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PubMed1985

Immunoglobulin VH gene structure and diversity in Heterodontus, a phylogenetically primitive shark.

A mouse VH probe has been used to identify and isolate VH homologs in a DNA library of Heterodontus francisci (horned shark). The complete nucleotide sequence of one VH gene, HXIA, has been determined and found to exhibit striking organizational homology and nucleotide identity with mammalian prototype VH genes. Metric analysis of the complete sequence is consistent with the early phylogenetic diversification of framework and complementarity-determining regions (CDR). Both the predicted amino acid sequence and the specific hybridization of the CDR2-specific, synthetic oligodeoxynucleotide probe in spleen mRNA suggest that HXIA is functionally expressed. A probe consisting of the entire coding region of this gene hybridizes with multiple components in Southern blot analysis of Heterodontus genomic DNA and together with the identification of additional unique VH+-lambda clones indicates that considerable complexity is associated with the germline VH gene family in a contemporary species that represents an early stage in the phylogenetic development of the vertebrates.

Amino Acid Sequence↗
PubMed2004

Using the framework of the kinematic theory for the definition of a movement primitive.

This article reviews the current status of the movement primitives problem, especially the question of their description and identification, and points out some challenges which remain unsolved by the approaches frequently adopted to study human movements. We use the framework of the kinematic theory proposed by Plamondon (1995 and 1998) as an example of a hybrid model that allows a precise and flexible quantitative description of human movements. It is shown that the theory can be used to encompass the various types of rapid movement encountered in the field. The principal aim of this article is to highlight the fact that the notion of movement primitives should not necessarily be confined to movements with a single velocity peak, as is still often assumed in many models. The model allows, for example, a simple description of a movement primitive, which might contain up to two direction reversals.

Biomechanical Phenomena↗
PubMed2002

Prospective study designs in outcomes research: the case of migraine.

Patient-reported outcomes (PROs), including resource utilisation, productivity and quality of life, are important outcomes in the field of migraine. Clinical trials have begun to incorporate PROs; however, not all research questions can be answered fully within the framework of a clinical trial design. Other prospective designs, including effectiveness trials, observational studies, and study hybrids may be used to answer many of the different research questions related to PROs. This paper reviews prospective study designs, their strengths and weaknesses, and examples of their application in migraine health-outcomes research. Guidance is provided for researchers in the selection of prospective research designs and the incorporation of PROs-research objectives.

Clinical Trials as Topic↗
PubMed2006

Rate-distortion optimized hybrid error control for real-time packetized video transmission.

The problem of application-layer error control for real-time video transmission over packet lossy networks is commonly addressed via joint source-channel coding (JSCC), where source coding and forward error correction (FEC) are jointly designed to compensate for packet losses. In this paper, we consider hybrid application-layer error correction consisting of FEC and retransmissions. The study is carried out in an integrated joint source-channel coding (IJSCC) framework, where error resilient source coding, channel coding, and error concealment are jointly considered in order to achieve the best video delivery quality. We first show the advantage of the proposed IJSCC framework as compared to a sequential JSCC approach, where error resilient source coding and channel coding are not fully integrated. In the USCC framework, we also study the performance of different error control scenarios, such as pure FEC, pure retransmission, and their combination. Pure FEC and application layer retransmissions are shown to each achieve optimal results depending on the packet loss rates and the round-trip time. A hybrid of FEC and retransmissions is shown to outperform each component individually due to its greater flexibility.

Algorithms↗
PubMedDate not supplied

Single- and dual-fractal analysis of hybridization binding kinetics: biosensor applications.

The diffusion-limited hybridization kinetics of analyte in solution to a receptor immobilized on a biosensor or immunosensor surface is analyzed within a fractal framework. The data may be analyzed by a single- or a dual-fractal analysis. This was indicated by the regression analysis provided by Sigmaplot. It is of interest to note that the binding rate coefficient and the fractal dimension both exhibit changes in the same direction for both the single-fractal and the dual-fractal analysis examples presented. For example, for a single-fractal analysis and for the hybridization of 10 nM 16CFl (oligonucleotide) to 16B immobilized via sulfosuccinimidyl-6-(biotinamido)hexanoate and streptavidin using chemical and thermal regeneration (Abel, A. P.; Weller, M. G.; Duveneck, G. L.; Ehrat, M. Widmer, H. M. Anal. Chem. 1996, 68, 2905-2912), an increase in the fractal dimension, Df from 1.211 (chemical regeneration) to 1.394 (thermal regeneration), leads to an increase in the binding rate coefficient, k, from 86.53 (chemical regeneration) to 100.0 (thermal regeneration). An increase in the degree of heterogeneity on the biosensor surface leads to an increase in the binding rate coefficient. When a dual-fractal analysis was utilized, an increase in the fractal dimension value from Df1 to Df2 leads to an increase in the binding rate coefficient value from k1 to k2. The fractional order of dependence of the binding rate coefficient, k1, on (a) the analyte (rRNA) concentration in solution and (b) on the fractal dimension, Df1, for the hybridization kinetics to detect Listeria species (Fliss, R.; St-Laurent, M.; Emond, E.; Simard, R. E.; Lemieux, R.; Ettriki, A.; Pandian, S. Appl. Microbiol. Biotechnol. 1995, 43, 717-724.) further reinforces the fractal nature of the system. The binding rate coefficient(s) expressions developed as a function of the analyte concentration in solution and the fractal dimension are of particular value since they provide a means to better control of biosensor or immunosensor performance.

Biosensing Techniques↗
PubMed1992

Horizontal transfer of P elements and other short inverted repeat transposons.

Evidence for horizontal transfer of the P family of transposable elements in the genus Drosophila is reviewed and evaluated, along with observations consistent with the recent invasion of Drosophila melanogaster by these elements. Some other examples of horizontal transfer involving other groups of transposable elements having short inverted terminal repeats are also briefly described. The sequential mechanistic steps likely to be involved in a horizontal transfer event are explored, including the requirement for suitable interspecific vectors or carriers. Finally, the frequency and significance of horizontal transfer of transposable elements are briefly discussed within an evolutionary framework.

Animals↗
PubMed2004

A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes.

BACKGROUND: The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. RESULTS: A total of 169 markers (21 microsatellites and 148 ESTs) were typed on the ChickRH6 RH panel, of which 134 were assigned to GGA5. The final map is composed of 73 framework markers extending over a 1315.6 cR distance. The remaining 61 markers were placed alongside the framework markers within confidence intervals. CONCLUSION: The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome.

Animals↗
PubMed1992

A radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 locus.

We describe a high-resolution radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 (NF2) gene. Eighty-five hamster-human somatic cell hybrids generated by X-irradiation and cell fusion were used to generate the radiation hybrid map. The presence or absence of 18 human chromosome 22-specific markers was determined in each hybrid by using Southern blot hybridization. Sixteen of the 18 markers were distinguishable by X-ray breakage in the radiation hybrids. Analysis of these data using two different mathematical models and two different statistical methods resulted in a single framework map consisting of 8 markers ordered with odds greater than 1000:1. The remaining nonframework markers were all localized to regions consisting of two adjoining intervals on the framework map with odds greater than 1000:1. Based on the RH map, the NF2 region of chromosome 22, defined by the flanking markers D22S1 and D22S28, is estimated to span a physical distance of approximately 6 Mb and is the most likely location for 9 of the 18 markers studied: D22S33, D22S41, D22S42, D22S46, D22S56, LIF, D22S37, D22S44, and D22S15.

Animals↗
PubMed1998

The INSL4 gene maps close to WI-5527 at 9p24.1-->p23.3 clustered with two relaxin genes and outside the critical region for the monosomy 9p syndrome.

The insulin like growth factor 4 (INSL4) gene belongs to the insulin gene superfamily and has been mapped by fluorescent in situ hybridization to 9p24. Expression of INSL4, of unknown function, has been recently detected in the perichondrium and ligaments of the human embryo. Here we have mapped INSL4 within the framework of a partial YAC contig covering the distal part of 9p to find out whether this gene lies within the critical region defined for the monosomy 9p syndrome. The gene was also located using a human-rodent radiation hybrid panel. INSL4 was found to be distal to the del(9p) critical region and excluded as a candidate for the syndrome. In addition, the positions of two relaxin genes (RLN1, RLN2) that belong to the same superfamily as INSL4 and which have also been mapped to chromosome 9, were refined. We have shown that the three genes are clustered in the same region.

Animals↗
PubMed2000

An evaluation of hybridization kinetics in biosensors using a single-fractal analysis.

The diffusion-limited hybridization kinetics of analyte in solution to receptor immobilized on a biosensor or immunosensor surface is analysed within a fractal framework. The data may be analysed by a single-fractal analysis. This was indicated by the regression analysis provided by Sigmaplot [Sigmaplot Users Manual (1993) Jandel Scientific, San Rafael, CA]. It is of interest to note that the binding-rate coefficient and the fractal dimension both exhibit changes in the same and in the opposite directions for the single example presented in each case. The binding-rate coefficient(s) expressions developed as a function of the analyte (DNA) concentration in solution and the fractal dimension are of particular value, since they provide a means to better control biosensor or immunosensor performance and provide physical insights into the hybridization process.

Base Sequence↗
PubMed1997

Molecular cloning of the RNA polymerase I transcription factor hUBF/NOR-90 (UBTF) gene and localization to 17q21.3 by fluorescence in situ hybridization and radiation hybrid mapping.

The 90-kDa nucleolus organizer region autoantigen (NOR-90) was previously shown to be identical to human upstream binding factor (hUBF), which has two molecular mass forms of 89 and 93 kDa, respectively. hUBF/NOR-90 is a member of the HMG-box DNA-binding protein family and is known to bind to enhancer regions upstream of the ribosomal RNA genes, which are clustered at NORs. The smaller version of UBF lacks an internal 111-bp region corresponding to 37 amino acids in the second HMG-box of the larger form. We isolated human genomic clones from a phage library and localized one of them by fluorescence in situ hybridization to chromosome 17q21.3. DNA sequence analysis showed that the 111-bp region represented a single exon, consistent with the previous notion that the two isoforms were products of alternative pre-mRNA splicing of a single gene in human. Radiation hybrid mapping placed this STS with very high probability (LOD > 19) to chromosome 17, approximately 3.77 cR distal to MIT framework marker UTR-9641. The order of the markers (a partial list) from this region was UTR-9641, SGC30031, WI-17308, D17S930, NOR53/33, WI-16100, D17S920, WI-16913, and WI-6808.

Alternative Splicing↗
PubMed2005

Cannabinoid mechanisms of pain suppression.

A large body of literature indicates that cannabinoids suppress behavioral responses to acute and persistent noxious stimulation in animals. This review examines neuroanatomical, behavioral, and neurophysiological evidence supporting a role for cannabinoids in suppressing pain at spinal, supraspinal, and peripheral levels. Localization studies employing receptor binding and quantitative autoradiography, immunocytochemistry, and in situ hybridization are reviewed to examine the distribution of cannabinoid receptors at these levels and provide a neuroanatomical framework with which to understand the roles of endogenous cannabinoids in sensory processing. Pharmacological and transgenic approaches that have been used to study cannabinoid antinociceptive mechanisms are described. These studies provide insight into the functional roles of cannabinoid CB1 (CB1R) and CB2 (CB2R) receptor subtypes in cannabinoid antinociceptive mechanisms, as revealed in animal models of acute and persistent pain. The role of endocannabinoids and related fatty acid amides that are implicated in endogenous mechanisms for pain suppression are discussed. Human studies evaluating therapeutic potential of cannabinoid pharmacotherapies in experimental and clinical pain syndromes are evaluated. The potential of exploiting cannabinoid antinociceptive mechanisms in novel pharmacotherapies for pain is discussed.

Animals↗
PubMed1999

A successful strategy for comparative mapping with human ESTs: 65 new regional assignments in the pig.

Large-scale sequencing of cDNAs from numerous tissues is currently being performed within the framework of the Human Genome Project. These expressed sequence tags (ESTs) are then mapped on a radiation hybrid panel to produce a high-resolution map of human genes. In this report, we estimate the efficiency of mapping these ESTs in the pig. A total of 344 human ESTs from Généthon were selected for amplification in other species by Zoo-PCR: 186 of these could be reproducibly amplified by use of pig DNA and the corresponding human primer pairs. One-hundred seven of these were tested on a porcine-rodent somatic cell hybrid panel, permitting regional localizations of 65 ESTs with agarose or single-strand conformation polymorphism analysis gels. The corresponding pig PCR products were sequenced: 60 ESTs matched significantly with the expected human sequences. Fifty-one of these localizations in the pig are in agreement with the comparative mapping data between humans and pigs based on heterologous chromosome painting. Seven ESTs that were localized in an unexpected region may indicate new chromosomal correspondences. This work significantly increases the number of genes mapped on the pig genome and demonstrates that this approach can be successfully applied to improve the gene density of mammalian genomic maps in chromosomal regions of interest, such as those in which QTL (Quantative Trait Loci) have been identified.

Animals↗
PubMed2002

Spinal and peripheral mechanisms of cannabinoid antinociception: behavioral, neurophysiological and neuroanatomical perspectives.

A large body of literature indicates that cannabinoids suppress behavioral responses to acute and persistent noxious stimulation. This review examines behavioral, neurophysiological and neuroanatomical evidence supporting a role for cannabinoids in suppressing nociceptive transmission at spinal and peripheral levels. The development of subtype-selective competitive antagonists and high-affinity agonists provides the pharmacological tools required to study cannabinoid antinociceptive mechanisms. These studies provide insight into the functional roles of cannabinoid receptor subtypes, CB1 and CB2, in cannabinoid antinociceptive mechanisms as revealed in animal models of acute and persistent (somatic inflammatory, visceral inflammatory, neuropathic) pain. Localization studies employing receptor binding and quantitative autoradiography, immunocytochemistry and in situ hybridization are reviewed to examine the distribution of cannabinoid receptors at these levels and provide a neuroanatomical framework with which to understand the roles of endogenous cannabinoids in sensory processing.

Animals↗
PubMed2000

Design and solution structure of a well-folded stack of two beta-hairpins based on the amino-terminal fragment of human granulin A.

Four amino acid substitutions were introduced into a peptide corresponding to the amino-terminal subdomain (30-31 residues) of human granulin A (HGA) in order to assess the contributions of a hydrophobic framework and other interactions to structure stabilization of the stack of two beta-hairpins. The resulting hybrid peptide, HGA 1-31 (D1V, K3H, S9I, Q20P) with four free cysteines, spontaneously formed a uniquely disulfide-bonded isomer with an expected [1-3, 2-4] disulfide pairing pattern. This peptide was characterized in detail by use of NMR and shown to assume a highly stable structure in solution, in contrast to the amino-terminal 1-30 fragment of human granulin A. The prototype peptide, or HGA 1-30 (C17S, C27S), had lower resistance to chemical reduction and proteolysis, broad NH and H(alpha) proton resonances, lower proton resonance dispersion, and no slowly exchanging amide protons. Two other peptides, HGA 1-30 (C17S, Q20P, C27S) and HGA 1-31 (D1V, K3H, S9I, C17S, C27S), with either Pro20 stabilizing a potential reverse turn or with a hydrophobic cluster consisting of Val1, His3, and Ile9, had sharper and slightly better dispersed NH and H(alpha) proton resonances, but still no slowly exchanging amide protons. The solution structure of HGA 1-31 (D1V, K3H, S9I, Q20P) indicates that it adopts a well-folded conformation of a stack of two beta-hairpins, as found for the amino-terminal subdomain of the prototypic carp granulin-1 with representative beta-hairpin stacks. These results highlight the importance of both hydrophobic and turn-stabilizing interactions for the structural integrity of the hairpin stack scaffold. The conformational stability appears to be maintained by a combination of the well-formed second beta-hairpin and two hydrophobic clusters, one located at the interface between the two beta-hairpins and the other on "top" of the first beta-hairpin. The implications of these findings for the design of conformationally stable hairpin stacks are discussed.

Amino Acid Sequence↗
PubMed1999

Interactions of Escherichia coli sigma(70) within the transcription elongation complex.

A functional transcription elongation complex can be formed without passing through a promoter by adding a complementary RNA primer and core Escherichia coli RNA polymerase in trans to an RNA-primed synthetic bubble-duplex DNA framework. This framework consists of a double-stranded DNA sequence with an internal noncomplementary DNA "bubble" containing a hybridized RNA primer. On addition of core polymerase and the requisite NTPs, the RNA primer is extended in a process that manifests most of the properties of in vitro transcription elongation. This synthetic elongation complex can also be assembled by using holo rather than core RNA polymerase, and in this study we examine the interactions and fate of the sigma(70) specificity subunit of the holopolymerase in the assembly process. We show that the addition of holopolymerase to the bubble-duplex construct triggers the dissociation of the sigma factor from some complexes, whereas in others the RNA oligomer is released into solution instead. These results are consistent with an allosteric competition between sigma(70) and the nascent RNA strand within the elongation complex and suggest that both cannot be bound to the core polymerase simultaneously. However, the dissociation of sigma(70) from the complex can also be stimulated by binding of the holopolymerase to the DNA bubble duplex in the absence of a hybridized RNA primer, suggesting that the binding of the core polymerase to the bubble-duplex construct also triggers a conformational change that additionally weakens the sigma-core interaction.

Base Sequence↗
PubMedDate not supplied

[Human vital function monitoring as a system with hybrid intelligence].

Monitoring system is considered in this work as a reanimatologist-monitor-patient-medium system. This work is an upgrade to the previous concept of monitoring systems as systems with hybrid intelligence acting under variable conditions of object and medium. Human cardiorespiratory system was considered within the framework of the P. K. Anokhin theory of functional systems. The problem of resuscitation was formulated for this system and volume of required information was determined. Environment characteristics in resuscitation and surgery departments were considered. The requirements for monitor were formulated on the basis of analysis of these systems. The law of mutual adaptation of reanimatologist and monitor was put forward and safety problems associated with human factor were considered. Implementation of these principles in the MITAR 01-R-D is described.

Artificial Intelligence↗
PubMed2001

Integration of cytogenetic landmarks into the draft sequence of the human genome.

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

Chromosome Aberrations↗