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PubMed1992

Bodymap: an image processing system for the measurement of body surface profiles encountered in skin expansion surgery.

A personal computer based image processing system for the mapping and subsequent analysis of local areas of the human body requiring no more than 180 degrees of vision is described. The operations of image capture and data extraction are undertaken in real time and photogrammetric reconstruction takes typically a further 30 s. Accuracy of the system has been assessed by photogrammetrically reconstructing 37 points whose coordinates had been precisely established by traditional survey techniques. An average discrepancy between surveyed and reconstructed positions of 0.485 mm was obtained; this level of accuracy compares highly favourably with results achieved using alternative methods and which do not have the level of automation inherent in the described system. The system has been developed specifically to provide quantitative values for parameters of particular interest in skin expansion surgery: consequently the post-reconstruction facilities available in this initial system are surface area and enclosed volume calculations and shaded surface display. Further development work currently in progress is also briefly discussed.

Body Surface Area↗

PubMed1995

From image processing to classification: II. Classification of electrophoretic patterns using self-organizing feature maps and feed-forward neural networks.

In a recent study, isoelectric focusing patterns were classified with a neural network using the back-propagation algorithm [1]. In order to further study the classification process and to generalize the presentation of electrophoretic patterns, Kohonen's self-organizing feature maps [2] were applied in this study. Although these feature maps are very efficient in many pattern recognition tasks, our data proved to be too complex for classification with an unsupervised system. Therefore, a second supervised network on top of the feature map was necessary. As in [3], a feed-forward network trained by the back-propagation algorithm was used. The final system allows us to correctly classify 90% of all wheat varieties. Moreover, the system proved to be reliable, reasonable in training time and shows the same accuracy in different experimental setups.

Algorithms↗

PubMed1992

Amino-terminal processing of actins mutagenized at the Cys-1 residue.

Most actins examined to date undergo a unique posttranslational modification termed processing, catalyzed by the actin N-acetylaminopeptidase. Processing is the removal of acetylmethionine from the amino terminus in class I actins with Met-Asp(Glu) amino termini. For class II actins with Met-X-Asp(Glu) amino termini, processing is the removal of the second residue as an N-acetylamino acid. Other cytosolic proteins with these amino termini are not processed suggesting that the reaction may be specific for actins. In actin, X is usually cysteine. However, there are some class II actins in which this residue is other than cysteine, suggesting a broader substrate specificity for actin N-acetylaminopeptidase than acetylmethionine or acetylcysteine. We constructed mutant actins in which this cysteine was replaced with serine, asparagine, glycine, aspartic acid, histidine, phenylalanine, and tyrosine and used these to determine the substrate specificity of rat liver actin N-acetylaminopeptidase in vitro. Amino-terminal acetylmethinonine was cleaved from adjacent aspartic acid, asparagine, or histidine, but not serine, glycine, phenylalanine, or tyrosine. Of the acetylated actin amino termini tested, only acetylmethionine and acetylcysteine were cleaved. Histidine was never N-acetylated and was not cleaved. When phenylalanine and tyrosine were adjacent to the initiator methionine, no initiator methionine was cleaved even though it was acetylated. These results suggest a narrow substrate specificity for the rat liver actin N-acetylaminopeptidase. They also demonstrate that the adjacent residue can effect actin N-acetylaminopeptidase specificity.

Actins↗

PubMed2003

Development of human protein reference database as an initial platform for approaching systems biology in humans.

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

BRCA1 Protein↗

PubMed2006

A RSK(y) relationship with promiscuous PKA.

Where, when, and with "whom" do molecules interact? Such relations in space and time are key concepts that currently engage investigators of cellular signaling processes. The notion of compartmentalized signaling grew out of studies of adenosine 3',5'-monophosphate (cAMP) signaling processes, and this area continues to generate exciting new paradigms. Distinct clouds of cAMP are formed and shaped within cells by tethered cAMP phosphodiesterases (PDEs). AKAPosomes, formed from distinct subpopulations of cAMP-dependent protein kinase (PKA) tethered to anchoring proteins (AKAPs) together with specific substrate molecules, interpret these gradients to generate individualized responses. PKA activity is also regulated by the interaction of other proteins with the regulatory (R) or catalytic (C) subunits of PKA, and a mechanism has been uncovered in which ribosomal S6 kinase (RSK1) interacts with either PKA subunit, depending on whether RSK1 has been phosphorylated and activated by extracellular signal-regulated kinase (ERK). Thus, inactive RSK1 binds the RI subunit of PKA to sensitize it to activation, whereas activated RSK1 binds the C subunit to desensitize PKA to cAMP activation. Cross-talk between the key cAMP and ERK signaling pathways provides a mechanism that, along with distinct mechanisms of both positive and negative attenuation provided by Raf and PDE4 isoforms, can be tailored on a cell type-specific basis.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2005

Mapping bone interstitial fluid movement: displacement of ferritin tracer during histological processing.

Bone interstitial fluid flow is thought to play a fundamental role in the mechanical stimulation of bone cells, either via shear stresses or cytoskeletal deformations. Recent evidence indicates that osteocytes are surrounded by a fiber matrix that may be involved in the mechanotransduction of external stimuli as well as in nutrient exchange. In our previous tracer studies designed to map how different-sized molecules travel through the bone porosities, we found that injected ferritin was confined to blood vessels and did not pass into the mineralized matrix. However, other investigators have shown that ferritin forms halo-shaped labeling that enters the mineralized matrix around blood vessels. This labeling is widely used to explain normal interstitial fluid movement in bone; in particular, it is said to demonstrate bulk centrifugal interstitial fluid movement away from a highly pressurized vascular porosity. In addition, appositional ferritin fronts are said to demonstrate centrifugal interstitial fluid movement from the medullary canal to the periosteal surface. The purpose of this study was to investigate the conflicting ferritin labeling results by evaluating the role of different histological processes in the formation of ferritin "halos." Ferritin was injected into the rat vasculature and allowed to circulate for 5 min. Samples obtained from tibiae were reacted for different times with Perl's reagent and then were either paraffin-embedded or sectioned with a cryostat. Halo-like labeling surrounding vascular pores was found in all groups, ranging from 1.2-3.9% for the samples treated with the shortest histological processes (unembedded, frozen sections) to 5.6-15% for the samples treated with the longest histological processes (paraffin-embedded sections). These results indicate that different histological processing methods are able to create ferritin "halos," with some processing methods allowing more redistribution of the ferritin tracer than others. Based on these results and the fact that "halo" labeling has not been found with any other tracer, as we seek to further delineate the movement of interstitial fluid and the role it plays in bone mechanotransduction, we believe that ferritin "halo" labeling should not be used to demonstrate physiological bone interstitial fluid flow.

Animals↗

PubMed1994

Identification of the essential cysteine and histidine residues of the turnip yellow mosaic virus protease.

The nonstructural protein expressed from ORF-206 of turnip yellow mosaic virus is proteolytically processed to produce N-terminal 150-kDa and C-terminal 70-kDa proteins. Through the use of linker insertion and deletion analyses coupled to in vitro translation, we have delimited the protease domain to residues 731-885 encoded by the 150-kDa coding region of ORF-206. The effects of substitutions of conserved residues within this region were studied in two assays: a direct assay for proteolysis occurring during in vitro translation and an assay for viral replication in turnip protoplasts. Replication was shown to be dependent on proteolytic maturation by the failure of a mutant with an inactive protease cleavage/recognition site to amplify in protoplasts. Substitutions at Cys783 and His869 were the only ones that resulted in undetectable signals in both assays, indicating that these are probable active sites residues, most likely of a papain-like protease. Domains putatively encoding similar proteases were detected in the genomes of other tymoviruses and viruses related to tymoviruses. The putative active site cysteine residues of these domains are followed by an aliphatic amino acid, whereas an aromatic amino acid at this position is typical of cellular and previously characterized viral papain-like proteases.

Amino Acid Sequence↗

PubMed2004

Using models of the myocyte for functional interpretation of cardiac proteomic data.

There has been significant progress towards the development of highly integrative computational models of the cardiac myocyte over the past decade. Models now incorporate descriptions of voltage-gated ionic currents and membrane transporters, mechanisms of calcium-induced calcium release and intracellular calcium cycling, mitochondrial ATP production and its coupling to energy-requiring membrane transport processes and mechanisms of force generation. There is an extensive literature documenting both the reconstructive and predictive abilities of these models and there is no question that an interplay between quantitative modelling and experimental investigation has become a central component of modern cardiovascular research. As data regarding the cardiovascular proteome in both health and disease emerge, integrative models of the myocyte are becoming useful tools for interpreting the functional significance of changes in protein expression and post-translational modifications (PTMs). Data of particular importance include information on: (a) changes of expressed protein level, (b) changes of protein PTMs, (c) protein localization, and (d) protein-protein interactions, as it is often possible to incorporate and interpret the functional significance of such findings using computational models. We provide two examples of how models may be used in this fashion. In the first example, we show how information on altered expression of the sarcoplasmic reticulum Ca2+-ATPase, when interpreted through the use of a computational model, has provided key insights into fundamental mechanisms regulating cardiac action potential duration. In the second example, we show how information on the effects of phosphorylation of L-type Ca2+ channels, when interpreted through the use of a model, provides insights on how this post-translational modification alters the properties of excitation-contraction coupling and risk for arrhythmia.

Animals↗

PubMed2004

Dog star rising: the canine genetic system.

Purebred dogs are providing invaluable information about morphology, behaviour and complex diseases, both of themselves and humans, by supplying tractable populations in which to map genes that control those processes. The diversification of dog breeds has led to the development of breeds enriched for particular genetic disorders, the mapping and cloning of which have been facilitated by the availability of the canine genome map and sequence. These tools have aided our understanding of canine population genetics, linkage disequilibrium and haplotype sharing in the dog, and have informed ongoing efforts of the need to identify quantitative trait loci that are important in complex traits.

Animals↗

PubMed2001

Use of (1)H NMR to study transport processes in porous biosystems.

The operation of bioreactors and the metabolism of microorganisms in biofilms or soil/sediment systems are strongly dictated by the transport processes therein. Nuclear magnetic resonance (NMR) spectroscopy or magnetic resonance imaging (MRI) allow nondestructive and noninvasive quantification and visualisation (in case of MRI) of both static and dynamic water transport phenomena. Flow, mass transfer and transport processes can be measured by mapping the (proton) displacement in a defined time interval directly in a so-called pulsed field gradient (PFG) experiment. Other methods follow the local intensity in time-controlled sequential images of water or labelled molecules, or map the effect of contrast agents. Combining transport measurements with relaxation-time information allows the discrimination of transport processes in different environments or of different fluids, even within a single picture element in an image of the porous biosystem under study. By proper choice of the applied NMR method, a time window ranging from milliseconds to weeks (or longer) can be covered. In this paper, we present an overview of the principles of NMR and MRI techniques to visualise and unravel complex, heterogeneous transport processes in porous biological systems. Applications and limitations will be discussed, based on results obtained in (model) biofilms, bioreactors, microbial mats and sediments.

Journal Article↗

PubMed1983

Electroanatomy of a unique amacrine cell in the rabbit retina.

Intracellular electrophysiological recordings were obtained from a specialized class of "starburst" amacrine cells by using an isolated superperfused retina-eyecup preparation of the rabbit. These cells were injected intracellularly with horseradish peroxidase and identified with light microscopy. A computer-controlled image-processing system was used to map and display the three-dimensional dendritic organization and provide information on length and sublaminar distribution of dendritic processes. Starburst amacrines show an unusual dendritic architecture that includes thin intermediate dendritic segments. Analysis with steady-state cable equations suggests that these thin segments may provide electrical isolation of distal processes, raising the possibility that a single dendrite, which lies beyond the thin segment, may constitute a functional subunit of the cell.

Action Potentials↗

PubMed1984

Widespread distribution of the major polypeptide component of MAP 1 (microtubule-associated protein 1) in the nervous system.

We prepared a monoclonal antibody to microtubule-associated protein 1 (MAP 1), one of the two major high molecular weight MAP found in microtubules isolated from brain tissue. We found that MAP 1 can be resolved by SDS PAGE into three electrophoretic bands, which we have designated MAP 1A, MAP 1B, and MAP 1C in order of increasing electrophoretic mobility. Our antibody recognized exclusively MAP 1A, the most abundant and largest MAP 1 polypeptide. To determine the distribution of MAP 1A in nervous system tissues and cells, we examined tissue sections from rat brain and spinal cord, as well as primary cultures of newborn rat brain by immunofluorescence microscopy. Anti-MAP 1A stained white matter and gray matter regions, while a polyclonal anti-MAP 2 antibody previously prepared in this laboratory stained only gray matter. This confirmed our earlier biochemical results, which indicated that MAP 1 is more uniformly distributed in brain tissue than MAP 2 (Vallee, R.B., 1982, J. Cell Biol., 92:435-442). To determine the identity of cells and cellular processes immunoreactive with anti-MAP 1A, we examined a variety of brain and spinal cord regions. Fibrous staining of white matter by anti-MAP 1A was generally observed. This was due in part to immunoreactivity of axons, as judged by examination of axonal fiber tracts in the cerebral cortex and of large myelinated axons in the spinal cord and in spinal nerve roots. Cells with the morphology of oligodendrocytes were brightly labeled in white matter. Intense staining of Purkinje cell dendrites in the cerebellar cortex and of the apical dendrites of pyramidal cells in the cerebral cortex was observed. By double-labeling with antibodies to MAP 1A and MAP 2, the presence of both MAP in identical dendrites and neuronal perikarya was found. In primary brain cell cultures anti-MAP 2 stained predominantly cells of neuronal morphology. In contrast, anti-MAP 1A stained nearly all cells. Included among these were neurons, oligodendrocytes and astrocytes as determined by double-labeling with anti-MAP 1A in combination with antibody to MAP 2, myelin basic protein or glial fibrillary acidic protein, respectively. These results indicate that in contrast to MAP 2, which is specifically enriched in dendrites and perikarya of neurons, MAP 1A is widely distributed in the nervous system.

Animals↗

PubMed2006

Simulation of machine-specific topographic indices for use across platforms.

PURPOSE: The objective of this project is to simulate the current published topographic indices used for the detection and evaluation of keratoconus to allow their application to maps acquired from multiple topographic machines. METHODS: A retrospective analysis was performed on 21 eyes of 14 previously diagnosed keratoconus patients from a single practice using a Tomey TMS-1, an Alcon EyeMap, and a Keratron Topographer. Maps that could not be processed or that contained processing errors were excluded from analysis. Topographic indices native to each of the three devices were recorded from each map. Software was written in ANSI standard C to simulate the indices based on the published formulas and/or descriptions to extend the functionality of The Ohio State University Corneal Topography Tool (OSUCTT), a software package designed to accept the input from many corneal topographic devices and provide consistent display and analysis. Twenty indices were simulated. Linear regression analysis was performed between each simulated index and the corresponding native index. A cross-platform comparison using regression analysis was also performed. RESULTS: All simulated indices were significantly correlated with the corresponding native indices (p < 0.01), with a mean R of 0.84, ranging from 0.42 to 0.99. Cross-platform comparisons were nonsignificant for specific indices and devices. CONCLUSION: Topographic indices native to three devices were successfully simulated. Cross-platform comparisons may be limited for specific indices.

Computer Simulation↗

PubMedDate not supplied

Use of 1H NMR to study transport processes in porous biosystems.

Biofilms↗

PubMed2003

A novel RING finger protein, human enhancer of invasion 10, alters mitotic progression through regulation of cyclin B levels.

The process of cellular morphogenesis is highly conserved in eukaryotes and is dependent upon the function of proteins that are centrally involved in specification of the cell cycle. The human enhancer of invasion clone 10 (HEI10) protein was identified from a HeLa cell library based on its ability to promote yeast agar invasion and filamentation. Through two-hybrid screening, the mitotic cyclin B1 and an E2 ubiquitin-conjugating enzyme were isolated as HEI10-interacting proteins. Mutation of the HEI10 divergent RING finger motif (characteristic of E3 ubiquitin ligases) and Cdc2/cyclin binding and phosphorylation sites alter HEI10-dependent yeast phenotypes, including delay in G(2)/M transition. In vertebrates, the addition of HEI10 inhibits nuclear envelope breakdown and mitotic entry in Xenopus egg extracts. Mechanistically, HEI10 expression reduces cyclin B levels in cycling Xenopus eggs and reduces levels of the cyclin B ortholog Clb2p in yeast. HEI10 is itself a specific in vitro substrate of purified cyclin B/cdc2, with a TPVR motif as primary phosphorylation site. Finally, HEI10 is itself ubiquitinated in egg extracts and is also autoubiquitinated in vitro. These and other points lead to a model in which HEI10 defines a divergent class of E3 ubiquitin ligase, functioning in progression through G(2)/M.

Adaptor Proteins, Signal Transducing↗

PubMed2005

The multiple personalities of the regulatory subunit of protein kinase CK2: CK2 dependent and CK2 independent roles reveal a secret identity for CK2beta.

Protein kinase CK2 (formerly casein kinase II), an enzyme that participates in a wide variety of cellular processes, has traditionally been classified as a stable tetrameric complex consisting of two catalytic CK2alpha or CK2alpha' subunits and two regulatory CK2beta subunits. While consideration of CK2 as a tetrameric complex remains relevant, significant evidence has emerged to challenge the view that its individual subunits exist exclusively within these complexes. This review will summarize biochemical and genetic evidence indicating that the regulatory CK2beta subunit exists and performs functions independently of CK2 tetramers. For example, unbalanced expression of catalytic and regulatory CK2 subunits has been observed in a variety of tissues and tumors. Furthermore, localization studies including live cell imaging have demonstrated that while the catalytic and regulatory subunits of CK2 exhibit extensive co-localization, independent mobility of the individual CK2 subunits can also be observed within cells. Identification of proteins that interact with CK2beta in the absence of catalytic CK2 subunits reinforces the notion that CK2beta has functions distinct from CK2 and begins to offer insights into these CK2-independent functions. In this respect, the discovery that CK2beta can interact with and modulate the activity of a number of other serine/threonine protein kinases including A-Raf, c-Mos and Chk1 is particularly striking. This review will discuss the interactions between CK2beta and these protein kinases with special emphasis on the properties of CK2beta that mediate these interactions and on the implications of these interactions in yielding new prospects for elucidation of the cellular functions of CK2beta.

Amino Acid Motifs↗

PubMed1998

Autoradiographic localisation of [3H]-SCH23390 and [3H]-spiperone binding sites in honey bee brain.

In the brain of the honey bee, dopamine receptors have been identified by using the vertebrate D1 dopamine antagonist [3H]-SCH23390 and the vertebrate D2 dopamine antagonist [3H]-spiperone. This study uses light microscope autoradiography to investigate the anatomical distributions of the binding sites labelled by [3H]-SCH23390 and [3H]-spiperone in tissue sections cut at three depths from the anterior surface of the brain. The binding of these radioligands differed significantly, in both density and distribution. Specific binding of [3H]-SCH23390, defined by using 5 x 10(-6) M cis-(Z)-flupentixol, was densest in regions of somata, such as the deutocerebral somatal rind, the somatal layer beneath the calyces of the mushroom bodies and the ventral protocerebral somatal group. High levels of [3H]-SCH23390 binding were also measured in the lateral protocerebrum. [3H]-Spiperone binding site density estimates were consistently lower than those of [3H]-SCH23390. Specific binding of [3H]-spiperone, determined by subtracting binding in the presence of 10(-4) M domperidone from the total binding, was highest in the alpha lobes, beta lobes, and calyces of the mushroom body neuropil. Relatively high binding was also measured in the central body and lateral protocerebral neuropil. These results suggest that the distribution of dopamine receptors in the brain of the bee is subtype specific, and they support the view that dopamine plays many roles in the insect central nervous system.

Animals↗

PubMed1998

Receptor autoradiographic mapping of the mesial motor and premotor cortex of the macaque monkey.

This study analyzes regional and laminar distribution patterns of neurotransmitter binding sites in the motor areas of the macaque mesial frontal cortex. Differences in distribution patterns are compared with the cytoarchitectonic parcellation. Binding sites were analyzed with quantitative in vitro receptor autoradiography in unfixed brains of five macaque monkeys. Alpha-amino-3-hydroxy-5-methyl-4-isoxalone propionic acid (AMPA), kainate, and N-methyl-D-aspartate (NMDA) binding sites were labeled with [3H]AMPA, [3H]kainate, and [3H]MK-801, respectively, muscarinic binding sites with [3H]pirenzepine or [3H]oxotremorine-M, noradrenergic binding sites with [3H]prazosin or [3H]UK-14304, gamma-aminobutyric acid (GABA)A binding sites with [3H]muscimol, and serotoninergic binding sites with [3H]ketanserine. Adjacent sections were stained with a modified Nissl method for cytoarchitectonic analysis. In the motor areas F1, F3, and F6, [3H]AMPA, [3H]pirenzepine, and [3H]oxotremorine-M binding was maximal in layers II, III, and V, and [3H]kainate binding was maximal in layers V and VI. Clear-cut changes in laminar distribution patterns of [3H]AMPA, [3H]kainate, and [3H]oxotremorine-M binding sites very closely matched corresponding cytoarchitectonic borders. Mean areal binding densities of all ligands to F1, F3, and F6 were plotted as polar plots for each area. A polygon was obtained for each area ("neurochemical fingerprint") when all the density values belonging to one area were connected with each other. The "neurochemical fingerprints" of F1, F3, and F6 were virtually identical in shape but increased in size from F1 to F6. This result reflects the functional similarity of these motor-related areas and possibly correlates with their differential involvement in motor control. Areas F1, F3, and F6 can thus be grouped into one "neurochemical family" of areas.

Animals↗