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PubMed1992

Thalassemic red cells determined by different technology of blood cell analysers.

Blood samples from 12 normal cases and 30 thalassemic patients were analyzed by four blood cell analysers (the H*1, Baker 9,000RX, Coulter JT, and Argos). These four machines had different technology: light scattering using laser beam (H*1) and electronic aperture impedance (Baker 9,000RX, Coulter JT, and Argos). Analysis of normal blood samples showed comparable red cell parameters between these four machines except the value of RDW. When the thalassemic blood samples were determined using these four types of blood cell counters, many red cell parameters showed significant difference. This indicates that thalassemic red cells which are known as the abnormal cells in terms of their volume, shape, intracellular hemoglobin content, and osmotic fragility, responded differently to the reagents and technology of blood cell analysis. Calibration of the instrument using qualitatively abnormal blood sample, is recommended.

Blood Cell Count↗
PubMed1980

The relationship between coding sequences and function in some heme binding proteins.

It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochrome c and cytochrome b5 chains (Argos and Rossmann 1979), it can be inferred that the cytochrome c gene will contain only one coding sequence while the cytochrome b5 gene will be composed of three exons as found in the globin gene.

Amino Acid Sequence↗
PubMed1989

Identification of four conserved motifs among the RNA-dependent polymerase encoding elements.

Four consensus sequences are conserved with the same linear arrangement in RNA-dependent DNA polymerases encoded by retroid elements and in RNA-dependent RNA polymerases encoded by plus-, minus- and double-strand RNA viruses. One of these motifs corresponds to the YGDD span previously described by Kamer and Argos (1984). These consensus sequences altogether lead to 4 strictly and 18 conservatively maintained amino acids embedded in a large domain of 120 to 210 amino acids. As judged from secondary structure predictions, each of the 4 motifs, which may cooperate to form a well-ordered domain, places one invariant amino acid in or proximal to turn structures that may be crucial for their correct positioning in a catalytic process. We suggest that this domain may constitute a prerequisite 'polymerase module' implicated in template seating and polymerase activity. At the evolutionary level, the sequence similarities, gap distribution and distances between each motif strongly suggest that the ancestral polymerase module was encoded by an individual genetic element which was most closely related to the plus-strand RNA viruses and the non-viral retroposons. This polymerase module gene may have subsequently propagated in the viral kingdom by distinct gene set recombination events leading to the wide viral variety observed today.

Amino Acid Sequence↗
PubMed1992

A functional protein hybrid between the glucose transporter and the N-acetylglucosamine transporter of Escherichia coli.

The glucose and N-acetylglucosamine-specific transporters (IIGlc/IIIGlc and IIGlcNAc) of the bacterial phosphotransferase system mediate carbohydrate uptake across the cytoplasmic membrane concomitant with substrate phosphorylation. The two transporters have 40% amino acid sequence identity. Eight chimeric proteins between the two transporters were made by gene reconstruction. All hybrid proteins could be expressed, some inhibited cell growth, and one was active. The active hybrid transporter consists of the transmembrane domain (residues 1-386) of the IIGlc subunit and the two hydrophilic domains (residues 370-648) of IIGlcNAc. The N-terminal hydrophilic domain of IIGlcNAc contains the transiently phosphorylated cysteine-412. The hybrid protein is specific for glucose, which indicates that the sugar specificity determinant is in the transmembrane domain and that the cysteine from which the phosphoryl group is transferred to the substrate is not part of the binding site. The protein sequence (LKTPGRED) at which the successful fusion occurred has the characteristic properties of an interdomain oligopeptide linker (Argos, P., 1990, J. Mol. Biol. 211, 943-958).

Acetylglucosamine↗
PubMed1994

Improving the sensitivity of the sequence profile method.

The sequence profile method (Gribskov M, McLachlan AD, Eisenberg D, 1987, Proc Natl Acad Sci USA 84:4355-4358) is a powerful tool to detect distant relationships between amino acid sequences. A profile is a table of position-specific scores and gap penalties, providing a generalized description of a protein motif, which can be used for sequence alignments and database searches instead of an individual sequence. A sequence profile is derived from a multiple sequence alignment. We have found 2 ways to improve the sensitivity of sequence profiles: (1) Sequence weights: Usage of individual weights for each sequence avoids bias toward closely related sequences. These weights are automatically assigned based on the distance of the sequences using a published procedure (Sibbald PR, Argos P, 1990, J Mol Biol 216:813-818). (2) Amino acid substitution table: In addition to the alignment, the construction of a profile also needs an amino acid substitution table. We have found that in some cases a new table, the BLOSUM45 table (Henikoff S, Henikoff JG, 1992, Proc Natl Acad Sci USA 89:10915-10919), is more sensitive than the original Dayhoff table or the modified Dayhoff table used in the current implementation. Profiles derived by the improved method are more sensitive and selective in a number of cases where previous methods have failed to completely separate true members from false positives.

Amino Acid Sequence↗
PubMed1995

Automatic recognition of hydrophobic clusters and their correlation with protein folding units.

A method is described to objectively identify hydrophobic clusters in proteins of known structure. Clusters are found by examining a protein for compact groupings of side chains. Compact clusters contain seven or more residues, have an average of 65% hydrophobic residues, and usually occur in protein interiors. Although smaller clusters contain only side-chain moieties, larger clusters enclose significant portions of the peptide backbone in regular secondary structure. These clusters agree well with hydrophobic regions assigned by more intuitive methods and many larger clusters correlate with protein domains. These results are in striking contrast with the clustering algorithm of J. Heringa and P. Argos (1991, J Mol Biol 220:151-171). That method finds that clusters located on a protein's surface are not especially hydrophobic and average only 3-4 residues in size. Hydrophobic clusters can be correlated with experimental evidence on early folding intermediates. This correlation is optimized when clusters with less than nine hydrophobic residues are removed from the data set. This suggests that hydrophobic clusters are important in the folding process only if they have enough hydrophobic residues.

Algorithms↗
PubMed1997

Origin and differentiation of supernumerary midline glia in Drosophila embryos deficient for apoptosis.

Drosophila embryos deficient for programmed cell death produce 9 midline glia (MG) in addition to the wild-type complement of 3.2 MG/segment. More than 3 of the supernumerary MG derive from the MGP (MG posterior) lineage and the remainder from the MGA/MGM (MG anterior and middle) lineage. There is one unidentified additional neuron in the mesectoderm of embryos deficient for apoptosis. The supernumerary MG are not diverted from other lineages nor do they arise from an altered pattern of mitosis. Instead, these MG appear to arise from a normally existing pool of 12 precursor cells, larger than anticipated by earlier studies. During normal development, MG survival is dependent upon signaling to the Drosophila EGF receptor. The persistence of supernumerary MG in embryos deficient for apoptosis does not alter the spatial pattern of Drosophila EGF receptor signaling. The number and position of MG which express genes dependent upon EGF receptor function, such as pointed or argos, are indistinguishable from wild type. Genes of the spitz group are required for Drosophila EGF receptor function. Surviving MG in spitz group/H99 double mutants continue to express genes characteristic of the MG, but the cells fail to differentiate into ensheathing glia and are displaced from the nerve cord.

Animals↗
PubMed1999

Tissue-specific regulation of vein/EGF receptor signaling in Drosophila.

Signaling by the Drosophila EGF receptor (DER) is modulated by four known EGF-like proteins: the agonists Vein (Vn), Spitz (Spi), and Gurken (Grk) and the antagonist Argos (Aos). DER is broadly expressed and thus tissue-specific regulation of ligand expression and activity is an important mechanism for controlling signaling. Here we investigate the tissue-specific regulation of Vn signaling by examining vn transcriptional control and Vn target gene activation in the embryo and the wing. The results show a complex temporal and spatial regulation of vn transcription involving multiple signaling pathways and tissue-specific activation of Vn target genes. In the embryo, vn is a target of Spi/DER signaling mediated by the ETS transcription factor PointedP1 (PntP1). This establishes a positive feedback loop in addition to the negative feedback loop involving Aos. The simultaneous production of Vn provides a mechanism for dampening Aos inhibition and thus fine-tunes signaling. In the larval wing pouch, vn is not a target of Spi/DER signaling but is expressed along the anterior-posterior boundary in response to Hedgehog (Hh) signaling. Repression by Wingless (Wg) signaling further refines the vn expression pattern by causing a discontinuity at the dorsal-ventral boundary. The potential for vn to activate DER target genes correlates with its roles in development: vn has a minor role in embryogenesis and does not induce DER target genes such as aos and pntP1 in the embryo. Conversely, vn has a major role in wing development and Vn/DER signaling is a potent inducer of DER target genes in the wing disc. Spi also has the potential to induce DER target genes in the wing disc. However, the ligands appear to evoke specific responses that result in different patterns of target gene expression. Finally, we show that other factors modulate the potential of Vn so that induction of Vn/DER target genes in the wing pouch is cell specific.

Animals↗
PubMed1992

A redefinition of the Asp-Asp domain of reverse transcriptases.

The rules defining the Asp-Asp domain of RNA-dependent polymerases deduced by Argos (1988) were tested in a set of 53 putative reverse transcriptases (RTs) sequences. Since it was found that some of these rules are not followed by RTs coded by bacteria, group II introns, and non-LTR retrotransposons, we present here a more strict definition of the Asp-Asp domain.

Amino Acid Sequence↗
PubMed1984

Transcription analysis of a Bacillus subtilis arg gene following cloning in Escherichia coli in an initially unstable hybrid plasmid.

Following shotgun cloning of EcoRI fragments of Bacillus subtilis DNA in pBR322, a hybrid plasmid pUL710 was isolated which complements argC but no other auxotrophs of E. coli K12. Restriction mapping, Southern blotting and other evidence suggest that pUL710 carries an insert of 1.6 kbp, and derives, by deletion of both vector and insert sequences, from a larger but unstable initial hybrid which carried a 12 kbp EcoRI fragment from the B. subtilis chromosome. RecE-dependent integration of pUL710 into the B. subtilis chromosome demonstrated homology between the insert DNA and the argO locus of B. subtilis. pUL710 was found to confer appreciable tetracycline resistance even though the deletion presumed to stabilise the hybrid had inactivated the tet promoter. The results of analysis by Tn5 mutagenesis, transcriptional fusions and run-off in vitro transcription suggest that both the cloned argC gene and the tetracycline gene in pUL710 are expressed from a B. subtilis promoter located very close to the EcoRI cloning site.

Aldehyde Oxidoreductases↗
PubMed1992

Method for calculating 3-D coordinates from molecular stereograms.

The three-dimensional coordinates for the alpha-carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective alpha-carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate the z-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values for xleft, yleft and xright, yright are provided in the first step. In the second step, the z-coordinate values are derived by varying z to minimize the bond distance error (Rossmann and Argos, 1980). In another approach, only a reference bond distance table is provided along with the table of xleft, yleft and xright, yright digitized values. In the first step, the viewing angle (phi), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (xerr and yerr) are calculated. In the second step, the z-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 A were obtained for both crambin and BPTI alpha-carbon atoms.

Algorithms↗
PubMed1997

Automated chemical synthesis: from resins to instruments.

Solid-phase organic synthesis is now a prevalent activity in drug discovery. In keeping with this keen interest is the need to develop reliable automated synthesis instrumentation as well as polymeric supports and linkers suitable for the full range of organic synthesis applications. In this paper, we review our activities in the development of new and enabling tools for automated chemical synthesis, including the following: (i) new solid supports such as ArgoGel (PS-PEG-based) and Argo-X203 (PS-based); and (ii) the Nautilus 2400 system, a fully closed and inert automated chemistry development workstation. Selected chemistry optimization and synthesis examples performed on the Nautilus and new solid supports will be described.

Automation↗
PubMed2000

Quantitative developmental genetic analysis reveals that the ancestral dipteran wing vein prepattern is conserved in Drosophila melanogaster.

Quantitative complementation tests provide a quick test of the hypothesis that a particular gene contributes to segregating phenotypic variation. A set of wild-type alleles is assayed for variation in their ability to complement the degree of dominance of the quantitative effect of a loss of function allele. Analysis of 15 loci known to be involved in wing patterning in Drosophila melanogaster suggests that the genes decapentaplegic, thickveins, EGFR, argos and hedgehog, each of which are involved in secreted growth factor signaling, may contribute to wing shape variation. The phenotype of one deficiency, Df(2R)Px2, which removes blistered/Plexate, is also highly sensitive to the wild-type genetic background and at intermediate expressivity reveals six ectopic veins. These form in the same locations as a projection of the ancestral pattern of dipteran wing veins on- to the D. melanogaster wing. This atavistic phenotype indicates that the wing vein prepatterning mechanism can be conserved in highly derived species, and implies that homoplasic venation patterns may be produced by derepression of vein primordia.

Animals↗
PubMed1988

The use of folding patterns in the search of protein structural similarities; a three-dimensional model of phosphoribosyl transferases.

A new way to predict the topologies of proteins of unknown three-dimensional structure is derived from the comparison of the distribution of the strongest predicted secondary structures with equivalent distributions recorded for proteins of known X-ray structures. As an illustration the tentative three-dimensional model of phosphoribosyl transferases which was proposed by Argos et al. is rediscussed.

Amino Acid Sequence↗
PubMed1993

Toscana virus genomic L segment: molecular cloning, coding strategy and amino acid sequence in comparison with other negative strand RNA viruses.

The complete nucleotide sequence of Toscana (TOS) virus (Bunyaviridae, Phlebovirus) L segment was determined. The L segment is 6404 nucleotides long, containing a single open reading frame (ORF) in the viral complementary sense coding for a protein of 2095 amino acids that, as in the case of negative strand RNA viruses, could be part of the RNA polymerase of TOS virus. This ORF is expressed by a messenger RNA (mRNA) as long as the genomic segment. Like the mRNAs expressed by the genomic segments of the other Bunyaviruses, the L mRNA has non-templated sequences at the 5' end. The comparison of TOS L protein sequence with the corresponding sequences of other negative strand RNA viruses showed a very high homology only with the Rift Valley Fever (RVF) virus. The residues conserved between the two proteins are mainly concentrated in the central region and contain three DD motifs proposed by Argos (1988) to be functional domains of DNA and RNA polymerases. The complete sequence of the Toscana virus L genomic segment has been deposited in the EMBL library with the accession number X68414.

Amino Acid Sequence↗
PubMed2004

PINning down the connections: transcription factors and hormones in leaf morphogenesis.

The past year has seen major advances in delineating the regulatory circuits that control leaf morphogenesis. Regulation of auxin transporters is pivotal in generating auxin gradients that define the sites of leaf inception. In addition, auxin acts via the ARGOS protein to regulate leaf size. HD-ZIPIII transcription factors controlled by micro-RNAs are required to specify adaxial identity in the leaf and vasculature. Elaboration of final leaf shape also depends on the regulated arrest of cell division, and the TCP and JAGGED transcription factors are key regulators of this process. Furthermore, the juxtaposition of abaxial and adaxial identities regulates leaflet placement in dissected leaf species.

Arabidopsis↗
PubMed2006

A multiple criteria analysis for household solid waste management in the urban community of Dakar.

Household solid waste management is a severe problem in big cities of developing countries. Mismanaged solid waste dumpsites produce bad sanitary, ecological and economic consequences for the whole population, especially for the poorest urban inhabitants. Dealing with this problem, this paper utilizes field data collected in the urban community of Dakar, in view of ranking nine areas of the city with respect to multiple criteria of nuisance. Nine criteria are built and organized in three families that represent three classical viewpoints: the production of wastes, their collection and their treatment. Thanks to the method PROMETHEE and the software ARGOS, we do a pair-wise comparison of the nine areas, which allows their multiple criteria rankings according to each viewpoint and then globally. Finding the worst and best areas in terms of nuisance for a better waste management in the city is our final purpose, fitting as well as possible the needs of the urban community. Based on field knowledge and on the literature, we suggest applying general and area-specific remedies to the household solid waste problems.

Belgium↗
PubMed2004

Fractal analysis of narwhal space use patterns.

Quantifying animal movement in response to a spatially and temporally heterogeneous environment is critical to understanding the structural and functional landscape influences on population viability. Generalities of landscape structure can easily be extended to the marine environment, as marine predators inhabit a patchy, dynamic system, which influences animal choice and behavior. An innovative use of the fractal measure of complexity, indexing the linearity of movement paths over replicate temporal scales, was applied to satellite tracking data collected from narwhals (Monodon monoceros) (n = 20) in West Greenland and the eastern Canadian high Arctic. Daily movements of individuals were obtained using polar orbiting satellites via the ARGOS data location and collection system. Geographic positions were filtered to obtain a daily good quality position for each whale. The length of total pathway was measured over seven different temporal length scales (step lengths), ranging from one day to one week, and a seasonal mean was calculated. Fractal dimension (D) was significantly different between seasons, highest during summer (D = 1.61, SE 0.04) and winter (D = 1.69, SE 0.06) when whales made convoluted movements in focal areas. Fractal dimension was lowest during fall (D = 1.34, SE 0.03) when whales were migrating south ahead of the forming sea ice. There were no significant effects of size category or sex on fractal dimension by season. The greater linearity of movement during the migration period suggests individuals do not intensively forage on patchy resources until they arrive at summer or winter sites. The highly convoluted movements observed during summer and winter suggest foraging or searching efforts in localized areas. Significant differences between the fractal dimensions on two separate wintering grounds in Baffin Bay suggest differential movement patterns in response to the dynamics of sea ice.

Journal Article↗