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PubMed1979

Sequence organization of the spacer DNA in a ribosomal gene unit of Xenopus laevis.

A detailed restriction map was constructed for a cloned Xenopus laevis rDNA fragment containing the nontranscribed spacer (NTS) and external transcribed spacer (ETS) together with a portion of both the 18S and 28S rRNA genes. The NTS was found to contain at least three distinct repetitious areas. Region 1 has a repeating unit of approximately 100 bp. The primary structure of this unit has been determined by DNA sequencing. Region 2 is very similar in organization to region 3, and both have an alternating 81/60 bp arrangement as revealed by restriction with Alu I and DNA sequencing. It can be shown that the 81 and 60 bp canons are virtually identical to one another excepting a deletion/insertion of a 21 bp segment. Region 3 differs from region 2 in having sites for Sma I with its 81 bp units. Between these repeated DNA sequences there are two identical, nonrepetitive DNA sequences, each of which is centered around a Bam Hl site. Most of the ETS has been sequenced. It was found to be nonrepetitive and extremely rich in Cs. Close to the 5' end of the 18S coding sequence there is a DNA stretch very rich in purines. About 2.25 kb upstream from the Eco Rl restriction site bisecting the 18S structural gene there is a unique sequence which may be homologous to the 5' end of the 40S precursor RNA. Present evidence suggests that the boundaries between NTS and ETS occur farther downstream than was suggested by electron microscopic data. Sequencing has revealed that the spacer DNA of X. laevis contains different kinds of simple DNA sequences, but no evidence has been found that spacer DNA once arose by saltation of a 15 bp segment. The most surprising finding was that the spacer sequences around the Bam restriction sites (the Bam islands) show high homology with a sequence near the NTS/ETS interface. From the restriction and sequencing analyses it can be deduced that in recent evolutionary times the DNA sequences near the 5' end of the ribosomal transcription unit were reduplicated twice and displaced into spacer by saltation of an intervening short DNA sequence (the 60/81 bp canons). Possible implications of these evolutionary events for spacer functions are consisdered. The sequencing has also provided a molecular basis for a whole range of conclusions arrived at previously by indirect approaches, and these are discussed.

Animals↗

PubMed2006

Xanthusbase: adapting wikipedia principles to a model organism database.

xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.

Databases, Nucleic Acid↗

PubMed2005

Examples of Fourier transform ion cyclotron resonance mass spectrometry developments: from ion physics to remote access biochemical mass spectrometry.

The application of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) for high resolution biomolecular analysis has increased greatly after 30 years of innovation since its conception in 1974. FT- ICR-MS can now routinely be used for the analysis of complex organic mixtures such as biological or petrochemical samples. Many of these new possibilities have been the results of many different instrumental developments. This paper provides a mini review of selected instrumental developments that now allow these measurements. The development of soft ionization techniques such as electrospray ionization and matrix assisted laser desorption and ionisation was crucial for the analysis of biological macromolecules. Improved ion transport optics led to an increase in sensitivity. New ICR cell designs complement the capabilities of FT-ICR-MS by allowing a more thorough study of the mechanism and kinetics of ion reactions in the gas-phase. A selected example of electron capture dissociation (ECD) employs these developments to investigate the role of peptide conformation in ECD. Improved electronics and software allow faster and more flexible experiments. All these improvements led to an increase in speed and sensitivity that are necessary to couple FT-MS to fast separation techniques such as nano-high performance liquid chromatography. The modern FT-ICR-MS instruments can be incorporated in virtual organizations allowing remote access to unique infrastructure. This concept of remote experimentation opens new possibilities for scientific collaborations between expert scientists at different locations and allows the efficient use of this expensive instrumentation.

Biochemical Phenomena↗

PubMed1989

[MR imaging of femoral head avascular necrosis with STIR sequence].

The uncomplicated bone necrosis is usually demarcated by reactive interface (RI). To analyze signal characteristics of RI, MR imaging of the hip was done using short TI IR (STIR) as well as short/long TR pulse sequences at 0.22 tesla. On STIR sequence the RI was observed as a high-signal line or ring with the shape identical to that of short TR image. The double line sign was not seen in early stage. The best explanation of high signal intensity of RI on STIR is that it has prolonged T1 and T2 secondary to high water content. It is concluded that STIR is an unique way to demonstrate RI in early osteonecrosis.

Adult↗

PubMed1993

Protein kinase C and annexins: unusual calcium response elements in the cell.

Protein kinase C and the annexins appear to share some unusual and potentially important membrane- and calcium-binding properties. While these proteins are calcium response elements, they are not calcium-binding proteins in the formal sense; at intracellular calcium concentrations, they only bind significant amounts of calcium when membranes or other suitable surfaces are present. The number of calcium ions bound per protein is large (> 8) and this stoichiometry, at the protein-membrane interface, may provide the large number of contact points needed for the very high-affinity interaction that is observed. The further ability of annexins and PKC to form structures with properties of integral membrane proteins may be important to provide a type of long-term cell signalling that produces a constitutively active kinase or ion channel activity. Selectivity for phospholipids in bilayer form is modest with respect to the acidic phospholipids but there is a surprising preference for phosphatidylethanolamine as the neutral phospholipid matrix. Along with other unusual properties, these proteins offer the potential for unique types of cell regulation events.

Animals↗

PubMed2005

Self-assembling bipyridinium multilayers.

The identification of strategies to assemble nanostructured films with engineered properties on solid supports can lead to the development of innovative functional materials. In particular, the self-assembly of electroactive multilayers from simple molecular building blocks on metallic electrodes can offer the opportunity to regulate the exchange of electrons between the underlying substrate and solution species. In this context, we designed an experimental protocol to prepare electroactive films from bipyridinium bisthiols. Specifically, we found that a compound incorporating two bipyridinium dications at its core and terminal thiol groups self-assembles into remarkably stable multilayers on polycrystalline gold. The surface coverage of the resulting films can be regulated by adjusting the exposure time of the gold substrate to the bipyridinium solution. Control experiments with appropriate model compounds demonstrate that both bipyridinium dications as well as both thiol groups must be present in the molecular skeleton to encourage multilayer growth. The resulting films transport electrons efficiently from the electrode surface to the film/solution interface. Indeed, they mediate the reduction of Ru(NH(3))(6)(3+) in the electrolyte solution but prevent the back oxidation of the resulting Ru(NH(3))(6)(2+). Furthermore, these polycationic bipyridinium films capture electrostatically Fe(CN)(6)(4-) tetraanions, which can also be exploited to transport electrons across the interfacial assembly. In fact, electrons can travel through the bipyridnium(2+/1+) couples to redox probes in solution and then back to the electrode through the Fe(CN)(6)(4/3-) couples. Thus, our original approach to self-assembling multilayers can produce stable electroactive films with unique electron transport properties, which can be regulated with a careful choice of the anionic components.

Journal Article↗

PubMed2002

Comparison of hedgehog and patched-1 protein expression in the cranial sutures of craniosynostotic and wild-type rabbits.

Craniosynostosis is characterized by premature fusion of the cranial sutures. At the molecular level, mutations in homeobox genes, transcription factors, and growth factor receptors have been implicated in the pathogenesis of this disorder, but the specific etiologic pathways have not yet been elucidated. To further study the molecular biology behind craniosynostosis, perisutural tissues in a unique rabbit model with congenital delayed-onset coronal craniosynostosis were examined for the presence of the hedgehog family of growth factors and their receptor, patched-1. Expression of desert hedgehog, Indian hedgehog, sonic hedgehog, and patched-1 was evaluated in four areas: suture, endosteum, periosteum, and osteocytes, using immuno-histochemistry (n = 8). Protein levels in affected animals were compared with protein levels in wild-type control rabbits (n = 8). Overall, sonic hedgehog, Indian hedgehog, and patched-1 protein levels were greater in affected animals. Specifically, areas of increased staining were seen along the bony interface of the endosteum and periosteum and in the osteocytes of the synostotic rabbits. Interestingly, in the suture, increased levels of Indian hedgehog and sonic hedgehog, but not patched-1, were seen. There was minimal expression of desert hedgehog in both rabbit types. The increased overall presence of hedgehog and patched-1 proteins in synostotic rabbits may be a reactive change to the disorder or part of the pathogenic process. Although the specific cause cannot be determined from the data, it is clear that the molecular milieu of the cranial sutures in synostotic rabbits is markedly different from that of wild-type rabbits.

Animals↗

PubMed2005

Digital chameleons: automatic assimilation of nonverbal gestures in immersive virtual environments.

Previous research demonstrated social influence resulting from mimicry (the chameleon effect); a confederate who mimicked participants was more highly regarded than a confederate who did not, despite the fact that participants did not explicitly notice the mimicry. In the current study, participants interacted with an embodied artificial intelligence agent in immersive virtual reality. The agent either mimicked a participant's head movements at a 4-s delay or utilized prerecorded movements of another participant as it verbally presented an argument. Mimicking agents were more persuasive and received more positive trait ratings than nonmimickers, despite participants' inability to explicitly detect the mimicry. These data are uniquely powerful because they demonstrate the ability to use automatic, indiscriminate mimicking (i.e., a computer algorithm blindly applied to all movements) to gain social influence. Furthermore, this is the first study to demonstrate social influence effects with a nonhuman, nonverbal mimicker.

Acculturation↗

PubMed2004

Virtual reality neurosurgery: a simulator blueprint.

OBJECTIVE: This article details preliminary studies undertaken to integrate the most relevant advancements across multiple disciplines in an effort to construct a highly realistic neurosurgical simulator based on a distributed computer architecture. Techniques based on modified computational modeling paradigms incorporating finite element analysis are presented, as are current and projected efforts directed toward the implementation of a novel bidirectional haptic device. METHODS: Patient-specific data derived from noninvasive magnetic resonance imaging sequences are used to construct a computational model of the surgical region of interest. Magnetic resonance images of the brain may be coregistered with those obtained from magnetic resonance angiography, magnetic resonance venography, and diffusion tensor imaging to formulate models of varying anatomic complexity. RESULTS: The majority of the computational burden is encountered in the presimulation reduction of the computational model and allows realization of the required threshold rates for the accurate and realistic representation of real-time visual animations. CONCLUSION: Intracranial neurosurgical procedures offer an ideal testing site for the development of a totally immersive virtual reality surgical simulator when compared with the simulations required in other surgical subspecialties. The material properties of the brain as well as the typically small volumes of tissue exposed in the surgical field, coupled with techniques and strategies to minimize computational demands, provide unique opportunities for the development of such a simulator. Incorporation of real-time haptic and visual feedback is approached here and likely will be accomplished soon.

Computer Simulation↗

PubMed1991

Public-academic linkages for culturally sensitive community mental health.

This paper traces the sixteen year history of a unique community mental health center which has combined academic and service provider roles in delivery of culturally appropriate care. Initially an arm of a department of psychiatry and derived from an anthropological research project, the center model was based on seven teams serving discrete ethnic communities, with subsequent development of a network of neighborhood-based "mini-clinics" as well as centralized aftercare facilities. The team staff-social scientists, clinicians, and paraprofessionals all of matching ethnicity to the populations served-became a core of "culture brokers" with a service, teaching, and research role at the interface of the university, medical center, and community. Subsequently the university was funded for a cross-cultural training institute for mental health professionals. Center staff extended training in culturally appropriate care to 174 mental health professionals from 97 facilities throughout the nation, as well as other spinoffs improving cultural expertise of staff in public sector agencies. Data on effectiveness of services and training are given and significant findings are discussed. The description includes the impact of historical shifts in funding, the effects of external events on community mental health center structure, and the current state of cross-cultural training and public-academic linkages in this particular program.

Aftercare↗

PubMed1990

Fetal tectum grafted as a cell suspension into the adult rat inferior colliculus.

The known structural and functional features of the inferior colliculus provided an advantageous substrate for examining the outcome of neural transplantation. In the present study, tissue from the midbrain tectum of Sprague-Dawley rat fetuses was removed at 15, 16 and 19 days of gestation (E15, E16 and E19), incubated as a dissociated cell suspension for 12 to 15 h in a medium containing True Blue for prelabeling, and injected into the central nucleus of the inferior colliculus (CNIC) of 28 normal male adult conspecifics. Viable tectal grafts were found in 57.5% of host animals with 65.2% located in CNIC. Grafts of E16 tissue had a survival rate of 84.2%, which was twice that of E15 or E19 donors, and there was no difference in graft survival rate in hosts sacrificed up to 6 months after the implantation procedure. Neurons prelabeled with True Blue and counterstained with thionin were identified as uniquely green stained cells in brightfield illumination and brilliant opaque cells in darkfield microscopy. Grafts were organized in tightly packed clusters of cells including large rounded polygonal and smaller cells similar in size to normal CNIC large and small multipolar neurons. Cell morphology of the larger ovoid and fusiform grafted neurons most closely resembled that of typical adult CNIC cell populations; other implanted cell types appeared immature even when host post-implant survival was extended. At longer post-implant intervals graft and host cells further intermingled, and both cellular and fibrous bridges were observed at the interface between host and graft tissue. The present work demonstrates the viability and development of homotypic cells grafted into a central auditory structure utilizing a simple method of prelabeling donor tissue with a fluorescent dye.

Animals↗

PubMed2001

Theoretical study of the mechanisms of substrate recognition by catalase.

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H(2)O(2) is only slightly larger than that for H(2)O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.

Catalase↗

PubMed1996

Phospholipase C beta2 association with phospholipid interfaces assessed by fluorescence resonance energy transfer. G protein betagamma subunit-mediated translocation is not required for enzyme activation.

Phospholipase C beta2 (PLC beta2) is activated by G protein betagamma subunits and calcium. The enzyme is soluble and its substrate, phosphatidylinositol 4,5-bisphosphate (PIP2), is present in phospholipid membranes. A potential mechanism for regulation of this enzyme is through influencing the equilibrium association of the enzyme with membrane surfaces. In this paper we describe a fluorescence resonance energy transfer (FRET) method for measuring the association of PLC beta2 with phospholipid bilayers. The method allows equilibrium measurements to be made under a variety of conditions, including those that support enzymatic activity and ability to be regulated by G proteins. Using this method it was found that PLC beta2 bound to vesicles containing anionic lipids and demonstrated a selective and unique interaction with PIP2-containing vesicles. The FRET data were corroborated with a centrifugation based method for estimating the affinity of PLC beta2 for vesicles. Apparently different modes of association of PLC beta2 with vesicles of different composition can be distinguished based on alterations in resonance energy transfer efficiency. Association of PLC beta2 with PIP2 vesicles requires an intact lipid bilayer, is blocked by neomycin, and is not affected by D-myo-inositol 1,4,5-trisphosphate (D-IP3). G protein betagamma subunits do not alter the affinity of PLC beta2 for lipid bilayers and at the PIP2 concentrations used to measure betagamma-dependent stimulation of PLC activity, the majority of the PLC beta2 is already associated with the vesicle surface. Furthermore, under conditions where betagamma subunits strongly activate PLC activity, the extent of association with vesicles is unaffected by betagamma subunits or calcium. These results indicate that activation of PLC beta2 by G protein betagamma subunits or Ca2+ in vitro does not involve translocation to the vesicle surface.

Animals↗

PubMed1986

Modification of the actin interface of skeletal myosin subfragment-1 by treatment with dibromobimane.

Recently, by treating the head portion of skeletal myosin subfragment-1 (S1) with the bifunctional agent dibromobimane, we introduced an intramolecular covalent cross-link which resulted in the stabilisation of an internal loop in the heavy chain structure of the head [Mornet et al. (1984) Proc. Natl Acad. Sci. USA 82, 1658-1662]. In order to define the functional properties of this new S1 conformational state, we have first determined the experimental conditions for the optimum modification of S1 by dibromobimane. We finally settled on a 60% yield of cross-linked S1. Because the modification occurs between the 50-kDa and the 20-kDa tryptic heavy chain fragments which have been postulated to be involved in the interaction of native S1 with actin, we have investigated the association of dibromobimane-treated S1 with actin, using chemical cross-linking of their rigor complex with 1-ethyl-3-[3-(dimethylamino)propyl] carbodiimide. The cross-linked species obtained were analyzed by polyacrylamide gel electrophoresis and compared with those known for unmodified S1. The carbodiimide-catalyzed linkage between actin and dibromobimane-modified S1 led to a singlet protein band migrating with an apparent molecular mass of 155 kDa, in contrast to the usual doublet bands of 175 kDa and 185 kDa produced with native S1. This result suggests that a change has occurred at the actin interface on the dibromobimane-treated S1 heavy chain. The covalent complex generated by carbodiimide cross-linking between actin and dibromobimane-modified S1 (27-kDa + 50-kDa + 20-kDa fragments) was submitted to chemical hydrolysis with hydroxylamine. The nature of the products identified is consistent with the conclusion that the internal freezing of the heavy chain structure by dibromobimane induces the loss of the ability to cross-linkage of the actin site on the 20-kDa domain but does not affect the conformation of the second site on the 50-kDa segment, which becomes the unique actin region cross-linkable by actin.

Actins↗

PubMed2006

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

Computational Biology↗

PubMed1999

Developing a framework for worldwide image communication.

The increasing mobility of the population and frequent changes in healthcare coverage, in both the government and private sectors, require integration of medical records not only longitudinally, but also across a variety of healthcare providers. Early in 1998, the federal government decided to solve this problem by constructing a framework for access to medical records by all of the government's health care facilities, called the Government Computer-Based Patient Record (GCPR). The government consortium chose a proposal by Litton PRC, a partnership of 11 companies with complementary areas of expertise. The framework is based on open systems, which use publicly available standards, and includes a Master Patient Information Locator that allows access to medical information from remote facilities, based on creating a unique identifier for each and every individual patient. PRC will use the Digital Imaging and Communications in Medicine (DICOM) imaging standard for radiology, supplemented by Health Level Seven (HL7).

Computer Communication Networks↗

PubMed2004

Solvent exchange method: a novel microencapsulation technique using dual microdispensers.

PURPOSE: A new microencapsulation method called the "solvent exchange method" was developed using a dual microdispenser system. The objective of this research is to demonstrate the new method and understand how the microcapsule size is controlled by different instrumental parameters. METHOD: The solvent exchange method was carried out using a dual microdispenser system consisting of two ink-jet nozzles. Reservoir-type microcapsules were generated by collision of microdrops of an aqueous and a polymer solution and subsequent formation of polymer films at the interface between the two solutions. The prepared microcapsules were characterized by microscopic methods. RESULTS: The ink-jet nozzles produced drops of different sizes with high accuracy according to orifice size of a nozzle, flow rate of the jetted solutions, and forcing frequency of the piezoelectric transducers. In an individual microcapsule, an aqueous core was surrounded by a thin polymer membrane; thus, the size of the collected microcapsules was equivalent to that of single drops. CONCLUSIONS: The solvent exchange method based on a dual microdispenser system produces reservoir-type microcapsules in a homogeneous and predictable manner. Given the unique geometry of the microcapsules and mildness of the encapsulation process, this method is expected to provide a useful alternative to existing techniques in protein microencapsulation.

Capsules↗

PubMed2006

PigGIS: Pig Genomic Informatics System.

Pig Genomic Information System (PigGIS) is a web-based depository of pig (Sus scrofa) genomic learning mainly engineered for biomedical research to locate pig genes from their human homologs and position single nucleotide polymorphisms (SNPs) in different pig populations. It utilizes a variety of sequence data, including whole genome shotgun (WGS) reads and expressed sequence tags (ESTs), and achieves a successful mapping solution to the low-coverage genome problem. With the data presently available, we have identified a total of 15 700 pig consensus sequences covering 18.5 Mb of the homologous human exons. We have also recovered 18 700 SNPs and 20 800 unique 60mer oligonucleotide probes for future pig genome analyses. PigGIS can be freely accessed via the web at http://www.piggis.org/ and http://pig.genomics.org.cn/.

Animals↗