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PubMed1991

Structure function analysis of the H-2 Abp gene.

The gene encoding the H-2 Ap class II beta chain was isolated from a B10.P genomic library and sequenced. This gene was also used to construct transfectants of the CH12 lymphoma clone CH12.LX, which express the Abp gene product in association with the endogenous A alpha k chain. We present here the first report of the complete nucleotide coding sequence of Abp. The predicted amino acid sequence of Abp reveals only five residues different from Abq, four of which are present in the mature peptide. These four amino acid changes could account for the differential susceptibility of H-2q vs H-2p mice to the development of collagen-induced arthritis (CIA). Antibodies specific for the transfected Abp protein induce CH12.LX cells to secrete immunoglobulin in the presence of antigen. Comparison of the amino acid sequence with other A beta chains that have been tested in signal transduction experiments suggests that amino acid 9 may be important to the signaling ability of class II A molecules.

Amino Acid Sequence↗
PubMed1998

Complete mitochondrial genome of a neotropical fruit bat, Artibeus jamaicensis, and a new hypothesis of the relationships of bats to other eutherian mammals.

The complete mitochondrial genome was obtained from a microchiropteran bat, Artibeus jamaicensis. The presumptive amino acid sequence for the protein-coding genes was compared with predicted amino acid sequences from several representatives of other mammalian orders. Data were analyzed using maximum parsimony, maximum likelihood, and neighbor joining. All analyses placed bats as the sister group of carnivores, perissodactyls, artiodactyls, and cetaceans (e.g., 100% bootstrap value with both maximum parsimony and neighbor joining). The data strongly support a new hypothesis about the origin of bats, specifically a bat/ferungulate grouping. None of the analyses supported the superorder Archonta (bats, flying lemurs, primates, and tree shrews). Our hypothesis regarding the relationship of bats to other eutherian mammals is concordant with previous molecular studies and contrasts with hypotheses based solely on morphological criteria and an incomplete fossil record. The A. jamaicensis mitochondrial DNA control region has a complex pattern of tandem repeats that differs from previously reported chiropteran control regions.

Animals↗
PubMed1998

Learning of sequential movements by neural network model with dopamine-like reinforcement signal.

Dopamine neurons appear to code an error in the prediction of reward. They are activated by unpredicted rewards, are not influenced by predicted rewards, and are depressed when a predicted reward is omitted. After conditioning, they respond to reward-predicting stimuli in a similar manner. With these characteristics, the dopamine response strongly resembles the predictive reinforcement teaching signal of neural network models implementing the temporal difference learning algorithm. This study explored a neural network model that used a reward-prediction error signal strongly resembling dopamine responses for learning movement sequences. A different stimulus was presented in each step of the sequence and required a different movement reaction, and reward occurred at the end of the correctly performed sequence. The dopamine-like predictive reinforcement signal efficiently allowed the model to learn long sequences. By contrast, learning with an unconditional reinforcement signal required synaptic eligibility traces of longer and biologically less-plausible durations for obtaining satisfactory performance. Thus, dopamine-like neuronal signals constitute excellent teaching signals for learning sequential behavior.

Algorithms↗
PubMed1992

The Bezold-Brücke effect in the color vision system of the honeybee.

Evidence is presented that intensity dependent color shifts (Bezold-Brücke effect) occur in the color vision system of the honeybee. The evidence comes from a fit between the choices of monochromatic lights in training experiments (Menzel, R., 1981; Journal of Comparative Physiology A, 141, 389-393) and the choice percentages derived now from recently presented quantitative predictions from the color opponent coding (COC) model for the bee (Backhaus, W., 1991; Vision Research, 31, 1381-1397) for the Bezold-Brücke effect. The only open parameter in the simulations of the training experiments is an experiment type dependent factor describing the weighting of color differences (judgement values) in the choice behavior. The results show (1) that the Bezold-Brücke effect exists in the bee. The results (2) confirm the color opponent coding (COC) model which was developed to describe the physiological components of the color vision system in the bee, (3) the general psychophysical assumptions about the structure of the color space, (4) the color difference formula, and (5) the general psychophysical assumptions about the (triadic) structure of judgements as tested in color similarity experiments.

Animals↗
PubMed1983

Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin.

We have isolated cDNA clones generated from the mRNA encoding the opsin apoprotein of bovine rhodopsin and used these cDNAs to isolate genomic DNA clones containing the complete opsin gene. Nucleotide sequence analysis of the cloned DNAs has yielded a complete amino acid sequence for bovine rhodopsin and provided an intron-exon map of its gene. The mRNA homologous sequences in the 6.4 kb gene consist of a 96 bp 5' untranslated region, a 1044 bp coding region, and a surprisingly long approximately 1400 bp 3' untranslated region, and are divided into five exons by four introns that interrupt the coding region. Secondary structure analysis predicts that the bovine rhodopsin chain, like that of bacteriorhodopsin, contains seven transmembrane segments. Interestingly, three of the four introns are immediately distal to the codons for three of these segments, and one of these introns marks the boundary between the C-terminal domain and a transmembrane domain.

Amino Acid Sequence↗
PubMed1990

Cloning and sequencing of two actin genes from Taenia solium (Cestoda).

Genomic and cDNA actin clones were isolated from Taenia solium gene libraries. The actin genes are interrupted by intervening sequences. Protein coding regions of both genes predict the same amino acid sequence. cDNA sequence data indicate that at least one gene is expressed at the larval stage. Results from Northern and Western blots showed that T. solium expresses an actin transcript of about 1,400 bases and a protein of 45,000 Da.

Actins↗
PubMed1993

Expression of Plasmodium falciparum lactate dehydrogenase in Escherichia coli.

A Plasmodium falciparum gene is described which encodes lactate dehydrogenase activity (P. falciparum LDH). The P. falciparum LDH gene contains no introns and is present in a single copy on chromosome 13. P. falciparum LDH was expressed in all asexual blood stages as a 1.6-kb mRNA. The predicted 316 amino acid protein coding region of P. falciparum LDH was inserted into the prokaryotic expression vector pKK223-3 and a 33-kDa protein having LDH activity was synthesized in Escherichia coli. P. falciparum LDH primary structure displays high amino acid similarity (50-57%) to vertebrate and bacterial LDH, but lacks the amino terminal extension observed in all vertebrate LDH. The majority of amino acid residues implicated in substrate and coenzyme binding and catalysis of other LDH are well conserved in P. falciparum LDH. However, several notable differences in amino acid composition were observed. P. falciparum LDH contained several distinctive single amino acid insertions and deletions compared to other LDH enzymes, and most remarkably, it contained a novel insertion of 5 amino acids within the conserved mobile loop region near arginine residue 109, a residue which is known to make contact with pyruvate in the ternary complex of other LDH. These results suggest that novel features of P. falciparum LDH primary structure may be correlated with previously characterized and distinctive kinetic, biochemical, immunochemical, and electrophoretic properties of P. falciparum LDH.

Amino Acid Sequence↗
PubMed1996

Cloning of PL33: a novel probable serpentine membrane receptor associated with human cytotrophoblast and lineage-specific HL-60 cell differentiation.

From a subtracted library of differentiating human cytotrophoblast cells, we have cloned a gene termed PL33, a novel probable member of the G-protein-linked seven transmembrane domain receptor family. The 496 amino acid open reading frame of PL33 codes for a protein of predicted molecular weight of 54.7 kDa. Northern blot analysis shows that the two mRNA transcripts of PL33 are expressed in testes, keratinocytes, differentiating cytotrophoblast and in monocyte/macrophage lineage-specific HL-60 cell differentiation.

Amino Acid Sequence↗
PubMed1994

Cloning, nucleotide sequence and expression of a hemolysin gene of Clostridium septicum.

A genomic library of Clostridium septicum NCTC547 strain was made in Escherichia coli by means of lambda gt10. The DNA insert of a hemolysin-positive (Hly+) lambda-clone was transferred into pUC19. The resulting plasmid, pCS21, confers a Hly+ phenotype on E. coli. Crude lysates of E. coli (pCS21) possessed a strong lytic activity on human erythrocytes and also a lethal effect on mice, characteristic of an alpha toxin. Nucleotide sequence analysis revealed that the insert DNA (5.2 kb) in pCS21 included at least one open reading frame of 1380 bp. The coding frame for hemolysin was predicted to be 1329 bp in size and to encode a protein of 49.8 kDa. It coincided with the molecular mass (48 kDa) of the alpha toxin secreted by C. septicum. Taken together, the data indicated that plasmid pCS21 indeed encoded an alpha toxin gene of C. septicum.

Amino Acid Sequence↗
PubMed1987

A set of cassettes and improved vectors for genetic and biochemical characterization of Pseudomonas genes.

A set of broad-host-range vectors allowing direct selection of recombinant DNA molecules to facilitate subcloning and expression analyses of Pseudomonas genes was constructed using Bg/II lacZ alpha cassette. Controlled expression vectors pVDtac39 and pVDtac24 were shown to be useful for determination of enzymatic activities encoded by the cloned DNA fragments and Mr determination of the corresponding polypeptides. A set of Pseudomonas putida xylE gene cassettes truncated at the 5' end was constructed for translational (protein) fusion studies. A protein fusion of the Pseudomonas aeruginosa algD gene, coding for GDPmannose dehydrogenase, and the truncated xylE gene cassette was used to verify the putative coding region and translational signals predicted from the algD nucleotide sequence.

Cloning, Molecular↗
PubMed1993

Cloning and sequencing an ovine interleukin-4-encoding cDNA.

We have cloned a cDNA containing the complete coding sequence of ovine(ov) interleukin 4 (IL4) by the polymerase chain reaction using primers based on the 5' and 3' untranslated regions of the human IL4 gene. RNA was isolated from phorbol myristate acetate- and calcium ionphore A23187-stimulated mesenteric lymph node cells. The ovIL4 cDNA is 535 bp in length and contains an open reading frame of 408 nucleotides (nt) coding for a 15.1-kDa IL4 precursor of 135 amino acids (aa). Cleavage of the putative signal peptide of 22 aa yields the mature form of 13.2 kDa. Analysis of the mature aa sequence shows two potential N-linked glycosylation sites and six Cys residues. Ovine and bovine IL4 are shorter than human, mouse and rat IL4, because of a 51-nt deletion in the coding region. Comparison of the predicted aa sequence shows that ovIL4 shares 92, 57, 37 and 42% identity with the bovine, human, mouse and rat IL4s, respectively.

Animals↗
PubMed1995

Using administratively collected hospital discharge data for AIDS surveillance.

The objectives of this study were twofold: to improve methods of identifying possible and acquired immunodeficiency syndrome (AIDS)-related hospital discharges in administrative databases and to measure AIDS-reporting completeness in Massachusetts both overall and by subgroup. We used fiscal year 1988 discharge data from the Massachusetts Rate Setting Commission (RSC) and data from the Massachusetts AIDS Reporting System (ARS). We identified 3362 discharges of adult patients (> 12 years old) from the RSC file that had diagnosis codes which are human immunodeficiency virus (HIV)-specific (042.x, 043.x, 044.x, or 795.8) or pertain to AIDS-defining "manifestations." Medical records of 650 patients apparently not reported to the ARS were reviewed. THe best set of codes overall consisted of either (a) the 042.x code or (b) the 043.x, 044.x, or 795.8 code plus selected manifestation codes (sensitivity, 93%; specificity, 86%; predictive value positive, 71%). Of the 927 AIDS cases identified from the 3362 discharges, only 36 had not been reported. AIDS cases among women (odds ratio (OR) = 2.9; 95% confidence interval (CI): 1.33 to 6.33), intravenous drug users (OR = 4.2; 95% CI: 2.20 to 8.02), and persons residing outside the Boston metropolitan area (OR = 2.3; 95% CI: 1.18 to 4.57) were more likely to be unreported than those among comparison groups.

AIDS-Related Opportunistic Infections↗
PubMed2005

Cloning, sequence analysis, and characterization of a novel beta-glucosidase-like activity from Pichia etchellsii.

Genomic DNA fragment encoding a novel beta-glucosidase-like activity of the yeast Pichia etchellsii was cloned and expressed in Escherichia coli. An open-reading frame of 1515bp, termed mugA, coding for a protein of predicted molecular mass of approximately 54kDa was confirmed for this activity. The sequence of the deduced protein did not show homology with the generic beta-glucosidases but a high degree of identity was seen with several Ser-Asp (SD)-rich cell-surface-associated proteins. The secondary structure prediction program 3D-PSSM indicated the protein to be composed of largely helical and coiled structures, which was confirmed by circular dichroism spectroscopy. The encoded protein, MUGA, was purified by about 53-fold and characterized as a monomer of 52.1kDa by SDS-PAGE and MALDI-TOF. The protein displayed high hydrolytic activity on methylumbelliferyl beta-d-glucoside but relatively very little hydrolysis of p-nitrophenyl beta-d-glucoside and gentiobiose, characteristic substrates for beta-glucosidases. The binding experiments performed between P. etchellsii cells and the purified E. coli expressed MUGA indicated binding with the cell surface, which was monitored by fluorescence microscopy. In competition experiments with the SD dipeptide, less protein was shown to bind to the cell surface, in a concentration-dependent manner.

Amino Acid Sequence↗
PubMed2003

p63/73 homologues in surf clam: novel signaling motifs and implications for control of expression.

To understand the role of p53 gene family members during invertebrate embryonic development, we used polymerase chain reaction (PCR) to identify p63/73 homologues in the marine mollusc Spisula solidissima. Here, we report the sequences of two distinct p63/73-like homologues, both cloned from Spisula embryos. The first, Ssp63/73alpha is 2699 nucleotide (nt); the second, Spp63/73beta is 3920 nt. The nucleotide sequences of the two variants are nearly identical up to their stop codons but diverge in their 3'-untranslated regions (UTRs). The deduced amino acid sequence of both Ssp63/73 variants is 597 amino acids, coding for a protein with predicted molecular weight of approximately 68 kDa. We conclude that the two unique transcripts, containing 3' UTRs of variable lengths, represent tandem alternate polyadenylation sites for the Ssp63/73 gene. While alternative splicing has been well documented in the p63/73 gene family, this is the first report of alternate polyadenylation site choice as a control point for p63/73 gene expression in any species. In order to identify specific post-transcriptional as well as post-translational signals potentially involved in regulation of p63/73-like expression, we compared Ssp63/p73 nucleotide and Ssp63/73 deduced amino acid sequences to corresponding regions of other mammalian and nonmammalian p63 and p73 homologues. Within the Spisula 3' UTRs we identified multiple AU-rich elements (AREs) which may control translation activation. Within the deduced amino acid sequence, we identified potential sites for sumoylation, a post-translational process that has been identified in mammalian p63 and p73 proteins. Identification of these novel signaling sites provides information about potential mechanisms controlling expression of multiple p63/73 isoforms during development.

3' Untranslated Regions↗
PubMed2006

Identification of two new members, XPLAC and XTES, of the XK family.

XK, a putative membrane transporter, is a component of the XK/Kell complex of the Kell blood group system. XK's substrate is unknown but absence of the protein, as occurs in the McLeod phenotype, is associated with red cell acanthocytosis and late onset central nervous system and neuromuscular abnormalities known as the McLeod syndrome. We have cloned two cDNAs, XPLAC (GenBank accession no. AY589511) and XTES (GenBank accession no. AY989815), which are closely related to XK and define them together as the XK family. XPLAC has a 2.9 kb cDNA that encodes 462 amino acids and XTES has a 1.6 kb cDNA coding 459 amino acids. The predicted molecular weights are 53.6 kDa for XPLAC and 53.4 kDa for XTES, which are similar to that of XK, which is 50.9 kDa. Unlike XK which is ubiquitously expressed XPLAC is expressed mostly in placenta and adrenal gland while XTES is exclusively expressed in primate testis. XPLAC has 37% and XTES has 31% amino acid identity with XK protein and they are predicted to have a similar topology to XK. XPLAC, like XK, has 3 exons and is located on X chromosome at q22.1, while XTES has 4 exons and is located at 22q11.1. Phylogenetic analysis shows that there are at least 5 additional vertebrate genes that are evolutionarily distantly related to the XK family. A domain with consensus sequences (ced-8 domain) for the extended family is described.

Acanthocytes↗
PubMed2006

The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum.

The complete nucleotide sequence of the Corynebacterium glutamicum ATCC 13032 genome was previously determined and allowed the reliable prediction of 3002 protein-coding genes within this genome. Using computational methods, we have defined 158 genes, which form the minimal repertoire for proteins that presumably act as transcriptional regulators of gene expression. Most of these regulatory proteins have a direct role as DNA-binding transcriptional regulator, while others either have less well-defined functions in transcriptional regulation or even more general functions, such as the sigma factors. Recent advances in genome-wide transcriptional profiling of C. glutamicum generated a huge amount of data on regulation of gene expression. To understand transcriptional regulation of gene expression from the perspective of systems biology, rather than from the analysis of an individual regulatory protein, we compiled the current knowledge on the defined DNA-binding transcriptional regulators and their physiological role in modulating transcription in response to environmental signals. This comprehensive data collection provides a solid basis for database-guided reconstructions of the gene regulatory network of C. glutamicum, currently comprising 56 transcriptional regulators that exert 411 regulatory interactions to control gene expression. A graphical reconstruction revealed first insights into the functional modularity, the hierarchical architecture and the topological design principles of the transcriptional regulatory network of C. glutamicum.

Amino Acids↗
PubMed2003

Human malaria parasites display a receptor for activated C kinase ortholog.

Receptors for activated C kinases (RACKs) are scaffold proteins that anchor diverse signaling proteins and are involved in modulating cell cycle. We report the cloning and cellular localization of a RACK ortholog (PfRACK) in the human malaria parasite Plasmodium falciparum. The full-length transcript obtained by 3(') and 5(') RACE has 1.4 kbp with a predicted ORF of 972 bp, coding for a protein with 323 residues of 35.8 kDa molecular weight and pI 6.38. PfRACK has 59% and 60% identity at the amino acid level to Chlamydomonas reinhardtii and Danio rerio RACKs, respectively, presenting seven WD40 motifs and retaining the conserved domains in repeats III (DVFSVSF) and VI (STINSLCF) that are important for PKC binding. Semi-quantitative RT-PCR revealed that PfRACK is constitutively expressed in the intraerythrocytic stages of P. falciparum. Using confocal microscopy, PfRACK was immunolocalized in all parasite stages, being conspicuously spread throughout the schizont. The high similarity of PfRACK to those previously described in other organisms, as well as its constitutive expression in Plasmodium asexual stages, suggests that it might play a key role in the regulatory processes of malaria parasite life cycle.

Amino Acid Sequence↗
PubMed2000

Color-opponent receptive fields derived from independent component analysis of natural images.

Independent Component Analysis (ICA) of images of natural scenes has been shown to generate basis functions, or filters, which resemble spatial [Bell & Sejnowski (1997). Vision Research, 37, 3327-3338; van Hateren & van der Schaaf (1998). Proceedings of the Royal Society of London B, 265, 359-366] and spatiotemporal [van Hateren & Ruderman (1998) Proceedings of the Royal Society of London B, 265, 2315-2320] receptive fields of simple cells of the striate cortex. ICA yields statistically independent components which provide for a redundancy-reduced representation of the data. Using one of several published algorithms [Lee (1998). Independent component analysis: theory and applications. Boston; Kluwer Academic], we applied linear ICA to color images of natural scenes. The resulting independent component filters (ICFs) separate into either luminance or color filters. The luminance filters are localized and oriented edge detectors as reported previously. The color filters resemble either blue-yellow or red-green double-opponent receptive fields with various orientations. An equal number of each type of filter (luminance, red-green, and blue-yellow) is obtained. Thus, ICA predicts that spatiochromatic information is coded in statistically independent luminance, blue-yellow, and red-green opponent pathways with a relatively equal representation and specific spatial profiles at the cortical level.

Algorithms↗