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PubMed1982

Pharmacology of GABA.

GABA-ergic systems are involved in all the main functions of the brain. In most brain regions impairment of this system produces epileptic activity. GABA-mediated inhibitory function can be enhanced by drugs of at least seven different types. They act on the metabolism or synaptic release of GABA, or its reuptake into neurones of glia, or on various components of the GABA receptor complex (GABA recognition site, "benzodiazepine" receptor or chloride ionophore). Among such compounds, those which act most specifically and potently on GABA receptors remain primarily research tools. Among compounds in clinical use, valproate, benzodiazepines, and anticonvulsant barbiturates al enhance GABA-mediated inhibition. In the future, new inhibitors of GABA uptake, new GABA agonists and potent inhibitors of GABA-transaminase are likely to become available. Trials of drugs enhancing GABA-ergic function have been made in a wide variety of neurological disorders. In most forms of epilepsy a therapeutic effect is evident. Real benefit from GABA therapies has not been demonstrated in the principal disorders of movement (Huntington's chorea, Parkinson's disease, dystonias), except in so far as they have a myoclonic or paroxysmal component. Among psychiatric disorders the acute symptoms of schizophrenia are exacerbated by enhanced GABA-ergic function. Abstinence syndromes (alcohol, barbiturate or narcotic withdrawal) are ameliorated by drugs enhancing GABA-ergic function, and there is some evidence for a beneficial action in anxiety states and mania. Attempts to relate the molecular neurobiology of GABA with clinical pharmacology are of very recent origin. Improved understanding of the variety of GABA receptor mechanisms will provide the key to the more selective pharmacological manipulations that are required for therapeutic success.

4-Aminobutyrate Transaminase↗
PubMed2004

Molecular dynamics simulations of papilloma virus E2 DNA sequences: dynamical models for oligonucleotide structures in solution.

The specificity of papilloma virus E2 protein-DNA binding depends critically upon the sequence of a region of the DNA not in direct contact with the protein, and represents one of the simplest known examples of indirect readout. A detailed characterization of this system in solution is important to the further investigation hypothesis of a structural code for DNA recognition by regulatory proteins. In the crystalline state, the E2 DNA oligonucleotide sequence, d(ACCGAATTCGGT), exhibits three different structural forms. We report herein studies of the structure of E2 DNA in solution based on a series of molecular dynamics (MD) simulations including counterions and water, utilizing both the canonical and various crystallographic structures as initial points of departure. All MDs converged on a single dynamical structure of d(ACCGAATTCGGT) in solution. The predicted structure is in close accord with two of the three crystal structures, and indicates that a significant kink in the double helix at the central ApT step in the other crystal molecule may be a packing effect. The dynamical fine structure was analyzed on the basis of helicoidal parameters. The calculated curvature in the sequence was found to originate primarily from YPR steps in the regions flanking the central AATT tract. In order to study the role of structural adaptation of the DNA in the binding process, a subsequent simulation on the 16-mer cognate sequence d(CAACCGAATTCGGTTG) was initiated from the crystallographic coordinates of the bound DNA in the crystal structure of the protein DNA complex. MD simulations starting with the protein-bound form relaxed rapidly back to the dynamical structure predicted from the previous simulations on the uncomplexed DNA. The MD results show that the bound form E2 DNA is a dynamically unstable structure in the absence of protein, and arises as a consequence of both structural changes intrinsic to the sequence and induced by the interaction with protein.

Animals↗
PubMed1999

DNA stretching and compression: large-scale simulations of double helical structures.

Computer-simulated elongation and compression of A - and B -DNA structures beyond the range of thermal fluctuations provide new insights into high energy "activated" forms of DNA implicated in biochemical processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG).poly(dC) and poly(dA).poly(dT) double helices, stretched from compressed states of 2.0 A per base-pair step to highly extended forms of 7.0 A per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of double-helical DNA identified in single crystals as well as non-canonical forms, such as the original "Watson-Crick" duplex with trans conformations about the P-O5' and C5'-C4' backbone bonds. The lowest energy minima correspond to canonical A and B -form duplexes. The calculations further reveal a number of unusual helical conformations that are energetically disfavored under equilibrium conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy versus stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identified by direct stretching experiments. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the observed sharp increase in force required to stretch single DNA molecules more than 1.6-1.65 times their canonical extension. Our extended duplexes also help to tie together a number of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochemical model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The crystalline TBP-bound DNA steps follow the calculated compression-elongation pattern of an unusual "vertical" duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition.Significantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy profiles show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy "activated" forms calculated here are critical for DNA processing, e.g. nucleo-protein recognition, DNA/RNA synthesis, and strand exchange.

Computer Simulation↗
PubMed1991

Cytotoxic T lymphocyte precursor cells specific for the major histocompatibility complex class I-like antigen, Qa-2, require CD4+ T cells to become primed in vivo and to differentiate into effector cells in vitro.

Experiments were performed to determine whether CD4+ T cells are required for the generation of cytotoxic T lymphocytes (CTL) specific for the nonpolymorphic major histocompatibility complex (MHC) class I-like antigen, Qa-2. Splenic T cells from BALB/cBy (Qa-2b) mice that had been immunized with irradiated BALB/cJ (Qa-2a) splenocytes generated CTL following in vitro stimulation with BALB/cJ splenocytes. These CTL lysed all Qa-2+, but not Qa-2- targets, regardless of the H-2 haplotypes of target cells or their non-MHC backgrounds. This apparent MHC class I-unrestricted recognition of Qa-2 antigen was confirmed using Qa-2-specific CTL clones. The Qa-2-primed CTL precursor cells (CTLp) and CTL were found to be CD8+ T cells. Primed splenocytes depleted of CD4+ T cells prior to culture failed to generate CTL, but addition of lymphokines to the culture restored the CTL generation. Stimulation of primed splenic T cells with irradiated Qa-2+ T blast cells, instead of splenocytes or B blast cells, led to little to no CTL generation, suggesting that MHC class II molecules are involved in the presentation of Qa-2 antigen to CD4+ T cells. This was also supported by the results of experiments using Qa-2+, class II- thymoma cells of BALB/c origin. Stimulation of the thymoma-primed splenic T cells with the mitomycin C-treated thymoma cells resulted in no generation of anti-Qa-2 CTL, despite the fact that high levels of CTL specific for minor histocompatibility (H) antigens and H-2d were generated by immunizing the corresponding allogeneic hosts with the thymoma. However, the addition of lymphokines rendered thymoma-primed T cells capable of generating anti-Qa-2 CTL. Both CD4+ and CD8+ T cell populations, isolated from the BALB/cJ splenocyte-primed responder cells, proliferated in vitro in response to the Qa-2+ splenocytes, suggesting that Qa-2-reactive CD4+ T cells were present in the immunized mice. Depletion of CD4+ T cells from thymectomized BALB/cBy mice with anti-L3T4 monoclonal antibodies markedly reduced, but did not eliminate anti-Qa-2 CTL generation. In contrast, depletion of CD8+ T cells led to a complete abrogation of the CTL response. Addition of lymphokines to the culture of responder cells depleted of either T cell subset did not restore their reactivity. It is concluded that anti-Qa-2 CTLp need "help" from CD4+ T cells to become primed in vivo. Furthermore, primed CTLp also need "help" or lymphokines provided by CD4+ T cells to differentiate into effector CTL in vitro.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1996

Reafference and attractors in the olfactory system during odor recognition.

Olfactory bulb activity has been postulated to be chaotic, as measured in the EEG, and to be subject to an attractor with many "wings" enabling classification of different learned odor classes. Two parallel questions are thus addressed by the work presented here: (1) what is the evidence for attractors in the olfactory system, which can mediate learned odor classes? and (2) how does the olfactory system enter a specific attractor or attractor wing associated with the learned odor during the classification process? Both of these questions address the wider notion of endogenous activity preparing the system for an expected stimulus, which is at the basis of the reafference principle. By viewing the brain as a distributed complex dynamical system with global attractors, these questions can be answered together. Rats were implanted with bipolar macroelectrodes in the Olfactory Bulb (OB), Prepyriform Cortex (PPC), Entorhinal Cortex (EC), and Dentate Gyrus (DG), and then trained in an operant paradigm to press a bar for a reward in the presence of one odor and to receive no reward in the presence of another odor. Local Field Potentials (LFP) were recorded simultaneously from the structures during the operant task. We present evidence for three endogenous events: (1) preafference, which is manifested both by the EC entering an attractor and a mid-range signal (15-30 Hz) which appears to be passed from the EC to the OB just before the OB enters an attractor; (2) afference, where the OB enters an attractor during the odor recognition period of the experiment and the LFP recordings indicate that the OB drives the other structures in all frequency bands, especially the high gamma band (65-100 Hz) associated with the OB burst frequency; and (3) reafference or post-afference, which is accompanied by a lower frequency gamma band signal (40-60 Hz) originating in the PPC and passed to both the OB and the EC just before the onset of the motor response to the odor. We use a new method, NECTAR (Nonparametric Exact Contingency Table Association Routine), related to mutual information, to verify what is seen with coherence and phase estimates, the apparent driving of each structure at different times in the odor trials, and to display evidence for non-periodic attractors governing both individual physiological structures and the system of structures. This is the first evidence of an endogenous, limbic event associated with sensory perceptual tuning in a mammal. These results are also the first experimental confirmation that the attractors governing olfactory activity involve multiple sites in the olfactory/limbic system and implement the process of attention.

Adaptation, Physiological↗
PubMed2004

Binary halftone image resolution increasing by decision tree learning.

This paper presents a new, accurate, and efficient technique to increase the spatial resolution of binary halftone images. It makes use of a machine learning process to automatically design a zoom operator starting from pairs of input-output sample images. To accurately zoom a halftone image, a large window and large sample images are required. Unfortunately, in this case, the execution time required by most of the previous techniques may be prohibitive. The new solution overcomes this difficulty by using decision tree (DT) learning. Original DT learning is modified to obtain a more efficient technique (WZDT learning). It is useful to know, a priori, sample complexity (the number of training samples needed to obtain, with probability 1 - delta, an operator with accuracy epsilon): we use the probably approximately correct (PAC) learning theory to compute the sample complexity. Since the PAC theory usually yields an overestimated sample complexity, statistical estimation is used to evaluate, a posteriori, a tight error bound. Statistical estimation is also used to choose an appropriate window and to show that DT learning has good inductive bias. The new technique is more accurate than a zooming method based on simple inverse halftoning techniques. The quality of the proposed solution is very close to the theoretical optimal obtainable quality for a neighborhood-based zooming process using the Hamming distance to quantify the error.

Algorithms↗
PubMed2001

Transcriptional regulation in Drosophila: the post-genome challenge.

Drosophila melanogaster has long been at the forefront of studies of transcriptional regulation in animals. Many fundamental ideas--such as cis control elements that act over long distances, the regulation of development by hierarchical cascades of transcription factors, dosage compensation, and position effect variegation--originated from studies of the fruit fly. The recent completion of the euchromatic DNA sequence of Drosophila is another breakthrough. The sequence data highlight important unanswered questions. For example, only one-fifth of the 124 Mb of Drosophila euchromatic DNA codes for protein. The function of the remaining 100 Mb of mostly unique DNA is largely unknown. Some proportion of this non-reading frame DNA must encode the functional recognition sites targeted by the approximately 700 sequence-specific DNA binding proteins that regulate transcription in Drosophila, but what proportion? Most or very little? Promoter sequences by definition contain all of the cis information that specifies how gene transcription is regulated. However, it has been difficult to decipher this information and predict the patterns of RNA expression. How do we break this "transcriptional code"? Mechanistic studies, using simple model promoters, indicate that transcription is controlled by the coordinate action of sequence-specific DNA binding proteins interacting with the general transcriptional machinery via intermediary adapters and chromatin remodeling activities. How can we integrate this biochemical information with data from genome-wide studies to describe the generation of highly complex patterns of transcription? Here, we discuss recent studies that may point the way ahead. We also highlight difficulties that the field faces in dissecting transcriptional control in the post-genome era.

Animals↗
PubMed2004

Cooperative self-assembly and molecular binding behavior of cyclodextrin-crown ether conjugates mediated by alkali metal ions.

In order to quantitatively investigate their molecular binding ability, a series of cyclodextrin-crown ether conjugates containing beta-cyclodextrin (beta-CyD) and crown ether units, i.e.N-(benzoaza-15-crown-5)acylaminomethylene tethered 6-diethylenetriamino-6-deoxy-beta-CyD, N-(benzoaza-15-crown-5)acylaminomethylene tethered 6-triethylenetetraamino-6-deoxy-beta-CyD and 4',5'-dimethylene-benzo-15-crown-5 tethered 6-diethylenetriamino-6-deoxy-beta-CyD, have been prepared as ditopic molecular receptors. Their inclusion complexation behavior with four representative fluorescent dyes, i.e. ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium 6-toluidino-2-naphthalenesulfonate (TNS), acridine red (AR) and rhodamine B (RhB), has been comprehensively investigated in aqueous NaH2PO4/Na2HPO4 or KH2PO4/K2HPO4 buffer solution (pH 7.20) by means of circular dichroism, fluorescence, and 2D NMR spectra. The results indicate that the self-assembly of crown ether modified beta-CyD mediated by potassium ion exhibits a dimeric structure, which significantly enhances the original binding ability and molecular selectivity of parent beta-CyD and its derivatives towards guest molecules through the cooperative binding of two hydrophobic CyD cavities with one guest. This cooperative binding mode of K+/CyD-crown ether systems are further confirmed by Job's experiments and 2D NMR investigations. Attributed to the positive contributions from the metal-ligated crown ether cap and K+-mediated dimerization of CyDs, the binding constant (Ks) values of CyD-crown ether conjugates toward ANS are 10-83 times higher than that of beta-CyD. The increased binding ability and molecular selectivity of CyD-crown ether conjugates are discussed from the viewpoints of size/shape-fit and multiple recognition mechanism.

Journal Article↗
PubMed1997

Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions?

The general transcription initiation factor TFIID was originally identified, purified, and characterized with a biochemical assay in which accurate transcription initiation is reconstituted with multiple, chromatographically separable activities. Biochemical analyses have demonstrated that TFIID is a multiprotein complex that directs preinitiation complex assembly on both TATA box-containing and TATA-less promoters, and some TFIID subunits have been shown to be molecular targets for activation domains in DNA-binding regulatory proteins. These findings have most commonly been interpreted to support the view that transcriptional activation by upstream factors is the result of enhanced TFIID recruitment to the core promoter. Recent insights into the architecture and cell-cycle regulation of the multiprotein TFIID complex prompt both a reassessment of the functional role of TFIID in gene activation and a review of some of the less well-appreciated literature on TFIID. We present a speculative model for diverse functional roles of TFIID in the cell, explore the merits of the model in the context of published data, and suggest experimental approaches to resolve unanswered questions. Finally, we point out how the proposed functional roles of TFIID in eukaryotic class II transcription fit into a model for promoter recognition and activation that applies to both eubacteria and eukaryotes.

Animals↗
PubMed1992

Three-dimensional structure of an angiotensin II-Fab complex at 3 A: hormone recognition by an anti-idiotypic antibody.

The elucidation of bioactive conformations of small peptide hormones remains an elusive goal to structural chemists because of the inherent flexibility of these molecules. Angiotensin II (AII), the major effector of the renin-angiotensin system, is an octapeptide hormone for which no clear structural models exist. Peptide hormones such as AII share the property that they bind to their receptors with high affinities, in spite of the fact that they must overcome an extremely large conformational entropy barrier to bind in one conformation. A "surrogate system" that consists of a high-affinity monoclonal antibody (MAb) and AII has been used to study a bound conformation of AII. The crystallographic structure of the complex reveals a structure of AII that is compatible with predicted bioactive conformations of AII derived from structure-activity studies and theoretical calculations. In the complex, the deeply bound hormone is folded into a compact structure in which two turns bring the amino and carboxyl termini close together. The antibody of this complex (MAb 131) has the unusual property that it was not generated against AII, but rather against an anti-idiotypic antibody reactive with a MAb to AII, which renders this antibody an anti-anti-idiotypic antibody. The high affinity for AII of the original MAb to AII was passed on to MAb 131 through a structural determinant on the anti-idiotypic antibody. Strikingly, the conformation of AII in this complex is highly similar to complementarity determining region loops of antibodies, possibly indicating that a true molecular mimic of bound AII was present on the anti-idiotypic antibody against which MAb 131 was elicited.

Amino Acid Sequence↗
PubMed2003

An ancient enzyme domain hidden in the putative beta-glucan elicitor receptor of soybean may play an active part in the perception of pathogen-associated molecular patterns during broad host resistance.

A successful defense against potential pathogens requires that a host organism is able to discriminate between self and nonself structures. Soybean (Glycine max L.) exploits a specific molecular pattern, a 1,6-beta-linked and 1,3-beta-branched heptaglucoside (HG), present in cell walls of the oomycetal pathogen Phytophthora sojae, as a signal compound eliciting the onset of defense reactions. The specific and high affinity HG-binding site is contained in the beta-glucan-binding protein (GBP), which in turn is part of a proposed receptor complex. The ability to perceive and respond to Phytophthora cell wall-derived beta-glucan elicitors is exclusive to plants that belong to the Fabaceae. However, we propose that the presence of the GBP is essential, but not sufficient for beta-glucan elicitor-dependent disease resistance because genes encoding GBP-related proteins can be retrieved from many plant species. Furthermore, we show that the GBP is composed of two different carbohydrateactive protein domains, one containing the beta-glucan-binding site, and the other related to glucan endoglucosidases of fungal origin. The glucan hydrolase displays most likely an endo-specific mode of action, cleaving only 1,3-beta-d-glucosidic linkages of oligoglucosides consisting of at least four moieties. Thus, the intrinsic endo-1,3-beta-glucanase activity of the GBP is perfectly suited during initial contact with Phytophthora to release oligoglucoside fragments enriched in motifs that constitute ligands for the high affinity binding site present in the same protein. The concept of innate immunity in plants receives substantial support by this highly sophisticated system using ancient enzyme modules as an active part of the recognition mechanism.

Amino Acid Motifs↗
PubMed1989

Evidence for an involvement of T4+ cytotoxic T cells in tumor immunity.

Cell-mediated immunity against cancer cells primarily involves class I major histocompatibility complex (MHC)-restricted cytotoxic T cells and natural killer (NK) cells. To investigate whether T4+ cytotoxic T cells also have a role in tumor-specific immunity, mice were immunized with a B cell lymphoma. T cell hybridomas were constructed from the immune spleen cells and analyzed for their cytotoxic ability against the immunizing lymphoma. A T4+, Lyt-1+ hybridoma cell line was developed (103L2) which specifically killed the immunizing tumor cells but not normal B cells or a range of other tumor cells of B or non-B origin. This cytotoxic hybridoma cell line differed from Lyt-2+ cytotoxic T lymphocyte cells and NK cells, commonly identified with cytotoxicity, in a number of important ways. First, the cells were class II MHC restricted; second, interleukin-2 was released from activated effector cells; and finally but most importantly, innocent nonparticipating bystander cells were also killed. The significance of this observation was that normal cells were protected, although a broad range of tumor cell types, including tumor antigen-negative mutants, were killed. It is therefore conceivable that T4+ cytotoxic T cells might play an important role in tumor immunity through the direct recognition and lysis of tumor cells while any tumor variants, arising due to antigen loss, would remain susceptible through the bystander killing effect and normal cells would remain unaffected. These results strongly suggest that tumor-reactive T4+ cytotoxic T cells belong to a new category of effector cells with an important role in tumor-specific immunity.

Animals↗
PubMed1996

Paracrine regulation of the renal microcirculation.

There has been an explosive growth of interest in the multiple interacting paracrine systems that influence renal microvascular function. This review first discusses the membrane activation mechanisms for renal vascular control. Evidence is provided that there are differential activating mechanisms regulating pre- and postglomerular arteriolar vascular smooth muscle cells. The next section deals with the critical role of the endothelium in the control of renal vascular function and covers the recent findings related to the role of nitric oxide and other endothelial-derived factors. This section is followed by an analysis of the roles of vasoactive paracrine systems that have their origin from adjoining tubular structures. The interplay of signals between the epithelial cells and the vascular network to provide feedback regulation of renal hemodynamics is developed. Because of their well-recognized contributions to the regulation of renal microvascular function, three major paracrine systems are discussed in separate sections. Recent findings related to the role of intrarenally formed angiotensin II and the prominence of the AT1 receptors are described. The possible contribution of purinergic compounds is then discussed. Recognition of the emerging role of extracellular ATP operating via P2 receptors as well as the more recognized functions of the P1 receptors provides fertile ground for further studies. In the next section, the family of vasoactive arachidonic acid metabolites is described. Possibilities for a myriad of interacting functions operating both directly on vascular smooth muscle cells and indirectly via influences on endothelial and epithelial cells are discussed. Particular attention is given to the more recent developments related to hemodynamic actions of the cytochrome P-450 metabolites. The final section discusses unique mechanisms that may be responsible for differential regulation of medullary blood flow by locally formed paracrine agents. Several sections provide perspectives on the complex interactions among the multiple mechanisms responsible for paracrine regulation of the renal microcirculation. This plurality of regulatory interactions highlights the need for experimental strategies that include integrative approaches that allow manifestation of indirect as well as direct influences of these paracrine systems on renal microvascular function.

Animals↗
PubMed1989

Primate evolution of a human chromosome 1 hypervariable repetitive element.

The clone designated hMF #1 represents a clustered DNA family, located on chromosome 1, consisting of tandem arrays displaying a monomeric length of 40 bp and a repetition frequency of approximately 7 x 10(3) copies per haploid genome. The sequence hMF #1 reveals multiple restriction fragment length polymorphisms (RFLPs) when human genomic DNA is digested with a variety of 4-6-bp recognition sequence restriction enzymes (i.e., Taq I, Eco RI, Pst I, etc.). When hamster and mouse genomic DNA was digested and analyzed, no cross-species homology could be observed. Further investigation revealed considerable hybridization in the higher primates (chimpanzee, gorilla, and orangutan) as well as some monkey species. The evolutionary relationship of this repetitive DNA sequence, found in humans, to that of other primates was explored using two hybridization methods: DNA dot blot to establish copy number and Southern DNA analysis to examine the complexity of the RFLPs. Homology to the hMF #1 sequence was found throughout the suborder Anthropoidea in 14 ape and New and Old World monkey species. However the sequence was absent in one species of the suborder Prosimii. Several discrepancies between "established" evolutionary relationships and those predicted by hMF #1 exist, which suggests that repetitive elements of this type are not reliable indicators of phylogenetic branching patterns. The phenomenon of marked diversity between sequence homologies and copy numbers of dispersed repetitive DNA of closely related species has been observed in Drosophila, mice, Galago, and higher primates. We report here a similar phenomenon for a clustered repeat that may have originated at an early stage of primate evolution.

Animals↗
PubMed2005

Fast SVM training algorithm with decomposition on very large data sets.

Training a support vector machine on a data set of huge size with thousands of classes is a challenging problem. This paper proposes an efficient algorithm to solve this problem. The key idea is to introduce a parallel optimization step to quickly remove most of the nonsupport vectors, where block diagonal matrices are used to approximate the original kernel matrix so that the original problem can be split into hundreds of subproblems which can be solved more efficiently. In addition, some effective strategies such as kernel caching and efficient computation of kernel matrix are integrated to speed up the training process. Our analysis of the proposed algorithm shows that its time complexity grows linearly with the number of classes and size of the data set. In the experiments, many appealing properties of the proposed algorithm have been investigated and the results show that the proposed algorithm has a much better scaling capability than Libsvm, SVMlight, and SVMTorch. Moreover, the good generalization performances on several large databases have also been achieved.

Algorithms↗
PubMedDate not supplied

The 26S proteasome Rpn10 gene encoding splicing isoforms: evolutional conservation of the genomic organization in vertebrates.

Recognition of polyubiquitinated substrates by the 26S proteasome is a key step in the selective degradation of various cellular proteins. The Rpn10 subunit of the 26S proteasome can bind polyubiquitin conjugates in vitro. We have previously reported the unique diversity of Rpn10, which differs from other multiple proteasome subunits, and that the mouse Rpn10 mRNA family is generated from a single gene by developmentally regulated alternative splicing. To determine whether such alternative splicing mechanisms occur in other species, we searched for Rpn10 isoforms in databases and in our original PCR products. Here we report the genomic organization of the Rpn10 gene in lower vertebrates and provide evidence for the competent generation of distinct forms of Rpn10 by alternative splicing through evolution.

Alternative Splicing↗
PubMed1996

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

Base Sequence↗
PubMed1999

Structural basis for recognition of phosphorylated high mannose oligosaccharides by the cation-dependent mannose 6-phosphate receptor.

Mannose 6-phosphate receptors (MPRs) play an important role in the targeting of newly synthesized soluble acid hydrolases to the lysosome in higher eukaryotic cells. These acid hydrolases carry mannose 6-phosphate recognition markers on their N-linked oligosaccharides that are recognized by two distinct MPRs: the cation-dependent mannose 6-phosphate receptor and the insulin-like growth factor II/cation-independent mannose 6-phosphate receptor. Although much has been learned about the MPRs, it is unclear how these receptors interact with the highly diverse population of lysosomal enzymes. It is known that the terminal mannose 6-phosphate is essential for receptor binding. However, the results from several studies using synthetic oligosaccharides indicate that the binding site encompasses at least two sugars of the oligosaccharide. We now report the structure of the soluble extracytoplasmic domain of a glycosylation-deficient form of the bovine cation-dependent mannose 6-phosphate receptor complexed to pentamannosyl phosphate. This construct consists of the amino-terminal 154 amino acids (excluding the signal sequence) with glutamine substituted for asparagine at positions 31, 57, 68, and 87. The binding site of the receptor encompasses the phosphate group plus three of the five mannose rings of pentamannosyl phosphate. Receptor specificity for mannose arises from protein contacts with the 2-hydroxyl on the terminal mannose ring adjacent to the phosphate group. Glycosidic linkage preference originates from the minimization of unfavorable interactions between the ligand and receptor.

Animals↗