Effect of electron beam and gamma radiation on drug-susceptible and drug-resistant Listeria monocytogenes strains in salmon under different temperature.

AIMS: To investigate the effect of gamma radiation and high energy electron beam doses on the inactivation of antibiotic-susceptible and antibiotic-resistant Listeria monocytogenes strains inoculated on the surface of raw salmon fillets stored at different temperature (-20, 4 and 25°C). METHODS AND RESULTS: The population of bacteria strains resistance to penicillin, ampicillin, meropenem, erythromycin and trimethoprim-sulfamethoxazole was generated. When using gamma irradiation, the theoretical lethal dose ranged from 1·44 to 5·68 kGy and for electron beam the values ranged from 2·99 to 6·83 kGy. The theoretical lethal dose for both radiation methods was higher for antibiotic-resistant strains. Gamma radiation proved to be a more effective method for extending salmon fillet shelf-life. The evaluation of pulsed-field gel electrophoresis electrophoregram revealed that the repair of radiation-caused DNA damage occurred faster in antibiotic-resistant L. monocytogenes strains. The number of live L. monocytogenes cells, 40 h after irradiation, also was higher in antibiotic-resistant strain suspension. CONCLUSIONS: The present study showed that gamma radiation was more effective in the elimination of the tested micro-organisms and food preservation, than a high energy electron beam. The antibiotic-resistant L. monocytogenes strains were more resistant to both radiation methods. SIGNIFICANCE AND IMPACT OF THE STUDY: There are a lot of research on the effect of radiation on the number of bacteria in food products. However, there is almost no information about the effect of strain properties, such as drug susceptibility, virulence, etc., on their resistance to ionizing radiation. An increasing number of drug resistant bacterial strains isolated from food, encourages to take up this research subject.

Recent insights into the evolution of genetic diversity of maize.

Evolutionary changes that occur within the maize genome can be divided into two classes: In the protein-coding regions, mutations that survive selective pressure primarily consist of single nucleotide polymorphisms which evolve at a relatively slow rate (10-9 mutations/ bp/generation), and functionally detrimental insertions are strongly selected against. In intergenic regions rapidly evolving (10-4 10-8 mutations/bp/generation) transposon insertions and deletions predominate. While genic single nucleotide changes are expected in part to result in amino acid sequence variants leading to the modification of protein properties (catalytic properties of enzymes, binding constants, etc.), transposable elements and other large insertions and deletions, when functionally relevant, are predicted to be regulatory in nature and may affect gene expression at distances of up to 100 kb away. Here, we discuss recent experimental evidence for massive dynamic changes of maize intergenic regions and the predicted functional consequences of genome diversity within this species.

High-throughput identification, database storage and analysis of SNPs in EST sequences.

Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation and disease-causing mutations in many genes. Due to their abundance and slow mutation rate within generations, they are thought to be the next generation of genetic markers that can be used in a myriad of important biological, genetic, pharmacological, and medical applications. There are several strategies both experimental, and in-silico for SNP discovery and mapping. Experimental SNP discovery consists of a number of labourious steps that make this process complex and expensive. In-silico discovery has been proposed as an alternative discovery method that makes use and takes advantage of large data sets with potential SNP information that have been generated with other purposes and have not been used as a SNP information source yet. However, in order to successfully apply the in-silico method to large data sets, the following challenges need to be addressed: First it is necessary to build an integrated SNP pipeline that handles data processing steps smoothly from the beginning (collecting sequence information) to end (SNPs in the database). Also, SNP detection tool parameters have to be optimized to satisfy specific goals of the project. Finally, SNP data could not be fully used until the in-silico method is validated experimentally. In this paper we present a design and implementation of an in-silico SNP detection software pipeline that exploits the existence of large EST (expressed sequence tag) data sets and effectively addresses the above challenges. First, the pipeline allows for smooth data transition between its different components by implementing data interfaces that translate the data formats of the different tools in the different stages. Second, we optimized PolyBayes parameters for SNP detection in maize EST. Finally, we implemented a user interface that along with the database structure created allows the scientist to perform preliminary analysis of the data and to perform basic statistics on the SNP data prior to experimental validation. The pipeline works with two different types of sequence assemblers (PHRAP (http://www.phrap.org/) and CAT from DoubleTwist (http://www.doubletwist.com/). It uses a Bayesian engine for SNP detection (PolyBayes), selects relevant polymorphism information which is then uploaded into a database. We detected 2439 SNPs and 822 insertion deletions (INDELs) with a PolyBayes probability higher than 0.99 on the public set of 68,000 maize ESTs. The user interface allowed us analyzing the polymorphism information right after discovery in several ways that allowed us to gain insight into the distribution and significance of the newly acquired data.

Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl.

The expression pattern of 1,529 yeast genes in response to sulfometuron methyl (SM) was analyzed by DNA microarray technology. SM, a potent herbicide, inhibits acetolactate synthase, a branched-chain amino acid biosynthetic enzyme. Exposure of yeast cells to 0.2 microg/ml SM resulted in 40% growth inhibition, a Gcn4p-mediated induction of genes involved in amino acid and cofactor biosynthesis, and starvation response. The accumulation of intermediates led to the induction of stress response genes and the repression of genes involved in carbohydrate metabolism, nucleotide biosynthesis, and sulfur assimilation. Extended exposure to SM led to a relaxation of the initial response and induction of sugar transporter and ergosterol biosynthetic genes, as well as repression of histone and lipid metabolic genes. Exposure to 5 microg/ml SM resulted in >98% growth inhibition and stimulated a similar initial expression change, but with no relaxation after extended exposure. Instead, more stress response and DNA damage repair genes become induced, suggesting a serious cellular consequence. Other salient features of metabolic regulation, such as the coordinated expression of cofactor biosynthetic genes with amino acid biosynthetic ones, were evident from our data. A potential link between SM sensitivity and ergosterol metabolism was uncovered by expression profiling and confirmed by genetic analysis.

The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4.

A 2.3-centimorgan (cM) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced, revealing the presence of 33 putative genes, including several apparently involved in disease resistance. Fourteen of the genes were confirmed by identifying the corresponding transcripts. Five genes, spanning 1.9 cM of the region, cross-hybridized with maize genomic DNA and were genetically mapped in maize, revealing a stretch of colinearity with maize chromosome 4. The Adh1 gene marked one significant interruption. This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. Several other genes, most notably genes similar to known disease resistance genes, showed no cross-hybridization with maize genomic DNA, suggesting sequence divergence or absence of these sequences in maize, which is in contrast to several other well-conserved genes, including Adh1 and Adh2. These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations. Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner-like element, which is new to rice. In contrast to maize, retroelements are less frequent in rice. Only 14.4% of this genome segment consist of retroelements. Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements, accounting for 18.8% of the total repetitive DNA.

Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants.

We investigated the transferability of 31 soybean (Glycine max) simple sequence repeat (SSR) loci to wild congeners and to other legume genera. Up to 65% of the soybean primer pairs amplified SSRs within Glycine, but frequently, the SSRs were short and interrupted compared with those of soybeans. Nevertheless, 85% of the loci were polymorphic within G. clandestina. Cross-species amplification outside of the genus was much lower (3%-13%), with polymorphism restricted to one primer pair, AG81. AG81 amplified loci in Glycine, Kennedia, and Vigna (Phaseoleae), Vicia (Vicieae), Trifolium (Trifolieae), and Lupinus (Genisteae) within the Papilionoideae, and in Albizia within the Mimosoideae. The primer conservation at AG81 may be explained by its apparent proximity to the seryl-tRNA synthetase gene. Interspecific differences in allele size at AG81 loci reflected repeat length variation within the SSR region and indels in the flanking region. Alleles of identical size with different underlying sequences (size homoplasy) were observed. Our findings and the emerging patterns in other plant studies suggest that in contrast to animals, successful cross-species amplification of SSRs in plants is largely restricted to congeners or closely related genera. Because mutations in both the SSR region and the flanking region contribute to variation in allele size among species, knowledge of DNA sequence is essential before SSR loci can be meaningfully used to address applied and evolutionary questions.

Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites.

A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 +/- 0.088 and 0.159 +/- 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants.

Genetic mapping and variability of seven soybean simple sequence repeat loci.

Microsatellites or simple sequence repeats are stretches of short tandemly repeated DNA sequence motifs, dispersed throughout the genomes of most eukaryotes. Simple sequence repeat polymorphisms (SSRPs) have recently been reported in plants. Here we present the genetic map position of seven different soybean (Glycine max (L.) Merr. and Glycine soja Sieb. and Zucc.) SSRPs contained in sequenced genes, four of which represent newly mapped positions for these genes. The other three SSRPs coincided with independently established RFLP map positions for the corresponding genes. When a set of 61 soybean accessions was screened at four of these loci by using agarose gels, the average number of alleles per locus was 7.75, the effective number of alleles (ne) was 2.57, and the level of allele differentiation (delta(t)) was 0.62. Allelic variation decreased sharply with increasing levels of domestication, with the level of differentiation going from 84% in the wild soybean to 43% in the elite germplasm. Variation levels observed on a subset made of 19 of the 61 lines were always higher for SSRPs than for RFLP markers, with the average number of alleles per locus going from 4.25 to 2.15. In comparison with RFLP markers, SSRPs are more informative and are easier to analyse but require more effort to develop.

Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification.

Simple sequence repeats (SSR), or microsatellites, are ubiquitous in eukaryotic genomes. Here we demonstrate the utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region. No sequencing is required to design the oligonucleotide primers. We tested primers anchored at 3' or 5' termini of the (CA)n repeats, extended into the flanking sequence by 2 to 4 nucleotide residues [3'-anchored primers: (CA)8RG, (CA)8RY, and (CA)7RTCY; and 5'-anchored primers: BDB(CA)7C, DBDA(CA)7, VHVG(TG)7 and HVH(TG)7T]. Radioactively labeled amplification products were analyzed by electrophoresis, revealing information on multiple genomic loci in a single gel lane. Complex, species-specific patterns were obtained from a variety of eukaryotic taxa. Intraspecies polymorphisms were also observed and shown to segregate as Mendelian markers. Inter-SSR PCR provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms. This application of (CA)n repeats may be extended to different microsatellites and other common dispersed elements.

A wheat HMW glutenin subunit gene reveals a highly repeated structure.

A wheat genomic library was screened with two synthetic oligonucleotides (24 and 25 bases in length) complementary to a partial cDNA clone encoding a glutenin gene [Thompson et al. (1983) Theor. Appl. Genet. 67, 87-96]. Glutenins are large molecular weight aggregated proteins of grain endosperm, and major determinants of bread making quality of wheat. Of the two clones obtained one was fully characterized. It contained the sequence of the high molecular weight subunit of glutenin. The amino acid sequence derived from the gene sequence reveals a mature protein (817 amino acids) with a highly repeated structure of two different motifs corresponding to the high glutamine (35.7%), glycine (20.1%) and proline (13.1%) content. The gene does not contain an intron, and possesses a typical eukaryotic promoter; the RNA initiation site is 25-30 bases downstream.

The nucleotide sequence of a UGA suppressor serine tRNA from Schizosaccharomyces pombe.

The UGA suppressor tRNA produced by Schizosaccharomyces pombe strain sup3-e was purified to homogeneity. It can be aminoacylated with a serine by a crude aminoacyl-tRNA synthetase preparation from S. pombe cells. By combining post-labeling fingerprinting and gel sequencing methods the nucleotide sequence of this tRNA was determined to be: pG-U-C-A-C-U-A-U-G-U-C-ac4C-G-A-G-D-G-G-D-D-A-A-G-G-A-m2G2-psi-U-A-G-A-N-U-U-C-A-i6A-A-psi-C-U-A-A-U-G-G-G-C-U-U-U-G-C-C-C-G-m5C-G-G-C-A-G-G-T-psi-C-A-m1A-A-U-C-C-U-G-C-U-G-G-U-G-A-C-G-C-C-A OH. The anticodon sequence u ca is complementary to the UGA codon.

Nucleotide sequence of tRNAPhe from the seeds of lupin (Lupinus luteus). Comparison of the major species with wheat germ tRNAPhe.

The nucleotide sequence of tRNAPhe of yellow lupin seeds (Lupinus luteus) is deduced from the composition of pancreatic and T1 ribonuclease digestion products and compared with tRNAPhe of wheat germ. Major lupin tRNAPhe, unlike pea tRNAPhe, differs from wheat germ tRNAPhe in the first base pair of stem TpsiC ("e").

Non-specific acetyl-CoA carboxylase and methylmalonyl-CoA carboxyltransferase in Streptomyces noursei var. polifungini.

1. Acetyl-CoA carboxylase (EC 6.4.1.2) and methylmalonyl-CoA carboxyltransferase (EC 2.1.3.1) have been isolated from mycelia of Streptomyces noursei var. polifungini, and purified about 50-fold. 2. Both enzymes carboxylate acetyl-CoA and propionyl-CoA; the respective Km values are 1.1 and 1.6 mM with acetyl-CoA carboxylase and 2.5 and 1.25 mM with carboxyltransferase. 3. The activities of both enzymes are inhibited by free fatty acids. Almost total inhibition of methylmalonyl-CoA carboxyltransferase was observed by 0.1 mM-butyrate or 0.1 mM-C14-C18 acids. Acetyl-CoA carobxylase was affected to the same extent by these compounds at concentration of about 1 mM. 4. The role of both carboxylating enzymes is biosynthesis of the antibiotic is discussed.

Acyl-CoA pool and acyl-CoA thioesterase in Streptomyces noursei var. polifungini.

The size of acyl-CoA pool in S. noursei var. polifungini was found to be associated with the antibiotic-synthesizing ability, and was negatively correlated with both the thio-esterase activity (acetyl-CoA hydrolase, EC 3.1.2.1) and its affinity towards acetyl-CoA and propionyl-CoA. The apparent Michaelis constants with acetyl-CoA and propionyl-CoA were 33 times 10(-5) and 6.6 times 10(-5) M in the low producing strain, and 8.5 times 10(-4) and 1.2 times 10(-4) M in the high producing strain, respectively.

Limiting reactions in activation of acyl units in biosynthesis of macrolide antibiotics.

Formation of propionyl phosphate in Streptomyces erythreus synthesizing a polypropionate erythronolide ring of erythromycin was found to be catalyzed by a specific propionate kinase. The isolated and 100-fold purified kinase was devoid of activity towards acetate and other monocarboxylic acids. The selection for higher antibiotic-synthesizing ability was associated with higher kinase activity and lower K(m) values towards propionate. This relation did not apply to the mutants of S. noursei var. polifungini producing polyene tetraene antibiotics of the nystatin type, composed of acetate and propionate units. Instead, the antibiotic-synthesizing ability was correlated with the activity of acetyl- and propionyl-coenzyme A carboxylase, responsible for the formation of malonyl- and methyl-malonyl-coenzyme A intermediates in the polymerization process.