Biomedical subjects

R A Prade

Publications and source records attributed to R A Prade.

7 recordsLinked to original sources

PubMed1996

Xylanases: from biology to biotechnology.

Xylan is the main carbohydrate found in the hemicellulosic fraction of plant tissues and accounts for one third of all renewable organic carbon available on earth. Xylanase, the major component of an enzymatic consortium, acts in nature by depolymerizing xylan molecules into monomeric pentosan units that are used by bacterial and fungal populations as a primary carbon source. Xylanase producers have been isolated from all ecological niches where plant material is deposited, and microorganisms often contain multiple loci encoding overlapping xylanolytic functions. The numerical excess of genes and the extensive sharing of structural features within beta-glycanase families suggests that extensive gene duplication and conversion events have occurred during xylanase evolution. Hydrolysis of beta-glycosidic linkages is sponsored by a general acid catalytic reaction common to all glycanases, whereas substrate recognition is specified by subsites that interact with adjacent glycosyl units. Under natural conditions xylanases are inducible by the products of their own action and subject to carbon catabolite repression. Bleaching paper pulps with xylanases is the first successful commercial application for these enzymes. The recovery of cellulosic textile fibers is the next logical application and bioconversion of biomass into fuels and chemicals, remains the ultimate target. Recent developments have shown that metabolic pathways can be transferred from one organism to another and proteins can be modified to gain conformational stability, suggesting that naturally occurring systems can be custom engineered to the situation in the fermentation tank. Thus, biotechnologies developed to transform biomass into marketable products that gradually substitute materials derived from non-renewable resources are becoming commercially worthwhile.

Bacteria↗

PubMed1996

On the consistency of a physical mapping method to reconstruct a chromosome in vitro.

During recent years considerable effort has been invested in creating physical maps for a variety of organisms as part of the Human Genome Project and in creating various methods for physical mapping. The statistical consistency of a physical mapping method to reconstruct a chromosome, however, has not been investigated. In this paper, we first establish that a model of physical mapping by binary fingerprinting of DNA fragments is identifiable using the key assumption-for a large randomly generated recombinant DNA library, there exists a staircase of DNA fragments across the chromosomal region of interest. Then we briefly introduce epi-convergence theory of variational analysis and transform the physical mapping problem into a constrained stochastic optimization problem. By doing so, we prove epi-convergence of the physical mapping model and epi-convergence of the physical mapping method. Combining the identifiability of our physical mapping model and the epi-convergence of a physical mapping method, finally we establish strong consistency of a physical mapping method.

Aspergillus nidulans↗

PubMed1994

A fast random cost algorithm for physical mapping.

Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational/statistical problem in genetics. Here we present a physical mapping algorithm for creating ordered genomic libraries or contig maps by using a random cost approach [Berg, A. (1993) Nature (London) 361, 708-710]. This random cost algorithm is 5-10 times faster than existing physical mapping algorithms and has optimization performance comparable to existing procedures. The speedup in the algorithm makes practical the widespread use of bootstrap resampling to assess the statistical reliability of links in the physical map as well as the use of more elaborate physical mapping criteria to improve map quality. The random cost algorithm is illustrated by its application in assembling a physical map of chromosome IV from the filamentous fungus Aspergillus nidulans.

Aspergillus nidulans↗

PubMed1994

The Penicillium chrysogenum and Aspergillus nidulans wetA developmental regulatory genes are functionally equivalent.

Aspergillus nidulans and Penicillium chrysogenum are related fungi that reproduce asexually by forming multicellular conidiophores and uninucleate conidia. In A. nidulans, spore maturation is controlled by the wetA (AwetA) regulatory gene. We cloned a homologous gene (PwetA) from P. chrysogenum to determine if spore maturation is regulated by a similar mechanism in this species. The PwetA and AwetA genes are similar in structure and functional organization. The inferred polypeptides share 77% overall amino acid sequence similarity, with several regions having > 85% similarity. The genes also had significant, local sequence similarities in their 5' flanking regions, including conserved binding sites for the product of the regulatory gene abaA. PwetA fully complemented an A. nidulans wetA deletion mutation, demonstrating that PwetA and its 5' regulatory sequences function normally in A. nidulans. These results indicate that the mechanisms controlling sporulation in A. nidulans and P. chrysogenum are evolutionarily conserved.

Amino Acid Sequence↗

PubMed1994

ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling.

In the program ODS_BOOTSTRAP we provide a methodology for quickly ordering clones in a genomic library into a physical map and for applying a statistical tool known as the bootstrap to assess the statistical reliability of a clonal ordering. Each clone is assigned a binary fingerprint by one of a variety of experimental approaches to physical mapping. For example, the binary fingerprints might be generated by hybridizing a panel of m probes to a library of n clones. The resulting n x m binary data matrix, X, is input to ODS_BOOTSTRAP, which utilizes the similarity in binary fingerprints of clones to construct a physical map. Under this particular implementation of bootstrap resampling, the m probes (or columns of the data matrix) are sampled randomly with replacement in the computer to generate a new n x m data matrix, X*, from which a second physical map is constructed. The resampling process is repeated 100 or more times to generate 100 or more X* matrices. The resulting 100 or more physical maps are compared with the original physical map based on the original data matrix X by counting how often links in the original physical map reappear. Three confidence statistics are introduced for each link in a physical map. The statistic C1 is defined as the percentage of time two neighboring clones on the original map reappear as neighbors under resampling. The statistic C2 is defined as the percentage of time that two neighboring clones i and j on the original map reappear as neighbors or that a clone with an identical binary fingerprint to clone i reappears as a neighbor to clone j. The statistic C3 is defined as the percentage of time that two neighboring clones on the original map reappear in the same contig under resampling.

Algorithms↗

PubMed1993

The Aspergillus nidulans brlA regulatory locus consists of overlapping transcription units that are individually required for conidiophore development.

The Aspergillus nidulans brlA locus controls conidiophore development in conjunction with the products of several other regulatory loci. In this paper, we show that the brlA locus consists of overlapping transcription units, designated alpha and beta, with alpha transcription initiating within beta intronic sequences. The predicted BrlA polypeptides differ by 23 amino acid residues at their N-termini. Targeted mutations specifically eliminating either the alpha or beta transcript led to developmental abnormalities similar to those produced by previously identified hypomorphic mutants, showing that both transcripts have essential functions for normal development. However, provision of additional doses of alpha in a beta- strain or of beta in an alpha- strain remediated the developmental defects, indicating that the polypeptides have redundant functions. It is likely that differential regulation of alpha and beta expression in the wild type is important for the initiation and temporal regulation of development.

Amino Acid Sequence↗

PubMed1982

Role of sulfhydryl compounds in the control of tyrosinase activity in Neurospora crassa.

It is known that Neurospora crassa mycelia cultured in standard concentrations (76 to 190 micrograms/ml) of sulfate accumulate a low molecular weight inhibitor of tyrosinase (monophenol, dihydroxyphenylalanine: oxygen oxidoreductase; EC 1.14.1.18.1.). This is not observed in cultures grown under sulfate-limiting conditions. The chemical nature of tyrosinase inhibition was investigated. It was shown to be due to the low molecular weight sulfhydryl fraction of the extracts, in which glutathione is predominant. The concentration of low molecular weight sulfhydryl compounds decreased sharply in mycelia submitted to various treatments which also derepressed tyrosinase, such as (i) starvation in phosphate buffer, (ii) treatment with cycloheximide, and (iii) mating. These results suggest that the concentration of sulfhydryl compounds may be of physiological significance in the control of tyrosinase activity in N. crassa.

Catechol Oxidase↗