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Interplay of ionic and structural heterogeneity on functional action potential duration gradients: Implications for arrhythmogenesis.

Action potential duration (APD) dispersion in the heart is governed by the underlying cellular architecture and the spatial distribution of the membrane properties. Understanding the contribution of each factor is important in designing more effective methods for the control of arrhythmias. Recent experimental studies have shown that the insertion of structural barriers in ionically heterogeneous tissue facilitates the formation of unidirectional block and discordant alternans. In this work, computational modeling is used to examine the effect of internal obstacles on the formation of functional APD gradients in ionically heterogeneous tissue. Intrinsic APD differences are introduced by assigning two discrete cell types to each half of a square domain. The combined effect of structural and ionic heterogeneities is shown to produce gradients in APD that are oblique to both the intrinsic gradients in APD and the physical boundary. Simulation results are presented that show that the magnitude and spatial extent of the subsequent APD gradients are modulated by the size and orientation of the obstacle, the degree of anisotropy, and the location of the pacing site. Long, thin internal obstacles are found to produce the greatest dispersion in APD. The combination of internal obstacles and ionic heterogeneities is shown to produce a substrate for re-entrant excitation following a pair of near threshold point stimuli. (c) 2002 American Institute of Physics.

Journal Article↗

Interaction of phosducin and phosducin isoforms with a 26S proteasomal subunit, SUG1.

PURPOSE: Retinal phosducin (Phd) and phosducin-like protein 1 (PhLP1) selectively bind G-protein beta/gamma subunits (Gbetagamma). Our laboratory has recently identified two phosducin-like orphan proteins (PhLOP1 and PhLOP2) that lack the ability to interact with Gbetagamma. In search of potential functional protein partner(s) for these phosducin orphans, we examined their protein-protein interactions using a yeast two-hybrid screen. METHODS: A bovine retina yeast expression cDNA library was screened with the GAL4 DNA binding domain (BD) fusion of PhLOP1. Quantitative analysis of the selected positives with PhLOP1 and other Phd isoforms was assessed by growth and beta-galactosidase activity. Further molecular, biochemical, and immunological detection methods utilizing glutathione S-transferase (GST)-Phd isoform fusion proteins and the potential partner were also performed. RESULTS: A member of the superfamily of putative ATPases was selected in the yeast two hybrid screen. Further characterization identified a direct interaction of this putative ATPase with PhLOP1, as well as Phd and PhLP1, but not with PhLOP2. A database search verified this ATPase as a bovine orthologue of the yeast SUG1 (ySUG1), a putative transcriptional mediator and a subunit of the 26S proteasome complex. Our experiments reveal that the carboxy-terminus of PhLOP1 is essential for the protein-protein interaction with SUG1, but it alone is not sufficient to mediate SUG1 interaction. CONCLUSIONS: Based on these experimental results, Phd, PhLP1 and PhLOP1 have protein-protein interaction with SUG1. PhLOP1, a truncated amino-terminal splice variant of Phd, is the best candidate for the interaction with SUG1 among the four Phd isoforms studied, which suggests a potential function for PhLOP1.

Adenosine Triphosphatases↗

[Measurement of pulmonary endothelial function; its potential clinical value].

For almost 10 years, numerous studies have shown that the pulmonary endothelium is endowed with a certain number of metabolic properties related to the uptake and hydrolysis of circulating vasoactive substances. Noradrenaline, serotonin, adenosine and possible certain prostaglandins are transported in the endothelial cells, according to processes which have now been clearly defined, and are there metabolised. Other compounds, including peptides (bradykinin, angiotensin I), or nucleotides (ATP, ADP, AMP) are hydrolysed in contact with the plasma membrane of the endothelium, without penetrating within the cell. For certain substrates (serotonin, angiotensin I), the properties of the pulmonary endothelial cell may be extended to systemic endothelial cells. For other substances, there would appear to be a specificity of endothelial function according to the site. It would appear that the lung, by virtue of its richness in endothelial cells, is capable of influencing concentrations of the circulating substances and, as a result, vascular tone. The existence of delicate processes of the uptake of substances has also been used to test the integrity of the cellular function of the pulmonary endothelium under experimental pathological condition, such as hyperoxia. However, before such a technique, based upon measurement os extraction of amines or other substances from various parts of the pulmonary circulation could be applied clinically, a critical consideration must be undertaken of the multiple factors involved in these processes. The major problem lies in the difficulty of distinguishing between dysfunction of the endothelial cells or a decrease in their number.

Endothelium↗

Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms.

A method of side-chain prediction without calculating the potential function is introduced. It is based on the assumption that similar side-chain conformations have a similar structural environment around the side chains. The environment information is represented by vectors that were obtained from principle component analysis and represented by the variance of positions of main-chain atoms around side chains. This information was added to the side-chain library (rotamer library) made from X-ray structures. Side-chain conformations were constructed using this side-chain library without using potential functions. An optimal solution was determined by comparing environmental information with the backbone conformation around the side chain to be predicted and native ones in the library. The method was performed for 15 proteins whose structures were known. The result for the root-mean-square deviation between the predicted and X-ray side-chain conformations was approximately 1.5 A (the value for core residues was approximately 1.1 A) and the percentage of predicted chi 1 angles correct within 40 degrees was approximately 65% (75% for the core). The computational time was short (approximately 60 s for the prediction of proteins with 200 amino acid residues). About 70% of the side-chain conformations were constructed by location of the main-chain atoms around the central C beta atom and the average of r.m.s.d. was approximately 1.4 A (for core residues the average was approximately 1.0 A).

Animals↗

Juxtaposition of CNR protocadherins and reelin expression in the developing spinal cord.

The CNR (cadherin-related neuronal receptors) family of protocadherins is of great interest because of their potential roles as molecular tags in the formation of specific synaptic connections, and as receptors for reelin, during neuronal migration, and cell body positioning. In order to know more about potential functions of CNRs we have mapped their expression during mouse nervous system development and compared their expression with that of reelin and its intracellular effector Dab1 in several tissues. In spinal cord, CNRs and Dab1 are expressed in motoneurons, while reelin is located in adjacent cells. In the hindbrain, there is a differential expression of CNRs and Dab1 in various motor nuclei. In the retina and olfactory system, we observe CNR and reelin expression but not that of Dab1. These results provide new insights into the potential functions of CNRs and their possible integration in the reelin pathway during development.

Animals↗

Assembly and analysis of the mouse immunoglobulin kappa gene sequence.

The mechanisms regulating V gene usage leading to the immunoglobulin (Ig) repertoire have been of interest for many years but are only partially defined. To gain insight into these processes, we have assembled the nucleotide sequence of the Mus musculus Igkappa locus using data recently made available from genome-wide sequencing efforts. We found the locus to be 3.21 Mb in length and mapped all known functional, pseudo- and relic V gene segments onto the sequence, along with known regulatory elements. We corrected errors in former gene assignments, positions and orientations and identified a novel Vkappa4 gene segment. This assembly allowed the establishment of a unified nomenclature for the V genes based on their relative positions similar to the nomenclature system adopted for the human Ig loci. The 5' boundary of the locus is defined by the presence of the tumor-associated calcium-signal transducer-2 gene located 19 kb upstream of Vkappa24-140, the most distal V gene. No non- Vkappa genes were found in the sequence of the locus. Detailed analysis of the sequences 0.5 kb upstream, within, and 0.5 kb downstream of each potentially functional V gene revealed interesting patterns of statistically significant clustering of transcription factor consensus binding sites, generally specific to a particular family. We found E boxes were clustered not only in promoter regions, but also nearby recombination signal sequences. Family members of Vkappa4/5 genes exhibit a conserved pattern of octamer sites in their downstream regions, as well as Ebf sites in their introns, and Lef-1 sites in their upstream regions. We discuss potential functional implications of these findings in the context of possible combinatorial mechanisms for targeting V genes for rearrangement. The assembled sequence and its analyses are available as a resource to the scientific community.

Animals↗

The histone H1 genes of the dipteran insect, Chironomus thummi, fall under two divergent classes and encode proteins with distinct intranuclear distribution and potentially different functions.

Four histone H1 genes of the midge, Chironomus thummi piger, and three H1 genes of the subspecies C. thummi thummi have been cloned and assigned to the four different H1 proteins from C. thummi larvae. Together with an earlier cloned H1 gene from C. thummi thummi [Hankeln, T. & Schmidt, E. R. (1991) Chromosoma 101, 25-31], these genes probably constitute the complete complement of H1 genes in both subspecies. They were found to fall under two classes that differ remarkably in their gene copy numbers, genomic organization, structure of flanking sequences, codon usage, and expression during embryonic development, and that encode H1 proteins of divergent structure. Histone H1 I-1 contains an inserted sequence, KAPKAPKAPKSPKAE in C. thummi piger, and KAPKAPKSPKAE in C. thummi thummi, that is lacking in the other H1 variants, H1 II-1, H1 II-2, and H1 III-1. In the immediate neighbourhood to the inserted sequence, a substitution in the H1 I-1 protein sequence dramatically enhances the potential to form a reversed turn. In early development, H1 I-1 is expressed at a higher rate than the other H1 genes. The transcripts have a size of about 1 kb; in addition, the H1 I-1 gene exhibited two minor transcripts of about 2.5 and > 3 kb size in middle blastoderm that are possibly polyadenylated. Together with our earlier finding that histone H1 I-1 is found in a limited number of polytene chromosome bands whereas the other H1 histones are uniformly distributed in chromatin, these results intimate functional differences between the two classes of H1 genes and their products.

Amino Acid Sequence↗

Event-related potentials and functional MRI: a comparison of localization in sensory, perceptual and cognitive tasks.

Combining ERP and fMRI methods to elucidate the time course and anatomical basis of information processing may provide a powerful new tool for understanding human brain function. Attempts to model the time course of fMRI activations by recording surface electromagnetic fields require a better understanding of the relationship between ERPs and fMRI activations. The results presented here show that good correspondence can be obtained between the location of ERP generators and fMRI activations in sensorimotor cortex, and in face perception and target detection tasks. However, difficulties in obtaining somatosensory fMRI activations with stimuli known to evoke robust SEPs, and the lack of fMRI activations within the hippocampus in tasks that elicit large hippocampal field potentials suggest that not all stimuli or tasks that evoke focal ERPs will evoke fMRI activations. This may be related to differences in the sensitivity of the fMRI that will be overcome with better technique and with more sensitive instruments. However, caution must be exercised in developing models that assume a one-to-one correspondence between ERP generators and fMRI activations.

Cognition↗

Molecular analysis of immunoglobulin genes in diffuse large B-cell lymphomas.

Diffuse large B-cell lymphoma (DLBCL) is a common type of non-Hodgkin's lymphoma (NHL) that is highly heterogeneous from both clinical and histopathologic viewpoints. The immunoglobulin (Ig) heavy (H) chain variable region genes were examined in 71 patients with untreated primary DLBCL. Fifty-eight potentially functional V(H) genes were detected in 53 DLBCL cases; V(H) genes were nonfunctional in 9 cases and were not detected in an additional 9 cases. The use of V(H) gene families by DLBCL tumors was unbiased without overrepresentation of any particular V(H) gene or gene family. Analysis of Ig mutations in comparison to the most closely related germline gene disclosed mutated V(H) genes in all but 1 DLBCL case. More than 2% difference from the most similar germline sequence was detected in 52 potentially functional and the 8 nonfunctional V(H) gene sequences, whereas less than 2% difference from the germline sequence was observed in 3 V(H) gene isolates. Only 3 V(H) gene isolates were unmutated. No correlation was found between V(H) gene use, mutation level, and International Prognostic Index (IPI) or survival. Six of 8 tested tumors showed evidence of ongoing somatic mutations. Evidence for positive or negative antigen selection pressure was observed in 65% of mutated DLBCL cases. Our findings indicate that the etiology and the driving forces for clonal expansion are heterogeneous, which may explain the well-known clinical and pathologic heterogeneity of DLBCL. (Blood. 2000;95:1797-1803)

B-Lymphocytes↗

Correlation between protein stability cores and protein folding kinetics: a case study on Pseudomonas aeruginosa apo-azurin.

This paper reports a combined computational and experimental study of the correlation between protein stability cores and folding kinetics. An empirical potential function was developed, and it was used for analyzing interaction energies among secondary structure elements. Studies on a beta sandwich protein, Pseudomonas aeruginosa azurin, showed that the computationally identified substructure with the strongest interactions in the native state is identical to the "interlocked pair" of beta strands, an invariant motif found in most sandwich-like proteins. Moreover, previous and new in vitro folding results revealed that the identified substructure harbors most residues that form native-like interactions in the folding transition state. These observations demonstrate that the potential function is effective in revealing the relative strength of interactions among various protein parts; they also strengthen the suggestion that the most stable regions in native proteins favor stable interactions early during folding.

Apoproteins↗

Modulation of eosinophil effector functions: the potential role of monoclonal antibodies and chemokine receptor antagonists.

Increased numbers of eosinophils in the peripheral blood and inflammatory tissue are characteristic features of allergic diseases such as allergic asthma, rhinoconjunctivitis, and atopic dermatitis. Tissue damage and propagation of inflammation is thought to be mediated by the interaction among Th2-like T cells, antigen-presenting cells, and eosinophils. In this process eosinophils are activated by several inflammatory mediators, leading to the influx of eosinophils at sites of inflammation and to tissue damage by the release of reactive oxygen species and toxic granule proteins. Therefore, agents that would be able to inhibit or antagonize mediator-induced eosinophil activation seem to be possibilities as new therapeutic strategies. In this review we will focus on the modulation of human eosinophil effector functions by monoclonal antibodies and chemokine receptor antagonists. We will discuss whether modulation of eosinophil effector functions might be successful as a possible future strategy of diseases that are accompanied by activated eosinophils. Even when these compounds show antagonistic effects on human eosinophils, in vitro future studies will be necessary to investigate whether chemokine receptor antagonists and monoclonal antibodies are suitable in vivo in an animal model prior to studies in humans.

Antibodies, Monoclonal↗

Potential of functional strains, isolated from traditional Maasai milk, as starters for the production of fermented milks.

The purpose of this research was the evaluation of technological features and of the ability of functional LAB strains with desirable sensory characteristics, to produce fermented milk. Eight strains of Lactobacillus plantarum, Lactobacillus acidophilus, Lactobacillus paracasei and Lactococcus lactis, isolated from Maasai traditional fermented milk in Kenya and previously tested for their probiotic properties, were selected for this investigation. Technological features such as growth kinetics in fresh heat-treated whole milk medium and survival in the final product during storage at 4 degrees C, were studied. The strains Lb. acidophilus BFE 6,059, Lb. paracasei BFE 5,264 and Lc. lactis BFE 6,049 showed the best potential and were thus selected for use as starter cultures in further trials with the objective to improve their technological performance and to optimise the sensory features of fermented milk obtained. The effects of fat (F), non-fat milk solids (S) and fermentation temperature (T), modulated according to a Central Composite Design, on fermentation rates and viability losses during refrigerated storage of the chosen starters, and on product texture parameters, were studied. From the data analysis, it was possible to select optimum conditions for enhancing positive sensory traits of final products and for improving the survival of these potentially probiotic cultures.

Animals↗

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.

A symplectic multiple-time-step (MTS) algorithm has been developed for the united-residue (UNRES) force field. In this algorithm, the slow-varying forces (which contain most of the long-range interactions and are, therefore, expensive to compute) are integrated with a larger time step, termed the basic time step, and the fast-varying forces are integrated with a shorter time step, which is an integral fraction of the basic time step. Based on the split operator formalism, the equations of motion were derived. Separation of the fast- and slow-varying forces leads to stable molecular dynamics with longer time steps. The algorithms were tested with the Ala(10) polypeptide chain and two versions of the UNRES force field: the current one in which the energy components accounting for the energetics of side-chain rotamers (U(rot)) can lead to numerically unstable forces and a modified one in which the the present U(rot) was replaced by a numerically stable expression which, at present, is parametrized only for polyalanine chains. With the modified UNRES potential, stable trajectories were obtained even when extending the basic time step to 15 fs and, with the original UNRES potentials, the basic time step is 1 fs. An adaptive multiple-time-step (A-MTS) algorithm is proposed to handle instabilities in the forces; in this method, the number of substeps in the basic time step varies depending on the change of the magnitude of the acceleration. With this algorithm, the basic time step is 1 fs but the number of substeps and, consequently, the computational cost are reduced with respect to the MTS algorithm. The use of the UNRES mesoscopic energy function and the algorithms derived in this work enables one to increase the simulation time period by several orders of magnitude compared to conventional atomic-resolution molecular dynamics approaches and, consequently, such an approach appears applicable to simulating protein-folding pathways, protein functional dynamics in a real molecular environment, and dynamical molecular recognition processes.

Algorithms↗

V(H) gene analysis of Burkitt's lymphoma in children from north-western Iran.

Cases of Burkitt's lymphoma (BL) from north-western Iran were investigated for the usage and somatic mutational pattern of their immunoglobulin variable region genes. Potentially functional V(H) genes were amplified from 6/12 of the tumour masses and all of these were derived from the V(H)3 family, with 4/6 being derived from the most commonly used V(H)3 family member, V3-23. All of the tumour sequences were mutated from their germline counterparts, to varying degrees, with a mean level of 5.8%, indicating that the cell of origin had encountered the germinal centre. Intraclonal sequence heterogeneity was also evident in 4/6 of the lymphomas, showing that the tumour cells had undergone further somatic mutation following neoplastic transformation. Analysis of the five potentially functional mutated V(H) sequences showed a significant clustering of replacement mutations in the complementarity-determining region 2, consistent with a role for antigen in selection of tumour cell sequences. The pattern of extensive somatic mutation, and intraclonal variation, in these mainly EBV+ve tumours, was similar to that previously reported in V(H) sequences of EBV+ve endemic BL (eBL) and EBV-ve sporadic BL (sBL), with the mean level of somatic mutation lying between those reported for eBL (7.7%) and sBL (4.0%). However, VH gene bias and the distribution of mutations in the Iranian cases showed features which differed from those reported for endemic or sporadic BL.

Amino Acid Sequence↗

Jekyll and Hyde: evolving perspectives on the function and potential of the adult liver progenitor (oval) cell.

The liver progenitor cell (LPC) has enormous potential for use in cell therapy to treat liver disease. Since liver regenerates readily from pre-existing hepatocytes, a role for LPCs and, indeed, their existence have been questioned. Research during the last decade has established that LPCs are an important alternative source of cells for liver regeneration. Their utility for cell therapy lies in their ability to generate both hepatocytes and cholangiocytes. However, they are observed in liver diseases that often lead to cancer and there is experimental evidence that implicates LPCs as the source of tumours. This article provides a brief history of the studies that established the functional importance of LPCs in liver disease. It focuses on mouse models that have led to the identification of factors that regulate LPC growth and differentiation and discusses LPCs derived from different sources. Recent promising results from both in vitro and vivo studies suggest that LPCs could be useful for cell therapy. In the context of liver disease, LPCs may indeed be the cell of the future and understandably "our favourite cell".

Aging↗

Kojic acid scavenges free radicals while potentiating leukocyte functions including free radical generation.

The effects of kojic acid, a compound that suppresses melanogenesis and is widely consumed in the Japanese diet with the belief that it is beneficial to health, were investigated on several aspects of leukocyte function. Kojic acid significantly decreased the levels of reactive oxygen species (ROS) (O2-, H2O2, OH.) generated by neutrophil and by a cell-free ROS-generating system. In contrast, it significantly enhanced neutrophil phagocytosis and ROS generation, and lymphocyte proliferation stimulated by phytohemagglutinin. In addition, calcium concentration, [Ca2+]i in human neutrophils was increased in the presence of kojic acid. These results suggest that kojic acid is a favorable agent in terms of host defense in that it enhances a number of activities of leukocytes, but scavenges ROS excessively released from cells or generated in the tissues or blood vessels that are potentially injurious to host tissues.

Calcium↗

Shoulder pain in hemiplegia.

Development of a painful shoulder in the hemiplegic patient is a significant and serious problem, because it can limit the patient's ability to reach his or her maximum functional potential. Several etiologies of shoulder pain have been identified, such as immobilization of the upper extremity, trauma to the joint structures, including brachial plexus injuries, and subluxation of the gleno-humeral joint. A review of the literature explains the basic anatomy and kinesiology of the shoulder complex, the various etiologies of hemiplegic shoulder pain, and the pros and cons of specific treatment techniques. This knowledge is essential for the occupational therapist to evaluate effectively techniques used to treat the patient with hemiplegic shoulder pain. More effective management of this problem will facilitate the patient's ability to reach his or her maximum functional potential.

Brachial Plexus↗

Multiple amphiphysin II splice variants display differential clathrin binding: identification of two distinct clathrin-binding sites.

Amphiphysin I and II are nerve terminal-enriched proteins that display src homology 3 domain-mediated interactions with dynamin and synaptojanin. It has been demonstrated that the amphiphysins also bind to clathrin, and we have proposed that this interaction may help to target synaptojanin and dynamin to sites of synaptic vesicle endocytosis. To understand better this potential functional role, we have begun to characterize clathrin-amphiphysin interactions. Using PCR from adult human cortex cDNA, we have cloned a number of amphiphysin II splice variants. In in vitro binding assays, the amphiphysin II splice variants display differential clathrin binding and define a 44-amino acid region mediating the interaction. Amphiphysin II truncation and deletion mutants identify two distinct clathrin-binding domains within this region: one with the sequence LLDLDFDP, the second with the sequence PWDLW. Both domains are conserved in amphiphysin I, and saturation binding analysis demonstrates that both sites bind clathrin with approximately equal affinity. The elucidation of clathrin as a splice-specific binding partner for amphiphysin II begins to address the potential functional role(s) for the multiple amphiphysin II splice variants and further supports an important function for clathrin-amphiphysin interactions in protein targeting during endocytosis.

Alternative Splicing↗