83 research outputs found
Using Shareholder Notes to Eliminate Section 357(c) Gain: Lessinger v. Commissioner, 872 F.2d 519 (2d Cir. 1989), Correct Result, Wrong Reason
No full textDespite the rather specific statutory framework of Subchapter C of the Internal Revenue Code, which addresses the tax consequences of corporate formation, the courts have repeatedly been called upon to provide a gloss to the statutes to address situations not contemplated by Congress.\u27 In Lessinger v. Commissioner, the Second Circuit encountered a factual situation that compelled the court to again gloss over the plain meaning of the words in the applicable Internal Revenue Code sections to reach the appropriate result. This Article examines the action taken by the Second Circuit in Lessinger and addresses the propriety of the judicial manipulation of statutory language. Further, it examines whether the court arrived at the correct result by using an incorrect approach. Lastly, the author proposes an alternative to the currently accepted interpretation of the statutory language that would make the Second Circuit\u27s approach in Lessinger unnecessary and would not necessitate further legislative action to bring the factual pattern presented by Lessinger within the ambit of the existing statutory objective
Using Shareholder Notes to Eliminate Section 357(c) Gain: Lessinger v. Commissioner, 872 F.2d 519 (2d Cir. 1989), Correct Result, Wrong Reason
No full textDespite the rather specific statutory framework of Subchapter C of the Internal Revenue Code, which addresses the tax consequences of corporate formation, the courts have repeatedly been called upon to provide a gloss to the statutes to address situations not contemplated by Congress.\u27 In Lessinger v. Commissioner, the Second Circuit encountered a factual situation that compelled the court to again gloss over the plain meaning of the words in the applicable Internal Revenue Code sections to reach the appropriate result. This Article examines the action taken by the Second Circuit in Lessinger and addresses the propriety of the judicial manipulation of statutory language. Further, it examines whether the court arrived at the correct result by using an incorrect approach. Lastly, the author proposes an alternative to the currently accepted interpretation of the statutory language that would make the Second Circuit\u27s approach in Lessinger unnecessary and would not necessitate further legislative action to bring the factual pattern presented by Lessinger within the ambit of the existing statutory objective
AMiGA: the arthropodan mitochondrial genomes accessible database
No full textFeijão P, Neiva LS, Azeredo-Espin AML d., Lessinger AC. AMiGA: the arthropodan mitochondrial genomes accessible database. Bioinformatics. 2006;22(7):902-903
TaxMan: a taxonomic database manager
No full textAbstract Background Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes) can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study. Results TaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level) and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy. Conclusion TaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of both annotation and BLAST similarity, it ensures that all available sequence data can be brought to bear on a phylogenetic problem, but remains fast enough to cope with many thousands of records. By automatically assisting in the selection of the best subset of taxa to address a particular phylogenetic problem, TaxMan greatly speeds up the process of generating multiple sequence alignments for phylogenetic analysis. Our results indicate that an automated phylogenetic workbench can be a useful tool when correctly guided by user knowledge.</p
Isolation And Characterization Of Polymorphic Microsatellite Loci For The Horn Fly, Haematobia Irritans (l.) (diptera: Muscidae)
No full textThe horn fly, Haematobia irritans (L.) (Diptera: Muscidae), is a cosmopolitan livestock pest that has caused a great negative impact on the animal production sector throughout the world. Here, we describe 10 polymorphic microsatellite loci isolated from H. irritans. The number of alleles found ranged from two to eight per locus and the expected heterozygosity from 0.1421 to 0.7702. These loci are potentially useful for the fine-scale genetic characterization of horn fly populations and provide fundamental information for pest management and planning of control programs. © 2008 The Authors.85971973Byford, R.L., Craig, M.E., Derouen, S.M., Al, E., Influence of permethrin, diazinon and ivermectin treatments on insecticide resistance in the horn fly (Diptera: Muscidae) (1999) International Journal of Parasitology, 29 (1), pp. 125-135Castiglioni, L., De Campos Bicudo, H.E., Molecular characterization and relatedness of Haematobia irritans (horn fly) populations, by RAPD-PCR (2005) Genetica, 124 (1), pp. 11-21Infante-Vargas, M.E., Azeredo-Espin, A.M.L., Genetic variability in mitochondrial DNA of screwworm, Cochiomyia hominivorax (Diptera: Calliphoridae), from Brazil (1995) Biochemical Genetics, 33, pp. 737-756Oliveira, M.T., De Azeredo-Espin, A.M., Lessinger, A.C., Evolutionary and structural analysis of the cytochrome c oxidase subunit I (COI) gene from Haematobia irritans, Stomoxys calcitrans and Musca domestica (Diptera: Muscidae) mitochondrial DNA (2005) DNA Sequence, 16 (2), pp. 156-160Oliveira, M.T., Da Rosa, A.C., Azeredo-Espin, A.M.L., Lessinger, A.C., Improving access to the control region and tRNA gene clusters of Dipteran mitochondrial DNA. (2006) Journal of Medical Entomology, 43 (3), pp. 636-639Oliveira, M.T., Azeredo-Espin, A.M.L., Lessinger, A.C., The Mitochondrial DNA Control Region of Muscidae Flies: Evolution and Structural Conservation in a Dipteran Context. (2007) Journal of Molecular Evolution, 64 (3), pp. 519-527Raymond, M., Rousset, F., Genepop (version 1.2): Population genetics software for exact tests and ecumenicism (1995) Journal of Heredity, 86 (3), pp. 248-249Rice, W.R., Analyzing tables of statistical tests (1989) Evolution, 43, pp. 223-225Rozen, S., Skaletsky, H.J., (1998) Primer 3, , http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi, Code available atSambrook, J., Maniatis, T., Fritsch, E.F., (1989) Molecular Cloning: A Laboratory Manual, , 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New YorkTorres, T.T., Azeredo-Espin, A.M.L., Development of new polymorphic microsatellite markers for the New World screw-worm Cochliomyia hominivorax (Diptera: Calliphoridae) (2005) Molecular Ecology Notes, 5, pp. 815-81
IFCC primary reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 °C. Part 9 : reference procedure for the measurement of catalytic concentration of alkaline phosphatase International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) Scientific Division, Committee on Reference Systems of Enzymes (C-RSE) (1))
No full textAbstract This paper is the ninth in a series dealing with reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 °C and the certification of reference preparations. Other parts deal with: Part 1. The concept of reference procedures for the measurement of catalytic activity concentrations of enzymes; Part 2. Reference procedure for the measurement of catalytic concentration of creatine kinase; Part 3. Reference procedure for the measurement of catalytic concentration of lactate dehydrogenase; Part 4. Reference procedure for the measurement of catalytic concentration of alanine aminotransferase; Part 5. Reference procedure for the measurement of catalytic concentration of aspartate aminotransferase; Part 6. Reference procedure for the measurement of catalytic concentration of γ-glutamyltransferase; Part 7. Certification of four reference materials for the determination of enzymatic activity of γ-glutamyltransferase, lactate dehydrogenase, alanine aminotransferase and creatine kinase at 37 °C; Part 8. Reference procedure for the measurement of catalytic concentration of α-amylase. The procedure described here is derived from the previously described 30 °C IFCC reference method. Differences are tabulated and commented on in Appendix 1
Evolutionary And Structural Analysis Of The Cytochrome C Oxidase Subunit I (coi) Gene From Haematobia Irritans, Stomoxys Calcitrans And Musca Domestica (diptera: Muscidae) Mitochondrial Dna
No full textThis work describes the molecular characterization of the cytochrome c oxidase subunit I (COI) gene of the mitochondrial DNA from three species of great medical and veterinary importance: the horn fly, Haematobia irritans, the stable fly, Stomoxys calcitrans and the house fly, Musca domestica (Diptera: Muscidae) (Linnaeus). The nucleotide sequence in all species was 1536 bp in size and coded for a 512 amino acid peptide. The nucleotide bias for an A + T-rich sequence is linked to three features: a high A + T content throughout the entire gene, a high A + T content in the third codon position, and a predominance of A + T-rich codons. An anomalous TCG (serine) start codon was identified. Comparative analysis among members of the Muscidae, Scatophagidae, Calliphoridae and Drosophilidae showed high levels of nucleotide sequence conservation. Analysis of the divergent amino acids and COI protein topologies among these three Muscidae species agreed with the evolutionary model suggested for the insect mitochondrial COI protein. The characterization of the structure and evolution of this gene could be informative for further evolutionary analysis of dipteran species. © 2005 Taylor & Francis Ltd.162156160Beard, C.B., Hamm, D.M., Collins, F.H., The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects (1993) Insect Mol Biol, 2, pp. 103-124Bernasconi, M.V., Valsangiacomo, C., Piffaretti, J.C., Ward, P.I., Phylogenetic relationships among Muscoidea (Diptera: Calyptratae) based on mitochondrial DNA sequences (2000) Insect Mol Biol, 9, pp. 67-74Caterino, M.S., Cho, S., Sperling, F.A.H., The current state of insect molecular systematics: A thriving Tower of Babel (2000) Annu Rev Entomol, 45, pp. 1-54Crozier, R.H., Crozier, Y.C., The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization (1993) Genetics, 133, pp. 97-117Foster, P.G., Jermiin, L.S., Hickey, D.A., Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria (1997) J Mol E, 44, pp. 282-288Greenberg, B., Flies and disease (1973) Biology and Disease Transmission, 2. , New Jersey: University Press PrincetownInfante, M.E., Azeredo-Espin, A.M.L., Genetic variability in mitochondrial DNA of screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), from Brazil (1995) Biochem Genet, 33, pp. 737-756Kumar, S., Tamura, K., Nei, M., (1993) MEGA: Molecular Evolutionary Genetics Analysis, Version 1.01, , University Park, Pennsylvania: The Pennsylvania State UniversityLessinger, A.C., Azeredo-Espin, A.M.L., Evolution and structural organisation of mitochondrial DNA control region of myiasis-causing flies (2000) Med Vet Entomol, 14, pp. 71-80Litjens, P., Lessinger, A.C., Azeredo-Espin, A.M.L., Characterization of the screwworm flies Cochliomyia hominivorax and Cochliomyia macellaria by PCR-RFLP of mitochondrial DNA (2001) Med Vet Entomol, 15, pp. 183-188Lunt, D.H., Zhang, D.-X., Szymura, J.M., Hewitt, G.M., The insect cytochrome oxidase I gene: Evolutionary patterns and conserved primers for phylogenetic studies (1996) Insect Mol Biol, 5, pp. 153-165Morlais, I., Severson, D.W., Complete mitochondrial DNA sequence and amino acid analysis of the cytochrome c oxidase subunit I (COI) from Aedes aegypti (2002) DNA Seq, 13, pp. 123-127Nirmala, X., Hypsa, V., Zurovec, M., Molecular phylogeny of Calyptratae (Diptera: Brachycera): The evolution of 18S and 16S ribosomal rDNAs in higher dipterans and their use in phylogenetic inference (2001) Insect Mol Biol, 10, pp. 475-485Saccone, C., De Giorgi, C., Gissi, C., Pesole, G., Reyes, A., Evolutionary genomics in Metazoa: The mitochondrial DNA as a model system (1999) Gene, 238, pp. 195-209Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H., Flook, P., Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers (1994) Ann Entomol Soc Am, 87, pp. 651-701Szalanski, A.L., Owens, C.B., Sequence change and phylogenetic signal in muscoid COII DNA sequences (2003) DNA Seq, 14, pp. 331-334Tajima, F., Nei, M., Estimation of evolutionary distance between nucleotide sequences (1984) Mol Biol Evol, 1, pp. 269-285Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools (1997) Nucleic Acids Research, 25, pp. 4876-488
Characterization Of The Screwworm Flies Cochliomyia Hominivorax And Cochliomyia Macellaria By Pcr-rflp Of Mitochondrial Dna.
No full textThe primary screwworm fly Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) is one of the most important insect pests of livestock in neotropical regions, whereas Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae), the secondary screwworm, is of medical and sanitary importance because of its role in the dissemination of pathogens. These two species share morphological similarities and both may occur in the same myiasis, but in different developmental stages. In this work, the usefulness of PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism) of mitochondrial DNA (mtDNA) for the unambiguous identification of C. hominivorax and C. macellaria was investigated. Two specific regions of mtDNA were amplified: 870bp from Cytochrome oxidase subunit I and 2100bp from the A+T rich/12S region from C. hominivorax and C. macellaria specimens from different areas of Brazil. Reliable species-specific PCR-RFLP results were obtained for the CO I region and the A+T rich/12S region using the restriction enzymes Dra I and Ssp I. These results confirm the conservation of CO I diagnostic restriction sites previously reported and demonstrate the usefulness of the control region sequences as an efficient marker for PCR-RFLP identification of Brazilian screwworm flies. The occurrences of intraspecific polymorphic patterns are discussed based on frequencies and potential conflicts for species identification. PCR-RFLP provides a potentially useful method for identifying samples from the areas where these species are monitored.15183-
Molecular mechanism of the hepatitis C vitus core protein chaperone properties : physicochemical investigation by fluorescence and surface plasmon resonance
No full textLa protéine core de virus de l’hépatite C (HCV) est l’une des dix protéines codées par l’ARN génomique de 9.6kb du virus. C’est une protéine chaperonne multifonctionnelle impliquée dans plusieurs processus viraux comme la prolifération cellulaire, la différentiation, l’encapsidation de l’ARN, la formation de la nucléocapside, et la variabilité génétique. Grâce à ses propriétés de chaperonne, le domaine D1 dimérise la région 3’ non traduite (3’UTR) de l’ARN génomique. Cependant le mécanisme de cette activité chaperonne ainsi que l’interaction entre la protéine Core et différents oligonucléotides de la partie 3’ de l’ARN restent inconnus. Dans ce but, nous avons utilisé différentes approches de fluorescence et la
résonance plasmonique de surface. Ainsi, en utilisant le peptide D1, correspondant à un fragment de la protéine core, ainsi que plusieurs dérivés de ce peptide nous avons caractérisé les paramètres de l’interaction et montré que la protéine core se lie spécifiquement aux oligonucléotides en tige-boucle de la partie 3’. Ensuite, nous avons suivi la conformation de ces oligonucléotides et montré que la protéine core n’est pas capable de déstabiliser leur
structure secondaire. Enfin, nous avons décrit au niveau moléculaire le mécanisme permettant à la protéine core d’hybrider des oligonucléotides complémentaires et montré que la cinétique d’hybridation repose sur une réaction à deux étapes impliquant un contact boucle-boucle. Ce
travail devrait nous permettre de mieux comprendre le rôle de la protéine core lors de l’encapsidation et la transcription de l’ARN et notamment dans les mécanismes de
recombinaison expliquant les variations génétiques du virus.Open reading frame (ORF) of 9.6kb HCV genomic RNA encodes at least 10 proteins, 4 structural and 6 non-structural, during translation process. The core is one of those 4 structural proteins and considered as a multifunctional chaperone involving in several viral processes like cell proliferation, differentiation, RNA packaging, nucleocapsid formation and recombinant genetic variability. With the virtue of its chaperone properties, Domain D1 dimerises the 3’ untranslated region (3’ UTR) of the genomic RNA. However, the mechanism of the core chaperone activity in the dimerisation of the genomic RNA and in binding with its
target nucleic acids are still unknown and were investigated in this present project. To reach this objective, we used fluorescence and surface plasmon resonance (SPR) techniques. By using the native D1 domain and peptides derived from this domain, we first characterized the binding parameters and the conformational changes associated with the binding of these peptides to the native and mutated sequences from HCV 3’ UTR sequences. Next, we investigated the destabilization of model and HCV ODNs secondary structure by the D1 domain and its mutants and found that core peptides only marginally destabilise the secondary structures of ODNs. In a last step, we described the molecular mechanisms of the core chaperone properties based on the hybridization kinetics of various HCV and model oligonucleotides. These chaperone properties of core are thought to intervene in processes like the encapsidation, the synthesis of the complementary strand of the genomic RNA and the recombination mechanisms participating to the genetic variability of the virus
Traceability of values for catalytic activity concentration of enzymes : a certified reference material for aspartate transaminase
No full textBackground: A new reference material for the liver enzyme aspartate transaminase (AST) (L-aspartate: 2-oxoglutarate-aminotransferase, EC 2.6.1.1), also called aspartate aminotransferase (ASAT), has been developed under the code ERM-AD457/IFCC. This certified reference material (CRM) for AST has been produced from a human type recombinant AST expressed in Escherichia coli and a buffer containing bovine serum albumin, and has been lyophilised.
Methods: The homogeneity and the stability of the material have been tested and the catalytic activity concentration has been characterised by 12 laboratories using the reference procedure for AST at 37 degrees C from the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC).
Results: The certified catalytic activity concentration and certified uncertainty of AST in the reconstituted material are (1.74 +/- 0.05) mkat/L or (104.6 +/- 2.7) U/L (with a coverage factor k = 2; 95% confidence interval).
Conclusions: Both the certified value and uncertainty are traceable to the International System of Units (SI). The material is aiming to control the IFCC reference procedure for AST at 37 degrees C, which will then be used to assign values to calibrants and control materials. The present paper highlights the scientific challenges and innovations which were encountered during the development of this new CRM
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