Efficient community detection in multilayer networks using boolean compositions.

Networks (or graphs) are used to model the dyadic relations between entities in complex systems. Analyzing the properties of the networks reveal important characteristics of the underlying system. However, in many disciplines, including social sciences, bioinformatics, and technological systems, multiple relations exist between entities.

GPU-Accelerated Flexible Molecular Docking.

Virtual screening is a key enabler of computational drug discovery and requires accurate and efficient structure-based molecular docking. In this work, we develop algorithms and software building blocks for molecular docking that can take advantage of graphics processing units (GPUs). Specifically, we focus on MedusaDock, a flexible protein-small molecule docking approach and platform.

Characteristics and safety assessment of intractable proteins in genetically modified crops.

Genetically modified (GM) crops may contain newly expressed proteins that are described as "intractable". Safety assessment of these proteins may require some adaptations to the current assessment procedures. Intractable proteins are defined here as those proteins with properties that make it extremely difficult or impossible with current methods to express in heterologous systems; isolate, purify, or concentrate; quantify (due to low levels); demonstrate biological activity; or prove equivalency with plant proteins.

Exploring antibiotic biosynthesis: Leo Vining's insights lead to new strategies in the quest for 'The 10 × '20 Initiative'.

The late Professor Leo Vining began his antibiotics research career as a visiting scientist in the laboratory of Selman Waksman at Rutgers University during the golden age of antibiotics. Through six decades of his distinguished career, Vining explored the biosynthesis of dozens of antibacterial and antifungal compounds produced by microorganisms. A number of underlying mechanisms of antibiotic biosynthesis were unraveled through his holistic approach and the findings laid the foundation to our understanding of regulation of antibiotic biosynthesis.

Preliminary safety assessment of a membrane-bound delta 9 desaturase candidate protein for transgenic oilseed crops.

A gene encoding delta 9 desaturase (D9DS), an integral membrane protein, is being considered for incorporation into oilseed crops to reduce saturated fatty acids and thus improve human nutritional value. Typically, a safety assessment for transgenic crops involves purifying heterologously produced transgenic proteins in an active form for use in safety studies. Membrane-bound proteins have been very difficult to isolate in an active form due to their inherent physicochemical properties.

Development of stable isotope and selenomethionine labeling methods for proteins expressed in Pseudomonas fluorescens.

Pseudomonas fluorescens is a robust protein expression system that is very well suited for high throughput protein expression for structural genomics studies. Since NMR spectroscopy and X-ray crystallography are both used by various investigators in structure elucidation studies, the availability of target proteins labeled with stable isotopes or selenomethionine is essential for the determination of protein structures. A completely defined medium for the expression and stable isotope labeling of proteins in P.

Expression of phosphinothricin N-acetyltransferase in Escherichia coli and Pseudomonas fluorescens: influence of mRNA secondary structure, host, and other physiological conditions.

Expression of a plant codon optimized pat gene encoding phosphinothricin acetyltransferase (PAT) in bacterial expression systems required modification of the 5' end of the pat ORF. Modifications necessary for improving the expression were identified by a coupled in vitro transcription and translation process. The dramatic improvement in the expression of PAT was due to the removal of a potential secondary structure that could have resulted in the inhibition of translational initiation.

Identification and characterization of the CYP52 family of Candida tropicalis ATCC 20336, important for the conversion of fatty acids and alkanes to alpha,omega-dicarboxylic acids.

Candida tropicalis ATCC 20336 excretes alpha,omega-dicarboxylic acids as a by-product when cultured on n-alkanes or fatty acids as the carbon source. Previously, a beta-oxidation-blocked derivative of ATCC 20336 was constructed which showed a dramatic increase in the production of dicarboxylic acids. This paper describes the next steps in strain improvement, which were directed toward the isolation and characterization of genes encoding the omega-hydroxylase enzymes catalyzing the first step in the omega-oxidation pathway.

Genes for the biosynthesis of spinosyns: applications for yield improvement in Saccharopolyspora spinosa.

Spinosyns A and D are the active ingredients in an insect control agent produced by fermentation of Saccharopolyspora spinosa. Spinosyns are macrolides with a 21-carbon, tetracyclic lactone backbone to which the deoxysugars forosamine and tri-O-methylrhamnose are attached. The spinosyn biosynthesis genes, except for the rhamnose genes, are located in a cluster that spans 74 kb of the S.

Rhamnose biosynthesis pathway supplies precursors for primary and secondary metabolism in Saccharopolyspora spinosa.

Rhamnose is an essential component of the insect control agent spinosad. However, the genes coding for the four enzymes involved in rhamnose biosynthesis in Saccharopolyspora spinosa are located in three different regions of the genome, all unlinked to the cluster of other genes that are required for spinosyn biosynthesis. Disruption of any of the rhamnose genes resulted in mutants with highly fragmented mycelia that could survive only in media supplemented with an osmotic stabilizer.

A cluster of genes for the biosynthesis of spinosyns, novel macrolide insect control agents produced by Saccharopolyspora spinosa.

Spinosyns A and D are the active ingredients in a family of insect control agents produced by fermentation of Saccharopolyspora spinosa. Spinosyns are 21-carbon tetracyclic lactones to which are attached two deoxysugars. Most of the genes involved in spinosyn biosynthesis are clustered in an 74 kb region of the S.

Cloning and analysis of the spinosad biosynthetic gene cluster of Saccharopolyspora spinosa.

Background: Spinosad is a mixture of novel macrolide secondary metabolites produced by Saccharopolyspora spinosa. It is used in agriculture as a potent insect control agent with exceptional safety to non-target organisms. The cloning of the spinosyn biosynthetic gene cluster provides the starting materials for the molecular genetic manipulation of spinosad yields, and for the production of novel derivatives containing alterations in the polyketide core or in the attached sugars.

DnrD cyclase involved in the biosynthesis of doxorubicin: purification and characterization of the recombinant enzyme.

Mutations in the Streptomyces peucetius dnrD gene block the ring cyclization leading from aklanonic acid methyl ester (AAME) to aklaviketone (AK), an intermediate in the biosynthetic pathway to daunorubicin (DNR) and doxorubicin. To investigate the role of DnrD in this transformation, its gene was overexpressed in Escherichia coli and the DnrD protein was purified to homogeneity and characterized. The enzyme was shown to catalyze the conversion of AAME to AK presumably via an intramolecular aldol condensation mechanism.

Production of the antitumor drug epirubicin (4'-epidoxorubicin) and its precursor by a genetically engineered strain of Streptomyces peucetius.

A fermentation method that bypasses the low-yielding semisynthesis of epirubicin (4'-epidoxorubicin) and 4'-epidaunorubicin, important cancer chemotherapy drugs, has been developed for Streptomyces peucetius. This bacterium normally produces the anthracycline antibiotics, doxorubicin and daunorubicin; the 4'-epimeric anthracyclines are formed by introducing the heterologous Streptomyces avermitilis avrE or Saccharopolyspora eryBIV genes into an S. peucetius dnmV mutant blocked in the biosynthesis of daunosamine, the deoxysugar component of these antibiotics.

Cloning and characterization of the Streptomyces peucetius dnmZUV genes encoding three enzymes required for biosynthesis of the daunorubicin precursor thymidine diphospho-L-daunosamine.

Characterization of the dnmZ, dnmU, and dnmV genes from the daunorubicin-producer Streptomyces peucetius by DNA sequence analysis indicated that these genes encode a protein of unknown function plus a putative thymidine diphospho-4-keto-6-deoxyglucose-3(5)-epimerase and thymidine diphospho-4-ketodeoxyhexulose reductase, respectively. Inactivation of each of the three genes by gene disruption and replacement in the wild-type strain demonstrated that all of them are required for daunosamine biosynthesis.

Functional characterization and transcriptional analysis of a gene cluster governing early and late steps in daunorubicin biosynthesis in Streptomyces peucetius.

Sequence analysis of the Streptomyces peucetius daunorubicin biosynthetic gene cluster revealed a partial (dnrQ) and two complete (dnrD and dnrP) open reading frames flanking dnrK. Bioconversion experiments showed that DnrD converts aklanonic acid methylester to aklaviketone and that DnrC is a methyltransferase that converts aklanonic acid to aklanonic acid methylester. The deduced dnrP gene product, homologous to known esterases, may catalyze the conversion of 10-carbomethoxy-13-deoxycarminomycin to its 10-carboxy derivative.

Functional characterization and transcriptional analysis of the dnrR1 locus, which controls daunorubicin biosynthesis in Streptomyces peucetius.

We previously proposed that the adjacent dnrIJ genes represent a two-component regulatory system controlling daunorubicin biosynthesis in Streptomyces peucetius on the basis of the homology of the DnrI and DnrJ proteins to other response regulator proteins and the effect of a dnrI::aphII mutation. In the present paper we report the results of work with the dnrI::aphII mutant in complementation, bioconversion, and transcriptional analysis experiments to understand the function of dnrI. For five putative operons in the sequenced portion of the S.

Characterization of the Streptomyces peucetius ATCC 29050 genes encoding doxorubicin polyketide synthase.

The dps genes of Streptomyces peucetius, encoding daunorubicin (DNR)-doxorubicin (DXR) polyketide synthase (PKS), are largely within an 8.7-kb region of DNA that has been characterized by Southern analysis, and gene sequencing, mutagenesis and expression experiments. This region contains nine ORFs, many of whose predicted products are homologous to known PKS enzymes.

Cloning and sequencing of a gene encoding carminomycin 4-O-methyltransferase from Streptomyces peucetius and its expression in Escherichia coli.

Sequence analysis of a portion of the Streptomyces peucetius daunorubicin biosynthetic gene cluster revealed a complete open reading frame (dnrK) that showed DNA and protein sequence homology to several O-methyltransferases. Expression of dnrK in Streptomyces lividans and Escherichia coli was done to show that this gene codes for carminomycin 4-O-methyltransferase. The deduced carminomycin 4-O-methyltransferase protein shows a conserved nucleotide binding site for its S-adenosyl-L-methionine cofactor.

Genetic control of polyketide biosynthesis in the genus Streptomyces.

The genetic control of polyketide metabolite biosynthesis in Streptomyces sp. producing actinorhodin, daunorubicin, erythromycin, spiramycin, tetracenomycin and tylosin is reviewed. Several examples of positively-acting transcriptional regulators of polyketide metabolism are known, including some two-component sensor kinase-response regulator systems.

Localization of the lysine epsilon-aminotransferase (lat) and delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (pcbAB) genes from Streptomyces clavuligerus and production of lysine epsilon-aminotransferase activity in Escherichia coli.

Lysine epsilon-aminotransferase (LAT) in the beta-lactam-producing actinomycetes is considered to be the first step in the antibiotic biosynthetic pathway. Cloning of restriction fragments from Streptomyces clavuligerus, a beta-lactam producer, into Streptomyces lividans, a nonproducer that lacks LAT activity, led to the production of LAT in the host. DNA sequencing of restriction fragments containing the putative lat gene revealed a single open reading frame encoding a polypeptide with an approximately Mr 49,000.

Lysine cataboism and α-aminoadipate synthesis in Streptomyces clavuligerus.

The intracellular α-aminoadipic acid pool in Streptomyces glavuligerus mycelium growing in a starch-peptone medium decreased during the late exponential and stationary phases when cephamycin was being produced; however, the amino acid accumulated extracellularly. Although the specific activity of lysine ɛ-aminotransferase (LAT) decreased during this period, there was no indication that the extracellular α-aminoadipic acid functioned as a precursor reserve for synthesis of the β-lactam antibiotic. Measurement of LAT activity in cultures grown in defined media with starch and various nitrogen sources indicated that the enzyme was synthesized preferentially only during early growth.

Cloning and location of a gene governing lysine epsilon-aminotransferase, an enzyme initiating beta-lactam biosynthesis in Streptomyces spp.

In actinomycetes that produce beta-lactam antibiotics of the cephem type, lysine epsilon-aminotransferase is the initial enzyme in the conversion of lysine to alpha-aminoadipic acid. We used a two-stage process ("chromosome walking") to screen a lambda library of Streptomyces clavuligerus genomic DNA for fragments that expressed lysine epsilon-aminotransferase activity in S. lividans.