8 research outputs found
Constant-Weight and Constant-Charge Binary Run-Length Limited Codes
Constant-weight and constant-charge binary sequences with constrained run
length of zeros are introduced. For these sequences, the weight and the charge
distribution are found. Then, recurrent and direct formulas for calculating the
number of these sequences are obtained. With considering these numbers of
constant-weight and constant-charge RLL sequences as coefficients of convergent
power series, generating functions are derived. The fact, that generating
function for enumerating constant-charge RLL sequences does not have a closed
form, is proved. Implementation of encoding and decoding procedures using
Cover's enumerative scheme is shown. On the base of obtained results, some
examples, such as enumeration of running-digital-sum (RDS) constrained RLL
sequences or peak-shifts control capability are also provided.Comment: 29 pages, submitted to IEEE Transactions on Information Theory. This
paper is a corrected version of a paper with the same title that appeared on
the arXiv in Feb. 2009. The major change is in Section VI, in which
Subsection D is now well define
Role of a novel iron transport system in Brucella pathogenicity and intracellular survival
The mbfA (membrane bound ferritin A) gene is carried by all Brucella species and is widely conserved in α-Proteobacteria. mbfA encodes a novel iron-export protein
comprising an N-terminal peroxide reductase (erythrin) domain and a C-terminal, membrane-embedded, iron-export domain (vacuolar iron transport, VIT). In this thesis,
for the first time, the role of mbfA in Brucella suis 1330 and Brucella melitensis 16M was investigated, and the contributions of the two domains towards a novel mechanism of oxidative-stress resistance was considered. In addition, any part played by MbfA in enhancing Brucella survival within the macrophage âBrucella-containing vacuoleâ (BCV) was investigated. The isolated erythrin domain was shown to bind two iron atoms (as expected) or zinc which stabilized the protein, but no substantive peroxidase activity was exhibited,
presumably due to lack of a reduction partner. mbfA complemented an E. coli mutant that was devoid of catalases/alkyl-hydroperoxidases, enhanced growth of a fur mutant with deregulated iron uptake, and impaired growth of a mutant lacking iron-uptake capacity. These findings support a role for MbfA in peroxide resistance and iron export. MbfA was shown to export 55Fe when expressed in E. coli, and this activity was found to be O2 and H2O2 dependent. Similar results were obtained using a Burkholderia multivorans mbfA mutant. In addition, MbfA mediated the decomposition of exogenous H2O2, which was mainly achieved by degradation of exogenous peroxide by exported iron. MbfA provided peroxide resistance in wildtype E. coli but only when
endogenous catalases/peroxidases were inhibited by NO. Thus, MbfA is not markedly NO inhibited. MbfA iron export was found to be partly dependent on the presence of
iron stores, in the form of bacterioferritin. A naturally-occurring single-nucleotide substitution in the proximal coding region of the mbfA gene renders this gene cryptic in B. melitensis (although mbfA appears
functional in all other Brucella spp.). Thus, a B. melitensis mbfA mutant exhibited no observable phenotype whereas a B. suis mbfA mutant displayed enhanced sensitivity to both Fe2+- and H2O2-mediated oxidative stress. It is hypothesized that MbfA exports ferric iron into the luminal space of the endosomal Brucella-containing vacuole (eBCV) to counteract both the respiratory burst generated by NADPH oxidase as well as the export of iron into the macrophage cytoplasm by NRAMP1. Exported iron causes disproportionation of peroxide externally, thus reducing the potential for harmful oxygen- and nitrogen-radical formation within the bacterial cell. Macrophage survival assays show that the absence of functional mbfA decreases intracellular survival during the early colonization phase in the eBCV, suggesting a reduced capacity to resist the redox stress of the endosomal and transient lysosomal compartments in the macrophage, which precede transition to the replicative BCV. Additionally, in vivo, mbfA contributes
significantly to the maintenance of chronic infection within the murine liver and spleen. Further, MbfA provided a greater advantage in NRAMP1+ macrophages, than
in NRAMP1- macrophages. This finding supports a role for MbfA in countering the iron export role of NRAMP1 within the phagolysosome, such that the purpose of this NRAMP1 actiy would be to preserve peroxide against iron-catalysed degradation. In summary, the results are therefore consistent with a role for mbfA in intracellular survival and redox stress resistance in Brucella
Metabonomic analysis of Drosophila mutants using high resolution mass spectrometry
The availability of fully sequenced genomes of model organisms such as Drosophila and their subsequent annotation has afforded opportunities for reverse genetics in a complex model organism. Metabonomics used as an aid to functional genomics can be used to understand the functions of genes in living systems. Thus metabonomics has been employed to study Drosophila samples extracted from whole animals at different developmental stages or in response to external stimuli or genetic mutation. With unmatched mass resolution, accuracy, and detection sensitivity, linear ion trap - Fourier Transform Orbitrap Mass Spectrometry (LTQ-Orbitrap-MS) has the potential for high throughput metabonomic analysis. Five different but linked studies are reported in this work. A global metabolic profiling method based on electrospray ionisation mass spectrometry was developed for Drosophila melanogaster metabolites. The method involved optimizing the extraction of Drosophila metabolites followed by analysis using liquid chromatography coupled with high-resolution mass spectrometry. The effect of extraction conditions and storage were studied, thus 750-800 metabolites were putatively identified in order to obtain the metabolite profiles of Drosophila reference strains and mutants. Metabolic studies were carried out to elucidate gene functions using established protocols. The online resource FlyAtlas.org provides detailed microarray-based expression data for the tissues and life-stages of Drosophila. Since downstream genes, such as urate oxidase are tubule-specific, an Orbitrap technology has been used to elucidate tissue specific metabolomes. Additionally, genetic interventions using designed RNA interference were also made and validated by qPCR and metabonomics. The method produced a new opportunity for metabonomics use in validating gene expressions. The xanthine oxidase inhibitor allopurinol was used to phenocopy the rosy mutation which caused the levels of xanthine and hypoxanthine to rise while the levels of uric acid fell. In addition, many unexpected metabolic changes followed this treatment with effects on the pentose phosphate pathway and tryptophan metabolism being the most marked. The yellow (y) gene was first discovered in Drosophila, but occurs in many insect species and in some bacteria. The y protein is similar to the major royal jelly proteins produced by bees. Metabolomic profiling was carried out on Oregon R (OR) and y Drosophila larvae at the third instar. There were numerous metabolic differences between the metabolic profiles of OR and y. Phenylalanine, tyrosine and DOPA were all elevated in y, as might be expected since the mutation blocks melanin biosynthesis. In addition, there were other metabolic effects including marked effects on to lysine metabolism. The white mutation of Drosophila, which affects ABC transporters, was studied with regards to its effect on pigment biosynthesis in Drosophila. In addition to the expected effects on pigments there were interesting male/female differences possibly related to the presence of the white gene in the X chromosome. In addition the effect of salt stess on wild type and white flies was studied. Overall, LTQ-Orbitrap-MS proved suitable for metabonomic analysis of both wild-type and mutant Drosophila and had potential in the analysis of metabolomes of single tissues. The possibility of using Orbitrap-based metabonomics in combination with Drosphila for drug testing is discussed and is a goal for the future.The availability of fully sequenced genomes of model organisms such as Drosophila and their subsequent annotation has afforded opportunities for reverse genetics in a complex model organism. Metabonomics used as an aid to functional genomics can be used to understand the functions of genes in living systems. Thus metabonomics has been employed to study Drosophila samples extracted from whole animals at different developmental stages or in response to external stimuli or genetic mutation. With unmatched mass resolution, accuracy, and detection sensitivity, linear ion trap - Fourier Transform Orbitrap Mass Spectrometry (LTQ-Orbitrap-MS) has the potential for high throughput metabonomic analysis. Five different but linked studies are reported in this work. A global metabolic profiling method based on electrospray ionisation mass spectrometry was developed for Drosophila melanogaster metabolites. The method involved optimizing the extraction of Drosophila metabolites followed by analysis using liquid chromatography coupled with high-resolution mass spectrometry. The effect of extraction conditions and storage were studied, thus 750-800 metabolites were putatively identified in order to obtain the metabolite profiles of Drosophila reference strains and mutants. Metabolic studies were carried out to elucidate gene functions using established protocols. The online resource FlyAtlas.org provides detailed microarray-based expression data for the tissues and life-stages of Drosophila. Since downstream genes, such as urate oxidase are tubule-specific, an Orbitrap technology has been used to elucidate tissue specific metabolomes. Additionally, genetic interventions using designed RNA interference were also made and validated by qPCR and metabonomics. The method produced a new opportunity for metabonomics use in validating gene expressions. The xanthine oxidase inhibitor allopurinol was used to phenocopy the rosy mutation which caused the levels of xanthine and hypoxanthine to rise while the levels of uric acid fell. In addition, many unexpected metabolic changes followed this treatment with effects on the pentose phosphate pathway and tryptophan metabolism being the most marked. The yellow (y) gene was first discovered in Drosophila, but occurs in many insect species and in some bacteria. The y protein is similar to the major royal jelly proteins produced by bees. Metabolomic profiling was carried out on Oregon R (OR) and y Drosophila larvae at the third instar. There were numerous metabolic differences between the metabolic profiles of OR and y. Phenylalanine, tyrosine and DOPA were all elevated in y, as might be expected since the mutation blocks melanin biosynthesis. In addition, there were other metabolic effects including marked effects on to lysine metabolism. The white mutation of Drosophila, which affects ABC transporters, was studied with regards to its effect on pigment biosynthesis in Drosophila. In addition to the expected effects on pigments there were interesting male/female differences possibly related to the presence of the white gene in the X chromosome. In addition the effect of salt stess on wild type and white flies was studied. Overall, LTQ-Orbitrap-MS proved suitable for metabonomic analysis of both wild-type and mutant Drosophila and had potential in the analysis of metabolomes of single tissues. The possibility of using Orbitrap-based metabonomics in combination with Drosphila for drug testing is discussed and is a goal for the future
Encoding of dklr-sequences using one weight set
The decoding function can be accomplished with a simple logic array. Note that the code above can easily be transformed into a (d = 1, k = 11) RLL code by representing the source word â2 â by â000000 â or â111111. â If Q, ~6 = 00, then represent the source word â2 â by â000000. â It should be appreciated that the smallest block-decodable conventional rate 2/3 (d = 1, k = 11) code requires a codeword length of n = 18. This clearly shows that a design of an RLL code which is not a (d, k) code plus precoder can be quite advantageous. IV. CONCLUSIONS We have presented a new rate 4/6 (d = 1, k = 11) runlength-limited code. The code is block-decodable, and it is particularly attractive as many commercially available Reed-Solomon codes operate in GF (2â). The encoder can be implemented with a simple 6-bit ROM, and decoding can be accomplished with a logic array
1997-1998 Louisiana Tech Catalog
The Louisiana Tech University Catalog includes announcements and course descriptions for courses offered at Louisiana Tech University for the academic year of 1997-1998.https://digitalcommons.latech.edu/university-catalogs/1017/thumbnail.jp