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Structure and function of neurons in the complex of the nucleus electrosensorius of Sternopygus and Eigenmannia: diencephalic substrates for the evolution of the jamming avoidance response.

The ability to discriminate the sign of the difference in frequency (DF) between two wavelike signals is integral to the jamming avoidance response (JAR) of weakly electric gymnotiform fish such as Eigenmannia. 'Whole-cell' intracellular recordings from neurons in the nucleus electrosensorius (nE) of Sternopygus, a gymnotiform that lacks the JAR, revealed that this nucleus receives information from both the ampullary and the tuberous electrosensory systems. Most tuberous units responded to DF stimuli, and many of these cells were DF sign-sensitive, i.e., they responded differently for one sign of DF. Although the distribution of ampullary units was somewhat restricted, sign-sensitive units were found in all areas of the nE in Sternopygus. Whole-cell recordings made in the nE of Eigenmannia revealed that, as in Sternopygus, sign-sensitive cells were not restricted to areas associated with control of the JAR. The diverse neurophysiology and connectivity of the nucleus electrosensorius suggests that, besides its role in the JAR of some members of the order, this nucleus likely serves as an interface between sensory input and neural circuits controlling other behaviors and endocrinological states in other gymnotiforms as well. The discovery of sign sensitivity in the nE of Sternopygus indicates that this property is not uniquely associated with the presence of a JAR; rather, the ability to discriminate the sign of DF may be relevant to many other behavioral contexts in gymnotiforms. Existing evidence indicates that the JAR evolved more than once in this group; the presence of sign sensitivity in ancestral gymnotiforms may have made this parallelism more likely.

Animals↗

A detailed study of the L2beta long-loop region of human chorionic gonadotrophin suggests it to be spatially close to, but not part of, the receptor-binding site.

An in-depth study of the L2beta long-loop region of human chorionic gonadotrophin (hCG), earlier identified to be a conformational bioneutralization epitope and receptor-binding site of the hormone, was carried out. The linear 38-57 hCGbeta peptide and the corresponding cyclic disulphide peptide were synthesized and antipeptide antibodies developed. Binding studies with antibodies to the linear peptide, and with hCGbeta, hCG and human LH suggest that part of the region is buried at the alpha/beta interface and part exposed in hCG. Observation of the surface exposure of residues 47-53 from the crystal structure of hCG was confirmed by epitope mapping studies of the region. The region is not unique to hCG as a majority of the antibodies to both the linear and cyclic peptides did not exhibit the required specificity. Competitive inhibition studies with the linear and cyclic peptides failed to show inhibition of radiolabelled hCG binding to its receptors. However, both the antipeptide antibodies were able to bioneutralize the hormone in an in vivo assay. Taken together, these results seem to indicate that the L2beta long-loop region is not a receptor-binding site of hCG but spatially close to it.

Analysis of Variance↗

At the interface of the immune system and the nervous system: how neuroinflammation modulates the fate of neural progenitors in vivo.

Neural stem and progenitor cells express a variety of receptors that enable them to sense and react to signals emanating from physiological and pathophysiological conditions in the brain as well as elsewhere in the body. Many of these receptors and were first described in investigations of the immune system, particularly with respect to hematopoietic stem cells. This emerging view of neurobiology has two major implications. First, many phenomena known from the hematopoietic system may actually be generalizable to stem cells from many organ systems, reflecting the cells' progenitor-mediated regenerative potential. Second, regenerative interfaces may exist between diverse organ systems; populations of cells of neuroectodermal and hematopoietic origin may interact to play a crucial role in normal brain physiology, pathology, and repair. An understanding of the origins of signals and the neural progenitors' responses might lead to the development of effective therapeutic strategies to counterbalance acute and chronic neurodegenerative processes. Such strategies may include modifying and modulating cells with regenerative potential in subtle ways. For example, stem cells might be able to detect pathology-associated signals and be used as "interpreters" to mediate drug and other therapeutic interventions. This review has focused on the role of inflammation in brain repair. We propose that resident astroglia and blood-born cells both contribute to an inflammatory signature that is unique to each kind of neuronal degeneration or injury. These cells play a key role in coordinating the neural progenitor cell response to brain injury by exerting direct and indirect environmentally mediated influence on neural progenitor cells. We suggest that investigations of the neural progenitor-immunologic interface will provide valuable data related to the mechanisms by which endogenous and exogenous neural progenitor cells react to brain pathology, ultimately aiding in the design of more effective therapeutic applications of stem cell biology. Such improvements will include: (1) ascertaining the proper timing for implanting exogenous neural progenitor cells in relation to the administration of anti-inflammatory agents; (2) identifying what types of molecules might be administered during injury to enhance the mobilization and differentiation of endogenous and exogenous neural progenitor cells while also inhibiting the detrimental aspects of the inflammatory reaction; (3) divining clues as to which molecules may be required to change the lesioned environment in order to invite the homing of reparative neural progenitor cells.

Animals↗

Classifying threats with a 14-MeV neutron interrogation system.

SeaPODDS (Sea Portable Drug Detection System) is a non-intrusive tool for detecting concealed threats in hidden compartments of maritime vessels. This system consists of an electronic neutron generator, a gamma-ray detector, a data acquisition computer, and a laptop computer user-interface. Although initially developed to detect narcotics, recent algorithm developments have shown that the system is capable of correctly classifying a threat into one of four distinct categories: narcotic, explosive, chemical weapon, or radiological dispersion device (RDD). Detection of narcotics, explosives, and chemical weapons is based on gamma-ray signatures unique to the chemical elements. Elements are identified by their characteristic prompt gamma-rays induced by fast and thermal neutrons. Detection of RDD is accomplished by detecting gamma-rays emitted by common radioisotopes and nuclear reactor fission products. The algorithm phenomenology for classifying threats into the proper categories is presented here.

Algorithms↗

The crystal structure of Plasmodium falciparum glutamate dehydrogenase, a putative target for novel antimalarial drugs.

Plasmodium falciparum is the main causative agent of tropical malaria, the most severe parasitic disease in the world. Growing resistance of Plasmodia towards available drugs is an increasing problem in countries where malaria is endemic. As Plasmodia are sensitive to oxidative stress, augmenting this in the parasite represents a promising principle for the development of novel antimalarial drugs. The NADP-dependent glutamate dehydrogenase (GDH) of P.falciparum is largely responsible for the production of NADPH in the parasite, which in turn serves as electron source for the antioxidative enzymes glutathione reductase and thioredoxin reductase. As GDH does not occur in the host erythrocyte, GDH is a particularly attractive target for drug therapy. The three-dimensional structure of P.falciparum GDH in the unligated state has been determined by X-ray crystallography to a resolution of 2.7A. Compared to the mammalian enzymes, two amino acid residues are exchanged in the putative active site of the parasite GDH. The most obvious differences between parasite and human GDH are the subunit interfaces of the hexameric proteins. In the parasite protein, several salt-bridges mediate contacts between the subunits whereas in the human enzyme these interactions are mainly of hydrophobic nature. Furthermore, P.falciparum GDH possesses a unique N-terminal extension that does not occur in any other GDH sequence so far studied. These findings might be exploited for the design of peptidomimetics capable of disrupting the oligomeric organisation of the parasite enzyme.

Amino Acid Sequence↗

Crystal structure of a bifunctional deaminase and reductase from Bacillus subtilis involved in riboflavin biosynthesis.

Bacterial RibG is an attractive candidate for development of antimicrobial drugs because of its involvement in the riboflavin biosynthesis. The crystal structure of Bacillus subtilis RibG at 2.41-A resolution displayed a tetrameric ring-like structure with an extensive interface of approximately 2400 A(2)/monomer. The N-terminal deaminase domain belongs to the cytidine deaminase superfamily. A structure-based sequence alignment of a variety of nucleotide deaminases reveals not only the unique signatures in each family member for gene annotation but also putative substrate-interacting residues for RNA-editing deaminases. The strong structural conservation between the C-terminal reductase domain and the pharmaceutically important dihydrofolate reductase suggests that the two reductases involved in the riboflavin and folate biosyntheses evolved from a single ancestral gene. Together with the binding of the essential cofactors, zinc ion and NADPH, the structural comparison assists substrate modeling into the active-site cavities allowing identification of specific substrate recognition. Finally, the present structure reveals that the deaminase and the reductase are separate functional domains and that domain fusion is crucial for the enzyme activities through formation of a stable tetrameric structure.

Amino Acid Sequence↗

Transmembrane domain sequence requirements for activation of the p185c-neu receptor tyrosine kinase.

The receptor tyrosine kinase p185c-neu can be constitutively activated by the transmembrane domain mutation Val664-->Glu, found in the oncogenic mutant p185neu. This mutation is predicted to allow intermolecular hydrogen bonding and receptor dimerization. Understanding the activation of p185c-neu has assumed greater relevance with the recent observation that achondroplasia, the most common genetic form of human dwarfism, is caused by a similar transmembrane domain mutation that activates fibroblast growth factor receptor (FGFR) 3. We have isolated novel transforming derivatives of p185c-neu using a large pool of degenerate oligonucleotides encoding variants of the transmembrane domain. Several of the transforming isolates identified were unusual in that they lacked a Glu at residue 664, and others were unique in that they contained multiple Glu residues within the transmembrane domain. The Glu residues in the transforming isolates often exhibited a spacing of seven residues or occurred in positions likely to represent the helical interface. However, the distinction between the sequences of the transforming clones and the nontransforming clones did not suggest clear rules for predicting which specific sequences would result in receptor activation and transformation. To investigate these requirements further, entirely novel transmembrane sequences were constructed based on tandem repeats of simple heptad sequences. Activation was achieved by transmembrane sequences such as [VVVEVVA]n or [VVVEVVV]n, whereas activation was not achieved by a transmembrane domain consisting only of Val residues. In the context of these transmembrane domains, Glu or Gln were equally activating, while Lys, Ser, and Asp were not. Using transmembrane domains with two Glu residues, the spacing between these was systematically varied from two to eight residues, with only the heptad spacing resulting in receptor activation. These results are discussed in the context of activating mutations in the transmembrane domain of FGFR3 that are responsible for the human developmental syndromes achondroplasia and acanthosis nigricans with Crouzon Syndrome.

Amino Acid Sequence↗

FindTarget: software for subtractive genome analysis.

In silico subtractive/differential genome analysis is a powerful approach for identifying genus- or species-specific genes, or groups of genes that are responsible for a unique phenotype. By this method, one searches for genes present in one group of bacteria and absent in another group. A software package has been developed, named FindTarget, that has a user-friendly web interface to facilitate differential genome analysis. The user chooses the genomes to compare, the similarity criteria and the thresholds to decide if a gene has a counterpart in another genome. The searches are based on BLASTP comparisons of proteomes. FindTarget also includes access to sequences, coloured multiple alignments, phylogenetic trees of conserved proteins and links to public annotated databases which provide a means for validation of the results. To illustrate this approach, a FindTarget search for genes putatively involved in the specificity of cell envelope synthesis of Gram-negative bacteria is presented. The results show that most of the identified genes are clearly involved in cell wall processes, underlining the power of such an approach in general and that of FindTarget in particular.

Bacterial Proteins↗

The role of secretory granules in peptide biosynthesis.

There are many events in the posttranslational processing of bioactive peptides that occur in secretory granules and not to any great extent in other cellular organelles and that do not appear as modifications of the structure of many conventional neurotransmitters. In addition, at least two very important steps are unique to peptide-containing granules: (1) the peptides must begin their trek to the secretory granule in the RER as a larger precursor, rather than being taken up as a finished or nearly finished product into a mature granule; (2) there is at least one crucial sorting step on the way from the RER to the secretory granule that must occur faithfully before the peptide correctly appears in the granule. As for small molecules such as the catecholamines, the posttranslational processing enzymes and any required cofactors must also be put into the granules if the final events of processing are to occur with fidelity. Many of the posttranslational processing enzymes are only beginning to be identified. It is clear from these studies on purified PAM and peptide alpha-amidation as it occurs in cells that correlating test tube studies with the functioning of secretory granules is a worthwhile, if difficult, pursuit. The unique milieu inside the granule is difficult to mimic in a test tube. Transfection of peptide-producing cells with cDNAs encoding precursors with specific alterations in processing sites offers perhaps the best way to interface the studies of secretory granules and the posttranslational processing enzymes that mediate those functions.

Animals↗

Elevated 5'-nucleotidase and alkaline phosphodiesterase activities in trout gill localize to endothelial (pillar) cells

Tissue homogenates from rainbow trout gill had three- to fivefold higher specific activity for 5'-nucleotidase (5'NT) and more than twofold greater alkaline phosphodiesterase (APD) activity than liver or kidney homogenates. In isolated plasma membranes, gill 5'NT activity was 3-5 times greater than that of the kidney or liver; gill and kidney plasma membranes had similar APD specific activities, both more than five times that of liver. 5'NT and APD activities were localized by histochemistry to the endothelial (pillar) cells of trout gill secondary lamellae. Staining was consistent with the concentration of both activities at the apical plasma membranes of pillar cells (i.e. at the lamellar microvascular surfaces). This localization may reflect a capacity for processing nucleotide metabolites circulating in the blood, perhaps relating to purinergic regulation of local lamellar hemodynamics. There was no histochemical evidence of either 5'NT or APD activity in the gill epithelial (pavement) cells that interface directly with the environment. In contrast, in trout kidney, both enzyme activities localized to the apical region of tubule epithelial cells. The absence of 5'NT and APD activity in pavement cells reinforces the unique structural and functional character of the gill-environment epithelial barrier. The results indicate that 5'NT and APD activities have particular potential application as markers in efforts to isolate and characterize specific gill plasma membrane fractions.

Journal Article↗

Crestal bone loss minimized when following the crestal preparation protocol: a histomorphometric study in dogs.

Initial breakdown of the implant-tissue interface generally begins at the crestal region in successfully osseointegrated implants. The purpose of this study was to evaluate the effect on crestal bone loss (CBL) around implants specially developed for immediate loading with a unique crestal drill. After 8 weeks postextraction, 6 young male mongrel dogs received 48 implants (XiVE) in the region corresponding to the 4 mandibular premolars. The implant sites were prepared according to the manufacturer's protocol with conventional standard drills. Before implant placement, the crestal drill was used in the experimental group but not in the control group. After a healing period of 12 weeks, the dogs were sedated and euthanized. Through linear measurements, from the top of the implant to the first bone-implant contact, the amount of CBL was determined. The histomorphometric results of CBL (mean +/- SEM) were 0.88 +/- 0.13 mm (range 0.0-3.0 mm) in the experimental group and 1.69 +/- 0.17 mm (range 0.0-4.2 mm) in the control group. The difference was statistically significant (P < .05) when the implants were used as the experimental units. The statistical analysis also revealed significance when the dogs were used as the experimental units (P < .05). When the median was used for analyses, the CBL was 0.44 mm for the experimental group and 1.91 mm for the control group. Crestal bone loss was minimized when the crestal preparation protocol was carefully followed by using the osseocondensating XiVE implant system.

Alveolar Bone Loss↗

Centrifugal assay for fluorescence-based cell adhesion adapted to the analysis of ex vivo cells and capable of determining relative binding strengths.

Cell adhesion assays are widely used to identify novel cellular ligands, novel cell surface receptors for these ligands and to elucidate the mechanisms responsible for the underlying cellular and molecular interactions. We report here the development of a novel centrifugal assay for fluorescence-based cell adhesion (CAFCA) that offers a number of advantages over the currently available assays. CAFCA is based on two centrifugation steps: one to allow for the synchronization of the initial cell-substratum contact and one to enable both a defined removal force to be exerted onto the cells for displacement of unbound cells and determination of the relative binding strengths of adhering cells. The fluorescently tagged cells are monitored in specifically devised, disposable microplate assemblies by a two-sided fluorescence detection through the computer-interfaced SPECTRAFLUOR microplate fluorometer. The assay is rapid, accurate, reproducible and adaptable to small numbers of delicate primary cells that can ideally be labeled with the fluorochrome calcein AM (or analogous vital fluorescent dyes). Most uniquely, CAFCA provides (i) means of assessing the precise number of cells bound to a given substratum out of the total amount of cells contained within the population to be analyzed and (ii) a means of establishing the attachment strengths (i.e., dynes/cell) in a high number of samples/conditions simultaneously. CAFCA is therefore expected to make a substantial methodological and conceptual contribution to the range of available assays aimed at examining cellular interactions in vitro and promises the potential of being able to transpose automated versions of these tests for routine use in laboratories.

Animals↗

Interproximal integrity of posterior partial-coverage ceramic restorations: sequence of delivery and finishing.

The conservative, nonretentive cavity design of partial-coverage ceramic restorations provides a number of distinct advantages over traditional cast-metal options. However, unique challenges are associated with precise delivery of the restoration and the cleanup of excess luting resin. Restorative success and long-term gingival health are dependent on interproximal integrity at the restoration-tooth interface. This article examines the variables that affect this integrity and introduces a number of innovative techniques that assure meticulous delivery of posterior partial-coverage ceramic restorations.

Acid Etching, Dental↗

[Point of care testing from clinical laboratory].

The point of care testing(POCT) becomes popular in the Japanese medical scenes. POCT has its unique technologies which makes convenient and fast turn around time(TAT) test available to the physicians. Can clinical laboratories challenge to this new technologies? The licensed medical technologists and clinical laboratory analyzers with advanced user interface improve TAT, and the well established technology can provide the best solution today, and. The synergy of the clinical laboratory tests and POCT will increase the productivity of patient care in the future.

Autoanalysis↗

TCDB: the Transporter Classification Database for membrane transport protein analyses and information.

The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10,000 references, encompassing approximately 3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at http://www.tcdb.org. The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.

Databases, Protein↗

Information retrieval using a "digital book shelf".

WALT (Washington University's Approach to Lots of Text), is a prototype interface designed to support information retrieval research. The WALT interface serves as a "front end" to a wide array of retrieval engines including those based on Boolean retrieval, latent semantic indexing, term frequency--inverse document frequency, and Bayesian inference techniques. The WALT interface is composed of seven distinct components: a document examination component known as the Document Browsing Area; four navigation components called the Book Shelf, the Book Spine, the Table of Contents, and the Path Clipboard; a term-based information retrieval component called Control Panel; and a relevance feedback component known as the Reader Feedback Panel. WALT's most unique feature may be it's use of "book shelf" and "book spine" metaphors both to facilitate navigation and to provide a histogram-based display showing documents deemed appropriate for answering user queries.

Books↗

C(15)H(24) Volatile Compounds Unique to Aflatoxigenic Strains of Aspergillus flavus.

Headspace volatiles from eight strains of Aspergillus flavus (four aflatoxigenic strains and four nonaflatoxigenic strains), grown for 1, 2, 3, 4, 8, and 10 days in submerged cultures, were collected in Tenax GC traps. The traps were desorbed onto a 50-m gas-liquid chromatography capillary column by heat and gas purge from an external direct injector device. The column was interfaced with a mass spectrometer data acquisition system. Peaks were identified by comparing retention times and mass spectra with those obtained from authentic compounds and by using a computer-assisted mass spectral data base. Aflatoxigenic strains of A. flavus produced several C(15)H(24) compounds (e.g., alpha-gurjunene, trans-caryophyllene, and cadinene) which peaked in 3-day cultures and were not present in earlier (1- and 2-day) or later (8- and 10-day) cultures. None of these volatiles were detected in nonaflatoxigenic strains of A. flavus. There was an apparent correlation between the release of C(15)H(24) volatile compounds and the initiation of aflatoxin biosynthesis, and a correlation between decline of aflatoxin synthesis and the disappearance of the C(15)H(24) compounds unique to aflatoxigenic A. flavus also existed.

Journal Article↗

Conformation of the gamma subunit at the gamma-epsilon-c interface in the complete Escherichia coli F(1)-ATPase complex by site-directed spin labeling.

Structure-function relationships of the gamma-epsilon-c subunit interface of F(O)F(1) ATP synthase, a region of subunit interactions important in coupling between catalysis and transport, were investigated by site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. The EPR line widths and collision accessibilities of 18 spin-labeled, unique cysteine F(1) mutants from gammaLeu198 to gammaLeu215 indicate an alternating pattern in the mobility and accessibility parameters for positions gamma201-209, which is reminiscent of a beta-strand. Labels at positions gamma204 and gamma210 show tertiary contact upon F(1) binding to F(O) and gammaD210C has reduced coupling efficiency. gammaE208C could not be spin labeled, but the uncoupling effects of gammaE208K are suppressed by second-site mutations in the polar loop of subunit c [Ketchum, C. J. and Nakamoto, R. K. (1998) J. Biol. Chem. 273, 22292-22297]. The restricted mobility and accessibility of spin labels in the odd-numbered positions between gamma201 and gamma207 plus the 2-4-fold higher values in k(cat) for ATP hydrolysis of these same mutant F(1) indicate that the interactions of these residues with the epsilon subunit mediate its inhibitory activity. Disrupted interactions with epsilon subunit also cause reduced coupling efficiency. We propose a model for the gamma-epsilon-c interface of Escherichia coli F(O)F(1) ATP synthase in which side chains from the odd-numbered residues of the gammaLys201-gammaTyr207 beta-strand directly and functionally interact with the epsilon subunit, while the even-numbered, acidic residues gammaAsp204, gammaGlu208, and gammaAsp210 interact with the F(O) sector, probably with subunit c. gamma Subunit interactions with both subunits in this region are important for coupling efficiency.

Amino Acid Substitution↗