization kernel is implemented in a parallelized way that enables simulation on PC grid architecture. Furthermore, this simulator includes a 1D interactive interface for pedagogic purpose illustrating the magnetization vector motion as well as the MRI contrasts.

Algorithms↗

PubMed1990

Interaction of the Escherichia coli Gal repressor protein with its DNA operators in vitro.

The binding of Escherichia coli Gal repressor to linear DNA fragments containing two binding sites (OE and OI) within the gal operon was analyzed in vitro with quantitative footprint and mobility-shift techniques. In vivo analysis of the regulation of the gal operon [Haber, R., & Adhya, S. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 9683-9687] has suggested the role of a regulatory "looped complex" mediated by the association of Gal repressor dimers bound at OE and OI. The binding of Gal repressor to a single site can be described by a model in which monomer and dimer are in equilibrium and only the dimer binds to DNA. At pH 7.0, 25 mM KCl, and 20 degrees C, the binding and dimerization free energies are comparable, suggesting that the equilibrium governing the formation of dimers may be important to regulation. The two intrinsic binding constants, delta GI and delta GE, and a constant describing cooperativity, delta GIE, were determined by footprint titration analysis as a function of pH, [KCl], and temperature. Only at 4 and 0 degrees C was delta GIE negative, signifying cooperative binding. These results are thought to be due to a weak dimer to tetramer association interface. delta GE and delta GI had maximal values between pH 6 and pH 7. The dependence of these constants on [KCl] corresponded to the displacement of approximately 2 ion equiv. The temperature dependence could be described by a change in the heat capacity, delta Cp, of -2.3 kcal mol-1 deg-1. Mobility-shift titration experiments conducted at 20 and 0 degrees C yielded values for delta GIE that were consistent with those resolved from the footprint analysis. Unique values of delta GIE were determined by analysis of mobility-shift titrations of Gal repressor with wild-type operator subject to the constraint that delta GE = delta GI: a procedure that eliminates the need to simultaneously analyze wild-type titrations with titrations of OE- and OI- operators.

Base Sequence↗

PubMed2006

Proteome-on-a-chip: mirage, or on the horizon?

Proteomics has emerged as the next great scientific challenge in the post-genome era. But even the most basic form of proteomics, proteome profiling, i.e., identifying all of the proteins expressed in a given sample, has proven to be a demanding task. The proteome presents unique analytical challenges, including significant molecular diversity, an extremely wide concentration range, and a tendency to adsorb to solid surfaces. Microfluidics has been touted as being a useful tool for developing new methods to solve complex analytical challenges, and, as such, seems a natural fit for application to proteome profiling. In this review, we summarize the recent progress in the field of microfluidics in four key areas related to this application: chemical processing, sample preconcentration and cleanup, chemical separations, and interfaces with mass spectrometry. We identify the bright spots and challenges for the marriage of microfluidics and proteomics, and speculate on the outlook for progress.

Animals↗

PubMed2003

Dissection of the functional surface of an anti-insect excitatory toxin illuminates a putative "hot spot" common to all scorpion beta-toxins affecting Na+ channels.

Scorpion beta-toxins affect the activation of voltage-sensitive sodium channels (NaChs). Although these toxins have been instrumental in the study of channel gating and architecture, little is known about their active sites. By using an efficient system for the production of recombinant toxins, we analyzed by point mutagenesis the entire surface of the beta-toxin, Bj-xtrIT, an anti-insect selective excitatory toxin from the scorpion Buthotus judaicus. Each toxin mutant was purified and analyzed using toxicity and binding assays, as well as by circular dichroism spectroscopy to discern the differences among mutations that caused structural changes and those that specifically affected bioactivity. This analysis highlighted a functional discontinuous surface of 1405 A(2), which was composed of a number of non-polar and three charged amino acids clustered around the main alpha-helical motif and the C-tail. Among the charged residues, Glu(30) is a center of a putative "hot spot" in the toxin-receptor binding-interface and is shielded from bulk solvent by a hydrophobic "gasket" (Tyr(26) and Val(34)). Comparison of the Bj-xtrIT structure with that of other beta-toxins that are active on mammals suggests that the hot spot and an adjacent non-polar region are spatially conserved. These results highlight for the first time structural elements that constitute a putative "pharmacophore" involved in the interaction of beta-toxins with receptor site-4 on NaChs. Furthermore, the unique structure of the C-terminal region most likely determines the specificity of excitatory toxins for insect NaChs.

Amino Acid Sequence↗

PubMed2004

Identification of a novel co-regulator interaction surface on the ligand binding domain of Nurr1 using NMR footprinting.

The nuclear receptor Nurr1 is a transcription factor essential for the development of midbrain dopaminergic neurons in vertebrates. Recent crystal structures of the Nurr1 ligand binding domain (LBD) and the Drosophila orthologue dHR38 revealed that, although these receptors share the classical LBD architecture, they lack a ligand binding cavity. This volume is instead filled with bulky hydrophobic side chains. Furthermore the "canonical" non-polar co-regulator binding groove is filled with polar side chains; thus, the regulation of transcription by this sub-family of nuclear receptor LBDs may be mediated by some other interaction surface on the LBD. We report here the identification of a novel co-regulator interface on the LBD of Nurr1. We used an NMR footprinting strategy that facilitates the identification of an interaction surface without the need of a full assignment. We found that non-polar peptides derived from the co-repressors SMRT and NCoR bind to a hydrophobic patch on the LBD of Nurr1. This binding surface involves a groove between helices 11 and 12. Mutations in this site abolish activation by the Nurr1 LBD. These findings give insight into the unique mechanism of action of this class of nuclear receptors.

Amino Acid Sequence↗

PubMed2004

topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association.

The database of topographic mapping of Single Nucleotide Polymorphism (topoSNP) provides an online resource for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease- associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology Information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. The current release also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. The database will be updated at regular intervals and can be accessed at: http://gila.bioengr.uic.edu/snp/toposnp.

Computational Biology↗

PubMed1982

Penguin egg-white and polar fish blood-serum proteins.

The development of, and findings in, a long-term research program on penguin proteins and polar fish blood proteins are described. Two of the egg-white proteins from the Adelie penguin (Pygoscelis adeliae) have unique properties: a glycoprotein named penalbumin that is a major constituent with some characteristics similar to ovalbumin, and an ovomucoid with strong inhibitory capacity for subtilisin as well as for bovine trypsin and alpha-chymotrypsin. The antifreeze glycoproteins from Antarctic fish (Trematomus borchgrevinki and Dissostichus mawsoni) and an Arctic fish (Boreogadus saida) appear to function noncolligatively by lowering the freezing temperature without affecting the melting point. Current evidence indicates that the antifreeze glycoprotein functions at the ice-solution interface, either on the ice surface or in a transition layer between the solution and the ice.

Animals↗

PubMed1994

Crystalline mitochondrial aspartate aminotransferase exists in only two conformations.

The subunits of the alpha 2-dimeric enzyme aspartate aminotransferase are composed of two distinct domains, one large and one small. The active sites are situated close to both the intersubunit and the interdomain interface. Binding of substrate analogues to the active site induces a large conformational change in the enzyme, whereby the small domain rotates by 13 degrees relative to the large domain and completely buries the ligand. We have determined the crystal structures of chicken mitochondrial aspartate aminotransferase (mAATase) in two new crystal forms. A comparison of the structures of mAATase in five crystal forms, including both the unliganded and the liganded enzyme, shows that mAATase exists in either one of two unique conformations, with only minimal adaptations to the crystal lattice. This suggests that both the open, unliganded and closed, liganded structure of mAATase are, to a large extent, stabilized by intramolecular interactions, and are consequently representative of functional states of the protein in solution. A 2-fold-symmetric packing interaction between small domains occurring identically in three crystal forms of mAATase is described.

Animals↗