Raman Hyperspectral Imaging for Detection of Watermelon Seeds Infected with Acidovorax citrulli

PubMed Central

Lee, Hoonsoo; Kim, Moon S.; Qin, Jianwei; Park, Eunsoo; Song, Yu-Rim; Oh, Chang-Sik

2017-01-01

The bacterial infection of seeds is one of the most important quality factors affecting yield. Conventional detection methods for bacteria-infected seeds, such as biological, serological, and molecular tests, are not feasible since they require expensive equipment, and furthermore, the testing processes are also time-consuming. In this study, we use the Raman hyperspectral imaging technique to distinguish bacteria-infected seeds from healthy seeds as a rapid, accurate, and non-destructive detection tool. We utilize Raman hyperspectral imaging data in the spectral range of 400–1800 cm−1 to determine the optimal band-ratio for the discrimination of watermelon seeds infected by the bacteria Acidovorax citrulli using ANOVA. Two bands at 1076.8 cm−1 and 437 cm−1 are selected as the optimal Raman peaks for the detection of bacteria-infected seeds. The results demonstrate that the Raman hyperspectral imaging technique has a good potential for the detection of bacteria-infected watermelon seeds and that it could form a suitable alternative to conventional methods. PMID:28946608

Management of cereal cyst nematodes, Heterodera spp., in Norway.

PubMed

Holgado, R; Andersson, S; Magnusson, C

2006-01-01

Cereal cyst nematodes, Heterodera spp., are known worldwide as parasites of cereals and grasses. Surveys of cereal fields in Norway have revealed that nematodes belonging to the H. avenae complex occur throughout the country, and that H. avenae (the oat cyst nematode) is the most common species, followed by H. filipjevi (the rye cyst nematode). Both species are of economic importance in Scandinavia. H. avenae has been found in two common pathotypes, Ha 11 and Ha 12. Work in Sweden, however, has detected three additional pathotypes, H. avenae "Knislinge", H. avenae "Ringsisen" and H. avenae "Våxtorp". These pathotypes were found also in the Norwegian surveys. In Sweden H. filipjevi has two pathotypes, "East" and "West". In Norway, only pathotype "West" has been detected so far. Nematode management practices must be based on the knowledge of the relationship between initial nematode density and yield, the population dynamics, and the measures capable of reducing or keeping the population density below the threshold for economic damage. Crop rotation and the use of cultivars with resistance are important measures for controlling cereal cyst nematodes. Several cereal cultivars with resistance to H. avenae are on the market. As to H. filipjevi, resistance may be found in some commercial cultivars, although no intentional breeding for resistance against this nematode species has been attempted. In 2004 and 2005 the majority of the cereal cultivars on the Norwegian market were tested for susceptibility/resistance towards H. avenae pathotype Ha 11, H. avenae pathotype "Våxtorp" and H. filipjevi pathotype "West". Management systems, based on careful nematode identification and good knowledge of appropriate resistant cultivars, are in operation in Norway. Resistant barley is generally recommended when nematode populations are high due to its high tolerance compared to resistant oats. Farmers implementing this program have reported increased cereal yields on the average of 1000 kg/ha. It has been calculated that by implementing this program in full the county of Vestfold could make an economic gain of 800,000 Euro annually.

Genetic basis and selection for life-history trait plasticity on alternative host plants for the cereal aphid Sitobion avenae.

PubMed

Dai, Xinjia; Gao, Suxia; Liu, Deguang

2014-01-01

Sitobion avenae (F.) can survive on various plants in the Poaceae, which may select for highly plastic genotypes. But phenotypic plasticity was often thought to be non-genetic, and of little evolutionary significance historically, and many problems related to adaptive plasticity, its genetic basis and natural selection for plasticity have not been well documented. To address these questions, clones of S. avenae were collected from three plants, and their phenotypic plasticity under alternative environments was evaluated. Our results demonstrated that nearly all tested life-history traits showed significant plastic changes for certain S. avenae clones with the total developmental time of nymphs and fecundity tending to have relatively higher plasticity for most clones. Overall, the level of plasticity for S. avenae clones' life-history traits was unexpectedly low. The factor 'clone' alone explained 27.7-62.3% of the total variance for trait plasticities. The heritability of plasticity was shown to be significant in nearly all the cases. Many significant genetic correlations were found between trait plasticities with a majority of them being positive. Therefore, it is evident that life-history trait plasticity involved was genetically based. There was a high degree of variation in selection coefficients for life-history trait plasticity of different S. avenae clones. Phenotypic plasticity for barley clones, but not for oat or wheat clones, was frequently found to be under significant selection. The directional selection of alternative environments appeared to act to decrease the plasticity of S. avenae clones in most cases. G-matrix comparisons showed significant differences between S. avenae clones, as well as quite a few negative covariances (i.e., trade-offs) between trait plasticities. Genetic basis and evolutionary significance of life-history trait plasticity were discussed.

New sources of adult plant and seedling resistance to Puccinia coronata f. sp. avenae identified among Avena sativa accessions of the national small grains collection

USDA-ARS?s Scientific Manuscript database

Accessions of cultivated oat (A. sativa L.) from the USDA-ARS Small Grains Collection in Aberdeen, ID were characterized for adult plant resistance (APR) and seedling resistance to crown rust, caused by Puccinia coronata f. sp. avenae (Pca). Initially, 607 oat accessions with diverse geographic orig...

Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa

USDA-ARS?s Scientific Manuscript database

A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plant...

De novo assembly and phasing of dikaryotic genomes from two isolates of Puccini coronata f. sp. avenae, the causal agent of oat crown rust

Treesearch

Marisa E. Miller; Ying Zhang; Vahid Omidvar; Jana Sperschneider; Benjamin Schwessinger; Castle Raley; Jonathan M. Palmer; Diana Garnica; Narayana Upadhyaya; John Rathjen; Jennifer M. Taylor; Robert F. Park; Peter N. Dodds; Cory D. Hirsch; Shahryar F. Kianian; Melania Figueroa

2018-01-01

Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting...

Large-Scale Identification and Characterization of Heterodera avenae Putative Effectors Suppressing or Inducing Cell Death in Nicotiana benthamiana

PubMed Central

Chen, Changlong; Chen, Yongpan; Jian, Heng; Yang, Dan; Dai, Yiran; Pan, Lingling; Shi, Fengwei; Yang, Shanshan; Liu, Qian

2018-01-01

Heterodera avenae is one of the most important plant pathogens and causes vast losses in cereal crops. As a sedentary endoparasitic nematode, H. avenae secretes effectors that modify plant defenses and promote its biotrophic infection of its hosts. However, the number of effectors involved in the interaction between H. avenae and host defenses remains unclear. Here, we report the identification of putative effectors in H. avenae that regulate plant defenses on a large scale. Our results showed that 78 of the 95 putative effectors suppressed programmed cell death (PCD) triggered by BAX and that 7 of the putative effectors themselves caused cell death in Nicotiana benthamiana. Among the cell-death-inducing effectors, three were found to be dependent on their specific domains to trigger cell death and to be expressed in esophageal gland cells by in situ hybridization. Ten candidate effectors that suppressed BAX-triggered PCD also suppressed PCD triggered by the elicitor PsojNIP and at least one R-protein/cognate effector pair, suggesting that they are active in suppressing both pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Notably, with the exception of isotig16060, these putative effectors could also suppress PCD triggered by cell-death-inducing effectors from H. avenae, indicating that those effectors may cooperate to promote nematode parasitism. Collectively, our results indicate that the majority of the tested effectors of H. avenae may play important roles in suppressing cell death induced by different elicitors in N. benthamiana. PMID:29379510

Life-history responses of insects to water-deficit stress: a case study with the aphid Sitobion avenae.

PubMed

Liu, Deguang; Dai, Peng; Li, Shirong; Ahmed, Syed Suhail; Shang, Zheming; Shi, Xiaoqin

2018-05-29

Drought may become one of the greatest challenges for cereal production under future warming scenarios, and its impact on insect pest outbreaks is still controversial. To address this issue, life-history responses of the English grain aphid, Sitobion avenae (Fabricius), from three areas of different drought levels were compared under three water treatments. Significant differences were identified in developmental time, fecundity and adult weight among S. avenae clones from moist, semiarid and arid areas under all the three water treatments. Semiarid and arid area clones tended to have higher heritability for test life-history traits than moist area clones. We identified significant selection of water-deficit on the developmental time of 1st instar nymphs and adult weight for both semiarid and arid area clones. The impact of intermediate and severe water-stress on S. avenae's fitness was neutral and negative (e.g., decreased fecundity and weight), respectively. Compared with arid-area clones, moist- and semiarid-area clones showed higher extents of adaptation to the water-deficit level of their respective source environment. Adult weight was identified as a good indicator for S. avenae's adaptation potential under different water-stress conditions. After their exposure to intermediate water-deficit stress for only five generations, adult weight and fecundity tended to decrease for moist- and semiarid-area clones, but increase for arid-area clones. It is evident from our study that S. avenae clones from moist, semiarid and arid areas have diverged under different water-deficit stress, and such divergence could have a genetic basis. The impact of drought on S. avenae's fitness showed a water-level dependent pattern. Clones of S. avenae were more likely to become adapted to intermediate water-deficit stress than severe water-deficit stress. After continuous water-deficit stress of only five generations, the adaptation potential of S. avenae tended to decrease for moist and semiarid area clones, but increase for arid area clones. The rapid shift of aphids' life-history traits and adaptation potential under drought could have significant implications for their evolutionary dynamics and outbreak risks in future climate change scenarios.

Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red Stripe in Argentina

PubMed Central

Fontana, Cecilia A.; Bassi, Daniela; Puglisi, Edoardo; Salazar, Sergio M.; Vignolo, Graciela M.; Coccocelli, Pier S.

2016-01-01

Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax avenae. The genome sequence from the first isolate of this bacterium in Argentina is presented here. The draft genome of the A. avenae T10_61 strain contains 5,646,552 bp and has a G+C content of 68.6 mol%. PMID:26847889

De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae.

PubMed

Kumar, Mukesh; Gantasala, Nagavara Prasad; Roychowdhury, Tanmoy; Thakur, Prasoon Kumar; Banakar, Prakash; Shukla, Rohit N; Jones, Michael G K; Rao, Uma

2014-01-01

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

De Novo Transcriptome Sequencing and Analysis of the Cereal Cyst Nematode, Heterodera avenae

PubMed Central

Kumar, Mukesh; Gantasala, Nagavara Prasad; Roychowdhury, Tanmoy; Thakur, Prasoon Kumar; Banakar, Prakash; Shukla, Rohit N.; Jones, Michael G. K.; Rao, Uma

2014-01-01

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction. PMID:24802510

Conversion of Isatin to Isatate as Related to Growth Promotion in Avena Coleoptile and Pisum Stem Sections 1

PubMed Central

Chen, H.-R.; Galston, A. W.; Milstone, L.

1966-01-01

Isatin, (indole 2,3-dione), which promotes elongation of Pisum stem sections at concentrations exceeding 0.1 mm, promotes elongation of Avena coleoptile sections only at higher concentrations, exceeding 1 mm. Aged isatin solutions are more active than fresh solutions, due to the slow, spontaneous conversion to isatate (o-aminophenylglyoxylate). A concentration of 0.1 mm aged isatin is as active in Avena coleoptile sections as in peas. Isatate has been independently synthesized and its auxin activity in both Avena coleoptile and Pisum stem sections confirmed. The synthetic isatate is more effective than isatin in both systems. This suggests that the auxin activity of isatin is due to its conversion to isatate. PMID:16656429

The effect of rodent seed predation on four species of California annual grasses.

PubMed

Borchert, M I; Jain, S K

1978-01-01

The effect of seed predation by Microtus californicus and Mus musculus on plant numbers of four species of California annual grasses was investigated for one year period on a grassland near Davis, California. In winter, mice utilized dead star thistle plants for cover when grasses in open areas were short, but moved into open areas when grass grew tall in spring.Using exclosures and plots sown with known quantities of seed, it was estimated that a mouse population (approximate density 120/acre) consumed 75% of Avena fatua seed, 44% of Hordeum leporinum seed, and 37% of Bromus diandrus seed. Mice showed a strong preference for Avena seed.Plant numbers of Avena and Hordeum were reduced by 62% and 30%, respectively. Hordeum, Lolium, and to a lesser extent, Bromus responded to a competitive release from Avena by increases in plant size and reproductive output. In addition, seed predation markedly increased seed to adult plant survivorship of Avena, Hordeum, and Bromus.Vertebrate seed predation is discussed as a potentially important factor in the yearly patterns of plant population regulation in California annual grasslands.

Influence of Aphelenchus avenae on Vesicular-arbuscular Endomycorrhizal Growth Response in Cotton.

PubMed

Hussey, R S; Roncadori, R W

1981-01-01

The influence of Aphelenchus avenae on the relationship between cotton (Gossypium hirsutum 'Stoneville 213') and Gigaspora margarita or Glomus etunicatus was assessed by its effect on the mycorrhizal stimulation of plant growth and microorganism reproduction. The mycophagous nematode usually did not suppress stimulation of shoot growth resulting from mycorrhizae (G. margarita) at inoculum levels of 3,000 or 6,000 nematodes per pot, but retarded root growth at 6,000 per pot. When the nematode inoculum was increased to 10, 40, or 80 thousand, G. margarita stimulation of shoot or root growth was retarded at the two higher rates. Shoot growth enhancement by G. etunicatus was suppressed by 10 thousand A. avenae but not by 40 or 80 thousand. A. avenae reproduced better when the nematode was added 3 wk after G. margarita than with simultaneous inoculations. Sporulation of both fungi was affected little by the mycophagous nematode. The high numbers of A. avenae required for an antagonistic effect probably precludes the occurrence of any significant interaction between these two organisms under field conditions.

Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis.

PubMed

Kong, Ling-An; Wu, Du-Qing; Huang, Wen-Kun; Peng, Huan; Wang, Gao-Feng; Cui, Jiang-Kuan; Liu, Shi-Ming; Li, Zhi-Gang; Yang, Jun; Peng, De-Liang

2015-10-16

Cereal cyst nematode Heterodera avenae, an important soil-borne pathogen in wheat, causes numerous annual yield losses worldwide, and use of resistant cultivars is the best strategy for control. However, target genes are not readily available for breeding resistant cultivars. Therefore, comparative transcriptomic analyses were performed to identify more applicable resistance genes for cultivar breeding. The developing nematodes within roots were stained with acid fuchsin solution. Transcriptome assemblies and redundancy filteration were obtained by Trinity, TGI Clustering Tool and BLASTN, respectively. Gene Ontology annotation was yielded by Blast2GO program, and metabolic pathways of transcripts were analyzed by Path_finder. The ROS levels were determined by luminol-chemiluminescence assay. The transcriptional gene expression profiles were obtained by quantitative RT-PCR. The RNA-sequencing was performed using an incompatible wheat cultivar VP1620 and a compatible control cultivar WEN19 infected with H. avenae at 24 h, 3 d and 8 d. Infection assays showed that VP1620 failed to block penetration of H. avenae but disturbed the transition of developmental stages, leading to a significant reduction in cyst formation. Two types of expression profiles were established to predict candidate resistance genes after developing a novel strategy to generate clean RNA-seq data by removing the transcripts of H. avenae within the raw data before assembly. Using the uncoordinated expression profiles with transcript abundance as a standard, 424 candidate resistance genes were identified, including 302 overlapping genes and 122 VP1620-specific genes. Genes with similar expression patterns were further classified according to the scales of changed transcript abundances, and 182 genes were rescued as supplementary candidate resistance genes. Functional characterizations revealed that diverse defense-related pathways were responsible for wheat resistance against H. avenae. Moreover, phospholipase was involved in many defense-related pathways and localized in the connection position. Furthermore, strong bursts of reactive oxygen species (ROS) within VP1620 roots infected with H. avenae were induced at 24 h and 3 d, and eight ROS-producing genes were significantly upregulated, including three class III peroxidase and five lipoxygenase genes. Large-scale identification of wheat resistance genes were processed by comparative transcriptomic analysis. Functional characterization showed that phospholipases associated with ROS production played vital roles in early defense responses to H. avenae via involvement in diverse defense-related pathways as a hub switch. This study is the first to investigate the early defense responses of wheat against H. avenae, not only provides applicable candidate resistance genes for breeding novel wheat cultivars, but also enables a better understanding of the defense mechanisms of wheat against H. avenae.

The impact of transgenic wheat expressing GNA (snowdrop lectin) on the aphids Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi.

PubMed

Miao, Jin; Wu, Yuqing; Xu, Weigang; Hu, Lin; Yu, Zhenxing; Xu, Qiongfang

2011-06-01

This study investigated the impact of transgenic wheat expressing Galanthus nivalis agglutinin (GNA), commonly known as snowdrop lectin, on three wheat aphids: Sitobion avenae (F.), Schizaphis graminum (Rondani), and Rhopalosiphum padi (L.). We compared the feeding behavior and the life-table parameters of aphids reared on GNA transgenic wheat (test group) and those aphids reared on untransformed wheat (control group). The results showed that the feeding behaviors of S. avenae and S. graminum on GNA transgenic wheat were affected. Compared with the control group, they had shorter initial probing period, longer total nonprobing period, shorter initial and total phloem sap ingestion phase (waveform E2), shorter duration of sustained ingestion (E (pd) > 10 min), and lower percentage of phloem phase of the total observation time. Moreover, S. graminum made more probes and had a longer total duration of extracellular stylet pathway (waveform C). The fecundity and intrinsic rate of natural increase (r(m)) of S. avenae and S. graminum on the transgenic wheat were lowered in the first and second generations, however, the survival and lifespan were not affected. The effects of the GNA expressing wheat on S. graminum and S. avenae were not significant in the third generation, suggesting rapid adaptation by the two aphid species. Despite the impact we found on S. avenae and S. graminum, transgenic GNA expressing wheat did not have any effects on R. padi.

Elevated CO2 changes interspecific competition among three species of wheat aphids: Sitobion avenae, Rhopalosiphum padi, and Schizaphis graminum.

PubMed

Sun, Yu Cheng; Chen, Fa Jun; Ge, Feng

2009-02-01

Effects of elevated CO2 (twice ambient) on the interspecific competition among three species of wheat aphids (Sitobion avenae, Rhopalosiphum padi, and Schizaphis graminum) and on wheat-aphid interactions were studied. Wheat plants had higher biomass and yield and lower water and nitrogen content of grain when grown under elevated CO2 than under ambient CO2; levels of condensed tannins, total phenols, and total nonstructural carbohydrates were also higher in wheat ears under elevated CO2. Compared with ambient CO2, elevated CO2 increased the abundance of R. padi when introduced solely but reduced its abundance when S. avenae was also present. The spatial distribution of wheat aphids was apparently influenced by CO2 levels, with significantly more S. avenae on ears and a more even distribution of R. padi on wheat plants under elevated CO2 versus ambient CO2. Elevated CO2 did not affect the abundance and spatial distribution of S. graminus when inoculated solely. Moreover, when S. avenae was present with either R. padi or S. graminum, spatial niche overlap was significantly decreased with elevated CO2. When three species co-occurred, elevated CO2 reduced spatial niche overlap between S. avenae and S. graminum and between R. padi and S. graminum. Our results suggest that increases in atmospheric CO2 would alleviate interspecific competition for these cases, which would accentuate the abundance of and the damage caused by these wheat aphids.

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust.

PubMed

Miller, Marisa E; Zhang, Ying; Omidvar, Vahid; Sperschneider, Jana; Schwessinger, Benjamin; Raley, Castle; Palmer, Jonathan M; Garnica, Diana; Upadhyaya, Narayana; Rathjen, John; Taylor, Jennifer M; Park, Robert F; Dodds, Peter N; Hirsch, Cory D; Kianian, Shahryar F; Figueroa, Melania

2018-02-20

Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae , is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae , which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae , resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of P. coronata f. sp. avenae . Copyright © 2018 Miller et al.

Assessment of Sublethal and Transgenerational Effects of Pirimicarb on the Wheat Aphids Rhopalosiphum padi and Sitobion avenae

PubMed Central

Desneux, Nicolas; Han, Peng; Gao, Xiwu

2015-01-01

The wheat aphids, Rhopalosiphum padi (Linnaeus) and Sitobion avenae (Fabricius), are key pests on wheat crops worldwide. Management practices rely primarily on insecticides. The pirimicarb (carbamate) is used extensively as an effective insecticide to control these two aphids. In addition to the mortality caused by pirimicarb, various sublethal effects may occur in aphids when exposed to low lethal or sublethal doses. Understanding the general effect of pirimicarb on aphids could help increasing rational use of this insecticide. Under laboratory conditions, we assessed the sublethal effects of a low lethal concentration of pirimicarb (LC25) on biological traits and acetylcholinesterase (AChE) activity of R. padi and S. avenae. Both direct and transgenerational effects, i.e. on parent and the F1 generations were assessed, respectively. We found that R. padi and S. avenae responded differentially to the LC25 of pirimicarb. The parent generation of R. padi showed a 39% decrease in fecundity and multiple transgenerational effects were observed in the F1 generation; overall juvenile development, reproductive period, adult longevity and lifespan were longer than those of the control group. By contrast, LC25 of pirimicarb showed almost no effects on S. avenae biological traits in both the parent and F1 generations; only the pre-reproductive duration was reduced in F1 generations. Demographic parameter estimates (e.g. rm) showed similar trend, i.e. significant negative effect on R. padi population growth and no effect on S. avenae. However, AChE activity decreased in both R. padi and S. avenae treated by the LC25 of pirimicarb. We demonstrated sublethal and transgenerational effects of pirimicarb in the two wheat aphid species; it hinted at the importance of considering sublethal effects (including hormesis) of pirimicarb for optimizing Integrated Pest Management (IPM) of wheat aphids. PMID:26121265

Life-history trait plasticity and its relationships with plant adaptation and insect fitness: a case study on the aphid Sitobion avenae.

PubMed

Dai, Peng; Shi, Xiaoqin; Liu, Deguang; Ge, Zhaohong; Wang, Da; Dai, Xinjia; Yi, Zhihao; Meng, Xiuxiang

2016-07-18

Phenotypic plasticity has recently been considered a powerful means of adaptation, but its relationships with corresponding life-history characters and plant specialization levels of insects have been controversial. To address the issues, Sitobion avenae clones from three plants in two areas were compared. Varying amounts of life-history trait plasticity were found among S. avenae clones on barley, oat and wheat. In most cases, developmental durations and their corresponding plasticities were found to be independent, and fecundities and their plasticities were correlated characters instead. The developmental time of first instar nymphs for oat and wheat clones, but not for barley clones, was found to be independent from its plasticity, showing environment-specific effects. All correlations between environments were found to be positive, which could contribute to low plasticity in S. avenae. Negative correlations between trait plasticities and fitness of test clones suggest that lower plasticity could have higher adaptive value. Correlations between plasticity and specialization indices were identified for all clones, suggesting that plasticity might evolve as a by-product of adaptation to certain environments. The divergence patterns of life-history plasticities in S. avenae, as well as the relationships among plasticity, specialization and fitness, could have significant implications for evolutionary ecology of this aphid.

A mutation (L1014F) in the voltage-gated sodium channel of the grain aphid, Sitobion avenae, is associated with resistance to pyrethroid insecticides.

PubMed

Foster, Stephen P; Paul, Verity L; Slater, Russell; Warren, Anne; Denholm, Ian; Field, Linda M; Williamson, Martin S

2014-08-01

The grain aphid, Sitobion avenae Fabricius (Hemiptera: Aphididae), is an important pest of cereal crops. Pesticides are the main method for control but carry the risk of selecting for resistance. In response to reports of reduced efficacy of pyrethroid sprays applied to S. avenae, field samples were collected and screened for mutations in the voltage-gated sodium channel, the primary target site for pyrethroids. Aphid mobility and mortality to lambda-cyhalothrin were measured in coated glass vial bioassays. A single amino acid substitution (L1014F) was identified in the domain IIS6 segment of the sodium channel from the S. avenae samples exhibiting reduced pyrethroid efficacy. Bioassays on aphids heterozygous for the kdr mutation (SR) or homozygous for the wild-type allele (SS) showed that those carrying the mutation had significantly lower susceptibility to lambda-cyhalothrin. The L1014F (kdr) mutation, known to confer pyrethroid resistance in many insect pests, has been identified for the first time in S. avenae. Clonal lines heterozygous for the mutation showed 35-40-fold resistance to lambda-cyhalothrin in laboratory bioassays, consistent with the reported effect of this mutation on pyrethroid sensitivity in other aphid species. © 2013 Society of Chemical Industry.

STRAIGHT-A STUDENTS DISLIKE PHYSICAL EDUCATION IN ADOLESCENCE: MYTH OR TRUTH? THE AVENA, AFINOS AND UP&DOWN STUDIES.

PubMed

Cañadas, Laura; Esteban-Cornejo, Irene; Ortega, Francisco B; Gomez-Martinez, Sonia; Casajús, José Antonio; Cabero, María Jesús; Calle, Maria E; Marcos, Ascensión; Veiga, Oscar L; Martinez-Gomez, David

2015-07-01

to examine if those adolescents who dislike physical education classes get better results on academic and cognitive performance than their peers. participants included 4 226 adolescents from the AVENA, AFINOS and UP&DOWN studies. Physical education enjoyment was assessed with a 7-point Likert scale. Cognitive performance in the AVENA study was assessed using the Spanish version of the SRA Test of Educational Ability. Academic performance in the AFINOS and UP&DOWN studies was assessed through Mathematics and Language grades and the average of both subjects. in the AVENA study we found differences in verbal ability among girls who dislike physical education and their peers (P = 0.033). In the AFINOS study, boys who dislike physical education had higher scores in Language than their peers (P = 0.024). In the UP&DOWN study girls who disliked physical education had higher scores in Language and in the average of Language and Mathematics than their peers (P < 0.001). in the AVENA and AFINOS studies adolescents who disliked physical education had similar results in cognitive and academic performance than their peers, but in the UP&DOWN study girls who disliked physical education showed higher results in academic performance than their peers. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae

PubMed Central

2010-01-01

Background Some organisms can survive extreme desiccation by entering a state of suspended animation known as anhydrobiosis. The free-living mycophagous nematode Aphelenchus avenae can be induced to enter anhydrobiosis by pre-exposure to moderate reductions in relative humidity (RH) prior to extreme desiccation. This preconditioning phase is thought to allow modification of the transcriptome by activation of genes required for desiccation tolerance. Results To identify such genes, a panel of expressed sequence tags (ESTs) enriched for sequences upregulated in A. avenae during preconditioning was created. A subset of 30 genes with significant matches in databases, together with a number of apparently novel sequences, were chosen for further study. Several of the recognisable genes are associated with water stress, encoding, for example, two new hydrophilic proteins related to the late embryogenesis abundant (LEA) protein family. Expression studies confirmed EST panel members to be upregulated by evaporative water loss, and the majority of genes was also induced by osmotic stress and cold, but rather fewer by heat. We attempted to use RNA interference (RNAi) to demonstrate the importance of this gene set for anhydrobiosis, but found A. avenae to be recalcitrant with the techniques used. Instead, therefore, we developed a cross-species RNAi procedure using A. avenae sequences in another anhydrobiotic nematode, Panagrolaimus superbus, which is amenable to gene silencing. Of 20 A. avenae ESTs screened, a significant reduction in survival of desiccation in treated P. superbus populations was observed with two sequences, one of which was novel, while the other encoded a glutathione peroxidase. To confirm a role for glutathione peroxidases in anhydrobiosis, RNAi with cognate sequences from P. superbus was performed and was also shown to reduce desiccation tolerance in this species. Conclusions This study has identified and characterised the expression profiles of members of the anhydrobiotic gene set in A. avenae. It also demonstrates the potential of RNAi for the analysis of anhydrobiosis and provides the first genetic data to underline the importance of effective antioxidant systems in metazoan desiccation tolerance. PMID:20085654

Development of a species-specific PCR assay for differentiation of Heterodera filipjevi and H. avenae

USDA-ARS?s Scientific Manuscript database

Heterodera avenae and H. filipjevi are economically important cyst nematodes that restrict production of cereal crops in the Pacific Northwest (PNW) USA and elsewhere in the world. Identification of these two species is critical for recommending and implementing effective management practices. Prime...

Effect of chitosan solution on the inhibition of Acidovorax citrulli causing bacterial fruit blotch of watermelon.

PubMed

Li, Bin; Shi, Yu; Shan, Changlin; Zhou, Qing; Ibrahim, Muhammad; Wang, Yanli; Wu, Guoxing; Li, Hongye; Xie, Guanlin; Sun, Guochang

2013-03-30

The production of watermelon in China has been seriously hampered by fruit blotch disease and limited control measures are now applied. Chitosan has been employed to control a variety of plant diseases and is considered to be the most promising biochemical to control this disease. The in vitro antibacterial effect of chitosan and its ability in protection of watermelon seedlings from bacterial fruit blotch were evaluated. Results showed that three types of chitosan, in particular, chitosan A at 0.40 mg mL⁻¹ significantly inhibited the growth of Acidovorax citrulli. The antibacterial activity of chitosan A was affected by chitosan concentration and incubation time. The direct antibacterial activity of chitosan may be attributed to membrane lysis evidenced by transmission electron microscopic observation. The disease index of watermelon seedlings planted in soil and the death rate of seedlings planted in perlite were significantly reduced by chitosan A at 0.40 mg mL⁻¹ compared to the pathogen control. Fresh and dry weight of watermelon seedlings planted in soil was increased by chitosan seed treatment, but not by chitosan leaf spraying. The results indicated that chitosan solution may have a potential in controlling bacterial fruit blotch of watermelon. © 2013 Society of Chemical Industry.

Screening wild oat accessions from Morocco for resistance to Puccinia coronata

USDA-ARS?s Scientific Manuscript database

Here we report the screening of 338 new accessions of 11 different wild oat species (Avena) from the USDA Small Grains Collection for resistance to crown rust (Puccinia coronata). Wild oat species were originally collected in Morocco by C. Al Faiz, INRAT Rabat: Avena agadiriana, A. atlantica, A. bar...

Comparative profiling of microRNAs in the winged and wingless English grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae)

USDA-ARS?s Scientific Manuscript database

English green aphid, Sitobion avenae (F.), show a classic polyphenic wing dimorphism among isogenic adults that is an intriguing model for the study of morphological plasticity in response to the environment. Short non-coding microRNA (miRNA) molecules regulate gene expression by post-transcriptiona...

Functional response of Hippodamia convergens to Sitobion avenae on wheat plants in the laboratory

USDA-ARS?s Scientific Manuscript database

We investigated predation by adult convergent lady beetle, Hippodamia convergens Guerin-Meneville, on English grain aphid, Sitobion avenae L., on wheat, Triticum aestivum L., plants in a laboratory arena and developed a functional response model for the number of aphids eaten by an adult female conv...

TOXICITY OF METHYL-TERT BYTYL ETHER (MTBE) TO PLANTS (AVENA SATIVA, ZEA MAYS, TRITICUM AESTIVUM, AND LACTUCA SATIVA)

EPA Science Inventory

Effects of Methyl tert-butyl ether (MTBE) on the germination of seeds and growth of the plant were studied in some laboratory experiments. Test plants were wild oat (Avena sative), sweet corn (Zea mays), wheat (Triticum aestivum), and lettuce (Lactuca sativa). Seed germination,...

Calcium bridges are not load-bearing cell-wall bonds in Avena coleoptiles

NASA Technical Reports Server (NTRS)

Rayle, D. L.

1989-01-01

I examined the ability of frozen-thawed Avena sativa L. coleoptile sections under applied load to extend in response to the calcium chelators ethyleneglycol-bis-(beta-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) and 2-[(2-bis-[carboxymethyl]amino-5-methylphenoxy)methyl]-6-methoxy-8-bis[car boxymethyl]aminoquinoline (Quin II). Addition of 5 mM EGTA to weakly buffered (0.1 mM, pH 6.2) solutions of 2(N-morpholino) ethanesulfonic acid (Mes) initiated rapid extension and wall acidification. When the buffer strength was increased (e.g. from 20 to 100 mM Mes, pH 6.2) EGTA did not initiate extension nor did it cause wall acidification. At 5 mM Quin II failed to stimulate cell extension or wall acidification at all buffer molarities tested (0.1 to 100 mM Mes). Both chelators rapidly and effectively removed Ca2+ from Avena sections. These data indicate that Ca2+ chelation per se does not result in loosening of Avena cells walls. Rather, EGTA promotes wall extension indirectly via wall acidification.

Dehydration-induced tps gene transcripts from an anhydrobiotic nematode contain novel spliced leaders and encode atypical GT-20 family proteins.

PubMed

Goyal, K; Browne, J A; Burnell, A M; Tunnacliffe, A

2005-06-01

Accumulation of the non-reducing disaccharide trehalose is associated with desiccation tolerance during anhydrobiosis in a number of invertebrates, but there is little information on trehalose biosynthetic genes in these organisms. We have identified two trehalose-6-phosphate synthase (tps) genes in the anhydrobiotic nematode Aphelenchus avenae and determined full length cDNA sequences for both; for comparison, full length tps cDNAs from the model nematode, Caenorhabditis elegans, have also been obtained. The A. avenae genes encode very similar proteins containing the catalytic domain characteristic of the GT-20 family of glycosyltransferases and are most similar to tps-2 of C. elegans; no evidence was found for a gene in A. avenae corresponding to Ce-tps-1. Analysis of A. avenae tps cDNAs revealed several features of interest, including alternative trans-splicing of spliced leader sequences in Aav-tps-1, and four different, novel SL1-related trans-spliced leaders, which were different to the canonical SL1 sequence found in all other nematodes studied. The latter observation suggests that A. avenae does not comply with the strict evolutionary conservation of SL1 sequences observed in other species. Unusual features were also noted in predicted nematode TPS proteins, which distinguish them from homologues in other higher eukaryotes (plants and insects) and in micro-organisms. Phylogenetic analysis confirmed their membership of the GT-20 glycosyltransferase family, but indicated an accelerated rate of molecular evolution. Furthermore, nematode TPS proteins possess N- and C-terminal domains, which are unrelated to those of other eukaryotes: nematode C-terminal domains, for example, do not contain trehalose-6-phosphate phosphatase-like sequences, as seen in plant and insect homologues. During onset of anhydrobiosis, both tps genes in A. avenae are upregulated, but exposure to cold or increased osmolarity also results in gene induction, although to a lesser extent. Trehalose seems likely therefore to play a role in a number of stress responses in nematodes.

First report of the cereal cyst nematode Heterodera filipjevi on winter wheat in Montana

USDA-ARS?s Scientific Manuscript database

Among the cereal cyst nematode complex, three species-Heterodera avenae, H. filipjevi and H. latipons-are the most destructive for wheat. Although H. avenae occurs in several U.S. states, H. filipjevi was discovered in the United States in Oregon in 2008 and has since been reported only in Washingto...

Genome-wide association mapping of barley yellow dwarf virus tolerance in spring oat (Avena sativa L.)

USDA-ARS?s Scientific Manuscript database

Barley yellow dwarf (BYD) is one of the most destructive diseases of cereal crops worldwide. Barley yellow dwarf viruses (BYDVs) are responsible for BYD and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-t...

Foraging by Hippodamia convergens for the aphid Sitobion avenae on wheat plants growing in greenhouse plots

USDA-ARS?s Scientific Manuscript database

We investigated predation by adult convergent lady beetle, Hippodamia convergens Guerin-Meneville, on English grain aphid, Sitobion avenae L., on wheat, Triticum aestivum L., growing in 1.8 x 1.8 m plantings in a greenhouse with a soil floor. The wheat was planted to simulate wheat in a typical pro...

Genetic variation and associations involving Fusarium head blight and deoxynivalenol accumulation in cultivated oat (Avena sativa L.)

USDA-ARS?s Scientific Manuscript database

Resistance in oats (Avena sativa L.) to infection by Fusarium graminearum was assessed in field trials in 2011-12 including 424 spring oat lines from North America and Scandinavia. Traits measured were Fusarium Head Blight (FHB), deoxynivalenol (DON) content, days to flowering (DTF) and days to matu...

Genome-wide association study for crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) resistance in an oat (Avena sativa) collection of commercial varieties and landraces.

PubMed

Montilla-Bascón, Gracia; Rispail, Nicolas; Sánchez-Martín, Javier; Rubiales, Diego; Mur, Luis A J; Langdon, Tim; Howarth, Catherine J; Prats, Elena

2015-01-01

Diseases caused by crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite alleles for rust and powdery mildew resistance in oat by association mapping to aid selection of resistant plants. To this aim, 177 oat accessions including white and red oat cultivars and landraces were evaluated for disease resistance and further genotyped with 31 simple sequence repeat and 15,000 Diversity Arrays Technology (DArT) markers to reveal association with disease resistance traits. After data curation, 1712 polymorphic markers were considered for association analysis. Principal component analysis and a Bayesian clustering approach were applied to infer population structure. Five different general and mixed linear models accounting for population structure and/or kinship corrections and two different statistical tests were carried out to reduce false positive. Five markers, two of them highly significant in all models tested were associated with rust resistance. No strong association between any marker and powdery mildew resistance at the seedling stage was identified. However, one DArT sequence, oPt-5014, was strongly associated with powdery mildew resistance in adult plants. Overall, the markers showing the strongest association in this study provide ideal candidates for further studies and future inclusion in strategies of marker-assisted selection.

Interactions of Seedborne Bacterial Pathogens with Host and Non-Host Plants in Relation to Seed Infestation and Seedling Transmission

PubMed Central

Dutta, Bhabesh; Gitaitis, Ronald; Smith, Samuel; Langston, David

2014-01-01

The ability of seed-borne bacterial pathogens (Acidovorax citrulli, Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato, Xanthomonas euvesicatoria, and Pseudomonas syringae pv. glycinea) to infest seeds of host and non-host plants (watermelon, tomato, pepper, and soybean) and subsequent pathogen transmission to seedlings was investigated. A non-pathogenic, pigmented strain of Serratia marcescens was also included to assess a null-interacting situation with the same plant species. Flowers of host and non-host plants were inoculated with 1×106 colony forming units (CFUs)/flower for each bacterial species and allowed to develop into fruits or umbels (in case of onion). Seeds harvested from each host/non-host bacterial species combination were assayed for respective bacteria by plating on semi-selective media. Additionally, seedlots for each host/non-host bacterial species combination were also assayed for pathogen transmission by seedling grow-out (SGO) assays under greenhouse conditions. The mean percentage of seedlots infested with compatible and incompatible pathogens was 31.7 and 30.9% (by plating), respectively and they were not significantly different (P = 0.67). The percentage of seedlots infested with null-interacting bacterial species was 16.8% (by plating) and it was significantly lower than the infested lots generated with compatible and incompatible bacterial pathogens (P = 0.03). None of the seedlots with incompatible/null-interacting bacteria developed symptoms on seedlings; however, when seedlings were assayed for epiphytic bacterial presence, 19.5 and 9.4% of the lots were positive, respectively. These results indicate that the seeds of non-host plants can become infested with incompatible and null-interacting bacterial species through flower colonization and they can be transmitted via epiphytic colonization of seedlings. In addition, it was also observed that flowers and seeds of non-host plants can be colonized by compatible/incompatible/null-interacting bacteria to higher populations; however, the level of colonization differed significantly depending on the type of bacterial species used. PMID:24936863

In vitro antioxidant activity and inhibitory effect, on oleic acid-induced hepatic steatosis, of fractions and subfractions from oat (Avena sativa L.) ethanol extract

USDA-ARS?s Scientific Manuscript database

Oats (Avena sativa L.) were extracted with 80% aqueous ethanol and the extract was successively isolated by liquid-liquid partition to yield n-hexane, ethyl acetate, n-butanol and water layers. Among these extractions the ethyl acetate (EA) layer exhibited the highest total phenolic content (TPC), t...

Unravelling mycorrhiza-induced wheat susceptibility to the English grain aphid Sitobion avenae

PubMed Central

Simon, Amma L.; Wellham, Peter A. D.; Aradottir, Gudbjorg I.; Gange, Alan C.

2017-01-01

Arbuscular mycorrhizal (AM) fungi are root symbionts that can increase or decrease aphid growth rates and reproduction, but the reason by which this happens is unknown. To investigate the underlying mechanisms of this interaction, we examined the effect of AM fungi on the English Grain aphid (Sitobion avenae) development, reproduction, attraction, settlement and feeding behaviour on two naturally susceptible varieties Triticum aestivum (L.) variety Solstice and T. monococcum MDR037, and two naturally resistant lines, T. monococcum MDR045 and MDR049. Mycorrhizal colonisation increased the attractiveness of T. aestivum var. Solstice to aphids, but there was no effect on aphid development on this variety. Using the Electrical Penetration Graph (EPG) technique, we found that mycorrhizal colonisation increased aphid phloem feeding on T. monococcum MDR037 and MDR045, colonisation also increased growth rate and reproductive success of S. avenae on these varieties. Mycorrhizas increased vascular bundle size, demonstrating that these fungi can influence plant anatomy. We discuss if and how this could be related to an enhanced success rate in phloem feeding in two varieties. Overall, we present and discuss how mycorrhizal fungi can affect the feeding behaviour of S. avenae in wheat, inducing susceptibility in a resistant variety. PMID:28406246

Unravelling mycorrhiza-induced wheat susceptibility to the English grain aphid Sitobion avenae

NASA Astrophysics Data System (ADS)

Simon, Amma L.; Wellham, Peter A. D.; Aradottir, Gudbjorg I.; Gange, Alan C.

2017-04-01

Arbuscular mycorrhizal (AM) fungi are root symbionts that can increase or decrease aphid growth rates and reproduction, but the reason by which this happens is unknown. To investigate the underlying mechanisms of this interaction, we examined the effect of AM fungi on the English Grain aphid (Sitobion avenae) development, reproduction, attraction, settlement and feeding behaviour on two naturally susceptible varieties Triticum aestivum (L.) variety Solstice and T. monococcum MDR037, and two naturally resistant lines, T. monococcum MDR045 and MDR049. Mycorrhizal colonisation increased the attractiveness of T. aestivum var. Solstice to aphids, but there was no effect on aphid development on this variety. Using the Electrical Penetration Graph (EPG) technique, we found that mycorrhizal colonisation increased aphid phloem feeding on T. monococcum MDR037 and MDR045, colonisation also increased growth rate and reproductive success of S. avenae on these varieties. Mycorrhizas increased vascular bundle size, demonstrating that these fungi can influence plant anatomy. We discuss if and how this could be related to an enhanced success rate in phloem feeding in two varieties. Overall, we present and discuss how mycorrhizal fungi can affect the feeding behaviour of S. avenae in wheat, inducing susceptibility in a resistant variety.

Characterization of three novel fatty acid- and retinoid-binding protein genes (Ha-far-1, Ha-far-2 and Hf-far-1) from the cereal cyst nematodes Heterodera avenae and H. filipjevi

USDA-ARS?s Scientific Manuscript database

Heterodera avenae and H. filipjevi are major parasites of wheat, reducing production worldwide. Both are sedentary endoparasitic nematodes, and their development and parasitism depend strongly on nutrients obtained from hosts. Secreted fatty acid- and retinoid-binding (FAR) proteins are nematode-spe...

De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

USDA-ARS?s Scientific Manuscript database

Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle Pca is dikaryotic with two separate haploid nuclei that may vary in virulence genotypes, which highlights the importance of understan...

Resistance of Wheat Accessions to the English Grain Aphid Sitobion avenae

PubMed Central

Hu, Xiang-Shun; Liu, Ying-Jie; Wang, Yu-Han; Wang, Zhe; Yu, Xin-lin; Wang, Bo; Zhang, Gai-Sheng; Liu, Xiao-Feng; Hu, Zu-Qing; Zhao, Hui-Yan; Liu, Tong-Xian

2016-01-01

The English grain aphid, Sitobion avenae, is a major pest species of wheat crops; however, certain varieties may have stronger resistance to infestation than others. Here, we investigated 3 classical resistance mechanisms (antixenosis, antibiosis, and tolerance) by 14 wheat varieties/lines to S. avenae under laboratory and field conditions. Under laboratory conditions, alatae given the choice between 2 wheat varieties, strongly discriminated against certain varieties. Specifically, the ‘Amigo’ variety had the lowest palatability to S. avenae alatae of all varieties. ‘Tm’ (Triticum monococcum), ‘Astron,’ ‘Xanthus,’ ‘Ww2730,’ and ‘Batis’ varieties also had lower palatability than other varieties. Thus, these accessions may use antibiosis as the resistant mechanism. In contrast, under field conditions, there were no significant differences in the number of alatae detected on the 14 wheat varieties. One synthetic line (98-10-30, a cross between of Triticum aestivum (var. Chris) and Triticum turgidum (var. durum) hybridization) had low aphid numbers but high yield loss, indicating that it has high antibiosis, but poor tolerance. In comparison, ‘Amigo,’ ‘Xiaoyan22,’ and some ‘186Tm’ samples had high aphid numbers but low yield loss rates, indicating they have low antibiosis, but good tolerance. Aphid population size and wheat yield loss rates greatly varied in different fields and years for ‘98-10-35,’ ‘Xiaoyan22,’ ‘Tp,’ ‘Tam200,’ ‘PI high,’ and other ‘186Tm’ samples, which were hybrid offspring of T. aestivum and wheat related species. Thus, these germplasm should be considered for use in future studies. Overall, S. avenae is best adapted to ‘Xinong1376,’ because it was the most palatable variety, with the greatest yield loss rates of all 14 wheat varieties. However, individual varieties/lines influenced aphid populations differently in different years. Therefore, we strongly recommend a combination of laboratory and long-term field experiments in targeted planting regions to identify varieties/lines that consistently show high resistance to S. avenae infestation. PMID:27249206

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

PubMed Central

Miller, Marisa E.; Zhang, Ying; Omidvar, Vahid; Sperschneider, Jana; Raley, Castle; Palmer, Jonathan M.; Garnica, Diana; Upadhyaya, Narayana; Rathjen, John; Taylor, Jennifer M.; Park, Robert F.; Dodds, Peter N.; Hirsch, Cory D.

2018-01-01

ABSTRACT Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae. PMID:29463655

Polyamine levels as related to growth, differentiation and senescence in protoplast-derived cultures of Vigna aconitifolia and Avena sativa

NASA Technical Reports Server (NTRS)

Kaur Sawhney, R.; Shekhawat, N. S.; Galston, A. W.

1985-01-01

We have previously reported that aseptically cultured mesophyll protoplasts of Vigna divide rapidly and regenerate into complete plants, while mesophyll protoplasts of Avena divide only sporadically and senesce rapidly after isolation. We measured polyamine titers in such cultures of Vigna and Avena, to study possible correlations between polyamines and cellular behavior. We also deliberately altered polyamine titer by the use of selective inhibitors of polyamine biosynthesis, noting the effects on internal polyamine titer, cell division activity and regenerative events. In Vigna cultures, levels of free and bound putrescine and spermidine increased dramatically as cell division and differentiation progressed. The increase in bound polyamines was largest in embryoid-forming callus tissue while free polyamine titer was highest in root-forming callus. In Avena cultures, the levels of total polyamines decreased as the protoplast senesced. The presence of the inhibitors alpha-difluoromethyl-arginine (specific inhibitor of arginine decarboxylase), alpha-difluoromethylornithine (specific inhibitor of ornithine decarboxylase) and dicyclohexylamine (inhibitor of spermidine synthase) reduced cell division and organogenesis in Vigna cultures. Addition of low concentration of polyamines to such cultures containing inhibitors or removal of inhibitors from the culture medium restored the progress of growth and differentiation with concomitant increase in polyamine levels.

New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.

USDA-ARS?s Scientific Manuscript database

Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD genomes) are well recognized; however, seed protein levels are modest and genetic resources for protein improvement are scarce. The wild tetraploid A. magna Ladiz. contains approximately 31% seed protein and has been hybr...

Exploring the origin of the D genome of oat by fluorescence in situ hybridization.

PubMed

Luo, Xiaomei; Zhang, Haiqin; Kang, Houyang; Fan, Xing; Wang, Yi; Sha, Lina; Zhou, Yonghong

2014-09-01

Further understanding of the origin of cultivated oat would accelerate its genetic improvement. In particular, it would be useful to clarify which diploid progenitor contributed the D genome of this allohexaploid species. In this study, we demonstrate that the landmarks produced by fluorescence in situ hybridization (FISH) of species of Avena using probes derived from Avena sativa can be used to explore the origin of the D genome. Selected sets of probes were hybridized in several sequential experiments performed on exactly the same chromosome spreads, with multiple probes of cytological preparations. Probes pITS and A3-19 showed there might be a similar distribution of pITS between the Ac and D genomes. These results indicated that the Ac genome is closely related to the D genome, and that Avena canariensis (AcAc) could be the D-genome donor of cultivated oat.

Biocontrol of Bacterial Fruit Blotch by Bacillus subtilis 9407 via Surfactin-Mediated Antibacterial Activity and Colonization

PubMed Central

Fan, Haiyan; Zhang, Zhanwei; Li, Yan; Zhang, Xun; Duan, Yongming; Wang, Qi

2017-01-01

In this study, Bacillus subtilis 9407 showed a strong antibacterial activity against Acidovorax citrulli in vitro and 61.7% biocontrol efficacy on melon seedlings 4 days post inoculation under greenhouse conditions. To understand the biocontrol mechanism of B. subtilis 9407, identify the primary antibacterial compound and determine its role in controlling bacterial fruit blotch (BFB), a srfAB deletion mutant (ΔsrfAB) was constructed. The ΔsrfAB which was deficient in production of surfactin, not only showed almost no ability to inhibit growth of A. citrulli but also decreased biofilm formation and reduced swarming motility. Colonization assay demonstrated that B. subtilis 9407 could conlonize on melon roots and leaves in a large population, while ΔsrfAB showed a four- to ten-fold reduction in colonization of melon roots and leaves. Furthermore, a biocontrol assay showed that ΔsrfAB lost the biocontrol efficacy. In summary, our results indicated that surfactin, which consists of C13- to C16-surfactin A was the primary antibacterial compound of B. subtilis 9407, and it played a major role in biofilm formation, swarming motility, colonization and suppressing BFB. We propose that the biocontrol activity of B. subtilis 9407 is the results of the coordinated action of surfactin-mediated antibacterial activity and colonization. This study reveals for the first time that the use of a B. subtilis strain as a potential biological control agent could efficiently control BFB by producing surfactin. PMID:29075242

Biocontrol of Bacterial Fruit Blotch by Bacillus subtilis 9407 via Surfactin-Mediated Antibacterial Activity and Colonization.

PubMed

Fan, Haiyan; Zhang, Zhanwei; Li, Yan; Zhang, Xun; Duan, Yongming; Wang, Qi

2017-01-01

In this study, Bacillus subtilis 9407 showed a strong antibacterial activity against Acidovorax citrulli in vitro and 61.7% biocontrol efficacy on melon seedlings 4 days post inoculation under greenhouse conditions. To understand the biocontrol mechanism of B. subtilis 9407, identify the primary antibacterial compound and determine its role in controlling bacterial fruit blotch (BFB), a srfAB deletion mutant (Δ srfAB ) was constructed. The Δ srfAB which was deficient in production of surfactin, not only showed almost no ability to inhibit growth of A. citrulli but also decreased biofilm formation and reduced swarming motility. Colonization assay demonstrated that B. subtilis 9407 could conlonize on melon roots and leaves in a large population, while Δ srfAB showed a four- to ten-fold reduction in colonization of melon roots and leaves. Furthermore, a biocontrol assay showed that Δ srfAB lost the biocontrol efficacy. In summary, our results indicated that surfactin, which consists of C13- to C16-surfactin A was the primary antibacterial compound of B. subtilis 9407, and it played a major role in biofilm formation, swarming motility, colonization and suppressing BFB. We propose that the biocontrol activity of B. subtilis 9407 is the results of the coordinated action of surfactin-mediated antibacterial activity and colonization. This study reveals for the first time that the use of a B. subtilis strain as a potential biological control agent could efficiently control BFB by producing surfactin.

Aphid Species Affect Foraging Behavior of Coccinella septempunctata (Coccinellidae: Coleoptera).

PubMed

Farooq, Muhammad Umar; Qadri, Hafiz Faqir Hussain; Khan, Muhammad Ahmad

2017-01-01

Flowers are admirable in scenic good looks and artistic beautification. These are also playing necessary roles in therapeutic preparations. Aphid is an important sucking pest of various flowers in ornamental territories and it is generally controlled by predators, so it was necessary to evaluate which aphid species affect the predator more or less. Biocontrol agent Coccinella septempunctata was used against cosmos aphid (Aphis spiraecola, rose aphid (Macrosiphum rosea), gul e ashrafi aphid (Aphis fabae), kaner aphid (Aphis nerii), chandni aphid (Sitobion avenae), dahlia aphid (Myzus persicae) and annual chrysanthemum aphid (Macrosiphoniella sanborni). The grub of C. septempunctata consumed 283.8±9.04 M. rosea, 487.7±12.6 M. sanborni, 432.75±16.02 A. spiraecola, 478.2±8.07 A. fabae, 552.3±9.04 M. persicae, 142±1.32 A. nerii and 498.5±13.09 S. avenae in its whole larval life. The M. persicae and M. rosea consuming grubs showed 100% adult emergence while, M. sanborni, A. spiraecola, A. fabae and S. avenae showed 96.58, 89.02, 94.78 and 75.45% adult emergence, respectively. The C. septempunctata has significant predatory potential against A. spiraecola, M. rosea, A. fabae, S. avenae, M. persicae and M. sanborni except A. nerii. Thus, further studies are needed to find out alternate predator to control A. nerii on ornamentals.

Identification of Mycobacterium avium subsp. hominissuis Isolated From Drinking Water

EPA Science Inventory

Mycobacterium avium (MA) is divided into four subspecies based primarily on host-range and consists of MA subsp. avium (birds), MA subsp. silvaticum (wood pigeons), MA subsp. paratuberculosis (broad, poorly-defined host range), and the recently described MA subsp. hominissuis (hu...

Comparative genomics of Campylobacter fetus from reptiles and mammals reveals divergent evolution in host-associated lineages

USDA-ARS?s Scientific Manuscript database

Campylobacter fetus currently comprises three recognized subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis, and C. fetus subsp. testudinum, which display a distinct host association. Both C. fetus subsp. fetus and C. fetus subsp. venerealis are associated with endothermic mammals, primar...

Cell wall and enzyme changes during the graviresponse of the leaf-sheath pulvinus of oat (Avena sativa)

NASA Technical Reports Server (NTRS)

Gibeaut, David M.; Karuppiah, Nadarajah; Chang, S.-R.; Brock, Thomas G.; Vadlamudi, Babu; Kim, Donghern; Ghosheh, Najati S.; Rayle, David L.; Carpita, Nicholas C.; Kaufman, Peter B.

1990-01-01

The graviresponse of the leaf-sheath pulvinus of oat (Avena sativa) involves an asymmetric growth response and asymmetric processes involving degradation of starch and cell wall synthesis. Cellular and biochemical events were studied by investigation of the activities of related enzymes and changes in cell walls and their constituents. It is suggested that an osmotic potential gradient acts as the driving factor for growth, while wall extensibility is a limiting factor in pulvinus growth.

Lactococcus lactis subsp. tructae subsp. nov. isolated from the intestinal mucus of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss).

PubMed

Pérez, Tania; Balcázar, José Luis; Peix, Alvaro; Valverde, Angel; Velázquez, Encarna; de Blas, Ignacio; Ruiz-Zarzuela, Imanol

2011-08-01

The species Lactococcus lactis currently includes three subspecies; L. lactis subsp. lactis and L. lactis subsp. cremoris, isolated from milk sources, and L. lactis subsp. hordniae, isolated from the leafhopper Hordnia circellata. In this study, three strains, designated L105(T), I3 and L101, were isolated from the intestinal mucus of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss). These strains were closely related to members of the species Lactococcus lactis. Strain L105(T) showed 99.4 % 16S rRNA gene sequence similarity to that of the type strains L. lactis subsp. lactis NCDO 604(T) and L. lactis subsp. hordniae NCDO 2181(T) and showed 99.9 % similarity to the type strain Lactococcus lactis subsp. cremoris NCDO 607(T). Analysis of two housekeeping genes, rpoB and recA, confirmed the close relationship between the novel strains and L. lactis subsp. cremoris with similarities of 99.3 and 99.7 %, respectively. The three strains could, however, be differentiated from their closest relatives on the basis of several phenotypic characteristics, as was the case for L. lactis subsp. lactis and L. lactis subsp. hordniae, which were also closely related on the basis of 16S rRNA, rpoB and recA gene sequence similarities. The strains isolated in this study represent a new subspecies, for which the name Lactococcus lactis subsp. tructae subsp. nov. is proposed. The type strain is L105(T) ( = LMG 24662(T)  = DSM 21502(T)).

The outer epidermis of Avena and maize coleoptiles is not a unique target for auxin in elongation growth

NASA Technical Reports Server (NTRS)

Cleland, R. E.

1991-01-01

A controversy exists as to whether or not the outer epidermis in coleoptiles is a unique target for auxin in elongation growth. The following evidence indicates that the outer epidermis is not the only auxin-responsive cell layer in either Avena sativa L. or Zea mays L. coleoptiles. Coleoptile sections from which the epidermis has been removed by peeling elongate in response to auxin. The magnitude of the response is similar to that of intact sections provided the incubation solution contains both auxin and sucrose. The amount of elongation is independent of the amount of epidermis removed. Sections of oat coleoptiles from which the epidermis has been removed from one side are nearly straight after 22 h in auxin and sucrose, despite extensive growth of the sections. These data indicate that the outer epidermis is not a unique target for auxin in elongation growth, at least in Avena and maize coleoptiles.

Association analysis of resistance to cereal cyst nematodes (Heterodera avenae) and root lesion nematodes (Pratylenchus neglectus and P. thornei) in CIMMYT advanced spring wheat lines for semi-arid conditions.

PubMed

Dababat, Abdelfattah A; Ferney, Gomez-Becerra Hugo; Erginbas-Orakci, Gul; Dreisigacker, Susanne; Imren, Mustafa; Toktay, Halil; Elekcioglu, Halil I; Mekete, Tesfamariam; Nicol, Julie M; Ansari, Omid; Ogbonnaya, Francis

2016-12-01

To identify loci linked to nematode resistance genes, a total of 126 of CIMMYT advanced spring wheat lines adapted to semi-arid conditions were screened for resistance to Heterodera avenae , Pratylenchus neglectus , and P. thornei , of which 107 lines were genotyped with 1,310 DArT. Association of DArT markers with nematode response was analyzed using the general linear model. Results showed that 11 markers were associated with resistance to H. avenae (pathotype Ha21), 25 markers with resistance to P. neglectus , and 9 significant markers were identified to be linked with resistance to P. thornei . In this work we confirmed that chromosome 4A (~90-105 cM) can be a source of resistance to P. thornei as has been recently reported. Other significant markers were also identified on chromosomal regions where no resistant genes have been reported for both nematodes species. These novel QTL were mapped to chromosomes 5A, 6A, and 7A for H. avenae ; on chromosomes 1A, 1B, 3A, 3B, 6B, 7AS, and 7D for P. neglectus ; and on chromosomes 1D, 2A, and 5B for P. thornei and represent potentially new loci linked to resistance that may be useful for selecting parents and deploying resistance into elite germplasm adapted to regions where nematodes are causing problem.

Biochemical and molecular characterization of Avena indolines and their role in kernel texture.

PubMed

Gazza, Laura; Taddei, Federica; Conti, Salvatore; Gazzelloni, Gloria; Muccilli, Vera; Janni, Michela; D'Ovidio, Renato; Alfieri, Michela; Redaelli, Rita; Pogna, Norberto E

2015-02-01

Among cereals, Avena sativa is characterized by an extremely soft endosperm texture, which leads to some negative agronomic and technological traits. On the basis of the well-known softening effect of puroindolines in wheat kernel texture, in this study, indolines and their encoding genes are investigated in Avena species at different ploidy levels. Three novel 14 kDa proteins, showing a central hydrophobic domain with four tryptophan residues and here named vromindoline (VIN)-1,2 and 3, were identified. Each VIN protein in diploid oat species was found to be synthesized by a single Vin gene whereas, in hexaploid A. sativa, three Vin-1, three Vin-2 and two Vin-3 genes coding for VIN-1, VIN-2 and VIN-3, respectively, were described and assigned to the A, C or D genomes based on similarity to their counterparts in diploid species. Expression of oat vromindoline transgenes in the extra-hard durum wheat led to accumulation of vromindolines in the endosperm and caused an approximate 50 % reduction of grain hardness, suggesting a central role for vromindolines in causing the extra-soft texture of oat grain. Further, hexaploid oats showed three orthologous genes coding for avenoindolines A and B, with five or three tryptophan residues, respectively, but very low amounts of avenoindolines were found in mature kernels. The present results identify a novel protein family affecting cereal kernel texture and would further elucidate the phylogenetic evolution of Avena genus.

Biology and management of Avena fatua and Avena ludoviciana: two noxious weed species of agro-ecosystems.

PubMed

Bajwa, Ali Ahsan; Akhter, Muhammad Javaid; Iqbal, Nadeem; Peerzada, Arslan Masood; Hanif, Zarka; Manalil, Sudheesh; Hashim, Saima; Ali, Hafiz Haider; Kebaso, Lynda; Frimpong, David; Namubiru, Halima; Chauhan, Bhagirath Singh

2017-08-01

Avena fatua and Avena ludoviciana are closely related grass weed species infesting a large number of crops around the world. These species are widely distributed in diverse agro-ecosystems from temperate to sub-tropical regions due to their unique seed traits, successful germination ecology, high competitive ability, and allelopathic potential. A. fatua is more widespread, adaptable, and problematic than A. ludoviciana. Both these species infest major winter and spring crops, including wheat, oat, barley, canola, maize, alfalfa, and sunflower, causing up to 70% yield losses depending on crop species and weed density. Chemical control has been challenged by large-scale herbicide resistance evolution in these weed species. A. fatua is the most widespread herbicide-resistant weed in the world, infesting about 5 million hectares in 13 countries. The use of alternative herbicides with different modes of action has proved effective. Several cultural practices, including diverse crop rotations, cover crops, improved crop competition (using competitive cultivars, high seed rates, narrow row spacing, altered crop geometry), and allelopathic suppression, have shown promise for controlling A. fatua and A. ludoviciana. The integrated use of these cultural methods can reduce the herbicide dose required, and lower dependency on herbicides to control these grasses. Moreover, integrated management may successfully control herbicide-resistant populations of these weed species. The use of integrated approaches based on the knowledge of biology and ecology of A. fatua and A. ludoviciana may help to manage them sustainably in the future.

Thermal Inactivation of Mycobacterium avium subsp. paratuberculosis in Artificially Contaminated Milk by Direct Steam Injection

PubMed Central

Butot, Sophie; Jagadeesan, Balamurugan; Bakker, Douwe; Donaghy, John

2016-01-01

ABSTRACT The efficiency of direct steam injection (DSI) at 105°C for 3 s to inactivate Mycobacterium avium subsp. paratuberculosis in milk at a pilot-plant scale was investigated. Milk samples were artificially contaminated with M. avium subsp. paratuberculosis and also with cow fecal material naturally infected with M. avium subsp. paratuberculosis. We also tested milk artificially contaminated with Mycobacterium smegmatis as a candidate surrogate to compare thermal inactivation between M. smegmatis and M. avium subsp. paratuberculosis. Following the DSI process, no viable M. avium subsp. paratuberculosis or M. smegmatis was recovered using culture methods for both strains. For pure M. avium subsp. paratuberculosis cultures, a minimum reduction of 5.6 log10 was achieved with DSI, and a minimum reduction of 5.7 log10 was found with M. smegmatis. The minimum log10 reduction for wild-type M. avium subsp. paratuberculosis naturally present in feces was 3.3. In addition, 44 dairy and nondairy powdered infant formula (PIF) ingredients used during the manufacturing process of PIF were tested for an alternate source for M. avium subsp. paratuberculosis and were found to be negative by quantitative PCR (qPCR). In conclusion, the results obtained from this study indicate that a >7-fold-log10 reduction of M. avium subsp. paratuberculosis in milk can be achieved with the applied DSI process. IMPORTANCE M. avium subsp. paratuberculosis is widespread in dairy herds in many countries. M. avium subsp. paratuberculosis is the causative agent of Johne's disease in cattle, and infected animals can directly or indirectly (i.e., fecal contamination) contaminate milk. Despite much research and debate, there is no conclusive evidence that M. avium subsp. paratuberculosis is a zoonotic bacterium, i.e., one that causes disease in humans. The presence of M. avium subsp. paratuberculosis or its DNA has been reported in dairy products, including pasteurized milk, cheese, and infant formula. In light of this, it is appropriate to evaluate existing mitigation measures to inactivate M. avium subsp. paratuberculosis in dairy products. The work conducted in this study describes the efficacy of direct steam injection, a thermal process commonly used in the dairy industry, to eliminate M. avium subsp. paratuberculosis and a surrogate bacterium in milk, thus ensuring the absence of M. avium subsp. paratuberculosis in dairy products subject to these process conditions. PMID:26944840

Molecular Characterization of Copper Resistance Genes from Xanthomonas citri subsp. citri and Xanthomonas alfalfae subsp. citrumelonis▿

PubMed Central

Behlau, Franklin; Canteros, Blanca I.; Minsavage, Gerald V.; Jones, Jeffrey B.; Graham, James H.

2011-01-01

Copper sprays have been widely used for control of endemic citrus canker caused by Xanthomonas citri subsp. citri in citrus-growing areas for more than 2 decades. Xanthomonas alfalfae subsp. citrumelonis populations were also exposed to frequent sprays of copper for several years as a protective measure against citrus bacterial spot (CBS) in Florida citrus nurseries. Long-term use of these bactericides has led to the development of copper-resistant (Cur) strains in both X. citri subsp. citri and X. alfalfae subsp. citrumelonis, resulting in a reduction of disease control. The objectives of this study were to characterize for the first time the genetics of copper resistance in X. citri subsp. citri and X. alfalfae subsp. citrumelonis and to compare these organisms to other Cur bacteria. Copper resistance determinants from X. citri subsp. citri strain A44(pXccCu2) from Argentina and X. alfalfae subsp. citrumelonis strain 1381(pXacCu2) from Florida were cloned and sequenced. Open reading frames (ORFs) related to the genes copL, copA, copB, copM, copG, copC, copD, and copF were identified in X. citri subsp. citri A44. The same ORFs, except copC and copD, were also present in X. alfalfae subsp. citrumelonis 1381. Transposon mutagenesis of the cloned copper resistance determinants in pXccCu2 revealed that copper resistance in X. citri subsp. citri strain A44 is mostly due to copL, copA, and copB, which are the genes in the cloned cluster with the highest nucleotide homology (≥92%) among different Cur bacteria. PMID:21515725

Dissecting the taxonomic heterogeneity within Propionibacterium acnes: proposal for Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov.

PubMed

Dekio, Itaru; Culak, Renata; Misra, Raju; Gaulton, Tom; Fang, Min; Sakamoto, Mitsuo; Ohkuma, Moriya; Oshima, Kenshiro; Hattori, Masahira; Klenk, Hans-Peter; Rajendram, Dunstan; Gharbia, Saheer E; Shah, Haroun N

2015-12-01

Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov. are described. These emanate from the three known phylotypes of P. acnes, designated types I, II and III. Electron microscopy confirmed the filamentous cell shape of type III, showing a striking difference from types I/II, which were short rods. Biochemical tests indicated that, in types I/II, either the pyruvate, l-pyrrolidonyl arylamidase or d-ribose 2 test was positive, whereas all of these were negative among type III strains. Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectra, which profile mainly their ribosomal proteins, were different between these two groups. Surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) spectra of all phylotypes revealed a specific protein biomarker that was overexpressed in type III strains compared with types I/II only when grown aerobically. Reference strains had high whole-genome similarity between types I (>91 %) and II (>75 %), but a considerably lower level of 72 % similarity with type III. recA and gyrB sequence dendrograms confirmed the distant relatedness of type III, indicating the presence of two distinct centres of variation within the species P. acnes. On the other hand, cellular fatty acid profiles and 16S rRNA gene sequence relatedness (>99.3 %) circumscribed the species. Thus, we propose two subspecies, Propionibacterium acnes subsp. acnes subsp. nov. for types I/II and Propionibacterium acnes subsp. elongatum subsp. nov. for type III. The type strain of Propionibacterium acnes subsp. acnes is NCTC 737T ( = ATCC 6919T = JCM 6425T = DSM 1897T = CCUG 1794T), while the type strain of Propionibacterium acnes subsp. elongatum is K124T ( = NCTC 13655T = JCM 18919T).

Role of Antibiosis in Competition of Erwinia Strains in Potato Infection Courts

PubMed Central

Axelrood, Paige E.; Rella, Manuela; Schroth, Milton N.

1988-01-01

Erwinia carotovora subsp. betavasculorum strains produced a bactericidal antibiotic in vitro that inhibited a wide spectrum of gram-negative and gram-positive bacteria. The optimum temperature for production was 24°C, and the addition of glycerol to culture media enhanced antibiotic production. Antibiotic production by these strains in the infection court of potato was the principal determinant enabling it to gain ascendancy over competing antibiotic-sensitive Erwinia carotovora subsp. carotovora strains. There was a complete correlation between antibiotic production by E. carotovora subsp. betavasculorum in vitro and inhibition of competing E. carotovora subsp. carotovora strains in planta. Inhibition of the latter by the former was apparent after 10 h of incubation in potato tuber wounds. Population densities of sensitive E. carotovora subsp. carotovora strains in mixed potato tuber infections with E. carotovora subsp. betavasculorum were approximately 106-fold lower after 48 h of incubation than in corresponding single sensitive strain infections. E. carotovora subsp. carotovora were not inhibited in tuber infections that were incubated anaerobically. This correlated with the absence of antibiotic production during anaerobic incubation in vitro. Antibiotic-resistant strains of E. carotovora subsp. carotovora were not inhibited in planta or in vitro by E. carotovora subsp. betavasculorum. Moreover, isogenic antibiotic-negative (Ant−) mutant E. carotovora subsp. betavasculorum strains were not inhibitory to sensitive E. carotovora subsp. carotovora strains in tuber infections. PMID:16347633

Electrophoretic Analysis of Diversity and Phylogeny of Pinus brutia and Closely Related Taxa

Treesearch

M. T. Conkle; G. Schiller; C. Grunwald

1988-01-01

Rangewide samples from mature natural stands of Pinus brutia Ten. subsp. brutia, subsp. stankewiczii (Sukaczew) Nahal, subsp. pithyusa (Stevenson) Nahal, and subsp. eldarica (Medw.) Nahal from throughout the eastern Mediterranean display a continuum of allozyme variation for...

Effect of Soil Slope on the Appearance of Mycobacterium avium subsp. paratuberculosis in Water Running off Grassland Soil after Application of Contaminated Slurry

PubMed Central

Alfaro, M.; Salazar, F.; Troncoso, E.; Mitchell, R. M.; Ramirez, L.; Naguil, A.; Zamorano, P.; Collins, M. T.

2013-01-01

The study assessed the effect of soil slope on Mycobacterium avium subsp. paratuberculosis transport into rainwater runoff from agricultural soil after application of M. avium subsp. paratuberculosis-contaminated slurry. Under field conditions, 24 plots of undisturbed loamy soil 1 by 2 m2 were placed on platforms. Twelve plots were used for water runoff: 6 plots at a 3% slope and 6 plots at a 15% slope. Half of the plots of each slope were treated with M. avium subsp. paratuberculosis-contaminated slurry, and half were not treated. Using the same experimental design, 12 plots were established for soil sampling on a monthly basis using the same spiked slurry application and soil slopes. Runoff following natural rainfall was collected and analyzed for M. avium subsp. paratuberculosis, coliforms, and turbidity. M. avium subsp. paratuberculosis was detected in runoff from all plots treated with contaminated slurry and one control plot. A higher slope (15%) increased the likelihood of M. avium subsp. paratuberculosis detection but did not affect the likelihood of finding coliforms. Daily rainfall increased the likelihood that runoff would have coliforms and the coliform concentration, but it decreased the M. avium subsp. paratuberculosis concentration in the runoff. When there was no runoff, rain was associated with increased M. avium subsp. paratuberculosis concentrations. Coliform counts in runoff were related to runoff turbidity. M. avium subsp. paratuberculosis presence/absence, however, was related to turbidity. Study duration decreased bacterial detection and concentration. These findings demonstrate the high likelihood that M. avium subsp. paratuberculosis in slurry spread on pastures will contaminate water runoff, particularly during seasons with high rainfall. M. avium subsp. paratuberculosis contamination of water has potential consequences for both animal and human health. PMID:23542616

The first closed genome sequence of Campylobacter fetus subsp. venerealis biovar intermedius

USDA-ARS?s Scientific Manuscript database

Campylobacter fetus venerealis biovar intermedius is a variant of Campylobacter fetus subsp. venerealis, the causative agent of Bovine Genital Campylobacteriosis. In contrast to Campylobacter fetus subsp. venerealis which is restricted to the genital tract of cattle, Campylobacter fetus subsp. vener...

Detoxification of Benzoxazolinone Allelochemicals from Wheat by Gaeumannomyces graminis var. tritici, G. graminis var. graminis, G. graminis var. avenae, and Fusarium culmorum

PubMed Central

Friebe, A.; Vilich, V.; Hennig, L.; Kluge, M.; Sicker, D.

1998-01-01

The ability of phytopathogenic fungi to overcome the chemical defense barriers of their host plants is of great importance for fungal pathogenicity. We studied the role of cyclic hydroxamic acids and their related benzoxazolinones in plant interactions with pathogenic fungi. We identified species-dependent differences in the abilities of Gaeumannomyces graminis var. tritici, Gaeumannomyces graminis var. graminis, Gaeumannomyces graminis var. avenae, and Fusarium culmorum to detoxify these allelochemicals of gramineous plants. The G. graminis var. graminis isolate degraded benzoxazolin-2(3H)-one (BOA) and 6-methoxy-benzoxazolin-2(3H)-one (MBOA) more efficiently than did G. graminis var. tritici and G. graminis var. avenae. F. culmorum degraded BOA but not MBOA. N-(2-Hydroxyphenyl)-malonamic acid and N-(2-hydroxy-4-methoxyphenyl)-malonamic acid were the primary G. graminis var. graminis and G. graminis var. tritici metabolites of BOA and MBOA, respectively, as well as of the related cyclic hydroxamic acids. 2-Amino-3H-phenoxazin-3-one was identified as an additional G. graminis var. tritici metabolite of BOA. No metabolite accumulation was detected for G. graminis var. avenae and F. culmorum by high-pressure liquid chromatography. The mycelial growth of the pathogenic fungi was inhibited more by BOA and MBOA than by their related fungal metabolites. The tolerance of Gaeumannomyces spp. for benzoxazolinone compounds is correlated with their detoxification ability. The ability of Gaeumannomyces isolates to cause root rot symptoms in wheat (cultivars Rektor and Astron) parallels their potential to degrade wheat allelochemicals to nontoxic compounds. PMID:9647804

rep-PCR-Mediated Genomic Fingerprinting: A Rapid and Effective Method to Identify Clavibacter michiganensis.

PubMed

Louws, F J; Bell, J; Medina-Mora, C M; Smart, C D; Opgenorth, D; Ishimaru, C A; Hausbeck, M K; de Bruijn, F J; Fulbright, D W

1998-08-01

ABSTRACT The genomic DNA fingerprinting technique known as repetitive-sequence-based polymerase chain reaction (rep-PCR) was evaluated as a tool to differentiate subspecies of Clavibacter michiganensis, with special emphasis on C. michiganensis subsp. michiganensis, the pathogen responsible for bacterial canker of tomato. DNA primers (REP, ERIC, and BOX), corresponding to conserved repetitive element motifs in the genomes of diverse bacterial species, were used to generate genomic fingerprints of C. michiganensis subsp. michiganensis, C. michiganensis subsp. sepedonicus, C. michiganensis subsp. nebraskensis, C. michiganensis subsp. tessellarius, and C. michiganensis subsp. insidiosum. The rep-PCR-generated patterns of DNA fragments observed after agarose gel electrophoresis support the current division of C. michiganensis into five subspecies. In addition, the rep-PCR fingerprints identified at least four types (A, B, C, and D) within C. michiganensis subsp. michiganensis based on limited DNA polymorphisms; the ability to differentiate individual strains may be of potential use in studies on the epidemiology and host-pathogen interactions of this organism. In addition, we have recovered from diseased tomato plants a relatively large number of naturally occurring avirulent C. michiganensis subsp. michiganensis strains with rep-PCR fingerprints identical to those of virulent C. michiganensis subsp. michiganensis strains.

Tulipa cinnabarina subsp. toprakii (Liliaceae), a new subspecies from southwestern Anatolia.

PubMed

Eker, İsmail; Yıldırım, Hasan; Altıoğlu, Yusuf

2016-01-01

A new subpecies, Tulipa cinnabarina subsp. toprakii subsp. nov. (Liliaceae) from Turkey is described. Diagnostic characters, descriptions, detailed illustrations, geographical distribution, conservation status and ecological observations on the new taxon are provided. It is also compared with the closely related Tulipa cinnabarina subsp. cinnabarina.

Genome size variation in the genus Avena.

PubMed

Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

2016-03-01

Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

PCR-Mediated Detection and Quantification of the Goss's Wilt Pathogen Clavibacter michiganensis subsp. nebraskensis Via a Novel Gene Target.

PubMed

McNally, R Ryan; Ishimaru, Carol A; Malvick, Dean K

2016-12-01

Goss's leaf blight and wilt of maize (corn) is a significant and reemerging disease caused by the bacterium Clavibacter michiganensis subsp. nebraskensis. Despite its importance, molecular tools for diagnosing and studying this disease remain limited. We report the identification of CMN_01184 as a novel gene target and its use in conventional PCR (cPCR) and SYBR green-based quantitative PCR (qPCR) assays for specific detection and quantification of C. michiganensis subsp. nebraskensis. The cPCR and qPCR assays based on primers targeting CMN_01184 specifically amplified only C. michiganensis subsp. nebraskensis among a diverse collection of 129 bacterial and fungal isolates, including multiple maize bacterial and fungal pathogens, environmental organisms from agricultural fields, and all known subspecies of C. michiganensis. Specificity of the assays for detection of only C. michiganensis subsp. nebraskensis was also validated with field samples of C. michiganensis subsp. nebraskensis-infected and uninfected maize leaves and C. michiganensis subsp. nebraskensis-infested and uninfested soil. Detection limits were determined at 30 and 3 ng of pure C. michiganensis subsp. nebraskensis DNA, and 100 and 10 CFU of C. michiganensis subsp. nebraskensis for the cPCR and qPCR assays, respectively. Infection of maize leaves by C. michiganensis subsp. nebraskensis was quantified from infected field samples and was standardized using an internal maize DNA control. These novel, specific, and sensitive PCR assays based on CMN_01184 are effective for diagnosis of Goss's wilt and for studies of the epidemiology and host-pathogen interactions of C. michiganensis subsp. nebraskensis.

Tulipa cinnabarina subsp. toprakii (Liliaceae), a new subspecies from southwestern Anatolia

PubMed Central

Eker, İsmail; Yıldırım, Hasan; Altıoğlu, Yusuf

2016-01-01

Abstract A new subpecies, Tulipa cinnabarina subsp. toprakii subsp. nov. (Liliaceae) from Turkey is described. Diagnostic characters, descriptions, detailed illustrations, geographical distribution, conservation status and ecological observations on the new taxon are provided. It is also compared with the closely related Tulipa cinnabarina subsp. cinnabarina. PMID:27698585

Stoichiometric Correlation of Malate Accumulation with Auxin-dependent K+-H+ Exchange and Growth in Avena Coleoptile Segments 12

PubMed Central

Haschke, Hans-Peter; Lüttge, Ulrich

1975-01-01

The action of auxin in the promotion of growth has been suggested in the literature to depend on cell wall acidification. In a former investigation by the present authors the electrochemical balance in auxin-induced proton extrusion was shown to be maintained by potassium net uptake. The present paper reports data demonstrating that the elongation of Avena coleoptile segments is accompanied by an accumulation of malate, which is stoichiometrically correlated with potassium uptake. We concluded that this malate accumulation is required in a mechanism regulating intracellular pH. PMID:16659374

Effect of Gibberellic Acid on the Plasticity and Elasticity of Avena Stem Segments 1

PubMed Central

Adams, Paul A.; Montague, Michael J.; Tepfer, Mark; Rayle, David L.; Ikuma, Hiroshi; Kaufman, Peter B.

1975-01-01

Extensibility characteristics of Avena stem segments treated with gibberellic acid (GA) were investigated in living internodes using a microgrowth method and in partially extracted cell walls subjected to Instron extensometer analysis. Both techniques showed that treatment with GA greatly increases internodal plasticity, but has virtually no effect on internodal elasticity. The increase in plasticity occurred 1 to 2 hours after the initiation of hormone treatment, which is similar to the time of onset of GA-enhanced growth and cell wall synthesis. Cycloheximide was shown to inhibit the effect of GA on plasticity. PMID:16659388

Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

PubMed Central

Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

1999-01-01

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412T, which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains. PMID:10508059

Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis.

PubMed

Torriani, S; Zapparoli, G; Dellaglio, F

1999-10-01

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412(T), which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.

Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov.

USDA-ARS?s Scientific Manuscript database

During independent diagnostic screenings of otariid seals in California (US) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established Campylobacter taxa, were cultured from abscesses and internal organs of different seal species. A polyphasic study was unde...

Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles.

PubMed

Fitzgerald, Collette; Tu, Zheng Chao; Patrick, Mary; Stiles, Tracy; Lawson, Andy J; Santovenia, Monica; Gilbert, Maarten J; van Bergen, Marcel; Joyce, Kevin; Pruckler, Janet; Stroika, Steven; Duim, Birgitta; Miller, William G; Loparev, Vladimir; Sinnige, Jan C; Fields, Patricia I; Tauxe, Robert V; Blaser, Martin J; Wagenaar, Jaap A

2014-09-01

A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like strains from humans (n = 8) and reptiles (n = 5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA-DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to C. fetus but clearly differentiated from recognized subspecies of C. fetus. Therefore, this unique cluster of 13 strains represents a novel subspecies within the species C. fetus, for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427(T) ( = ATCC BAA-2539(T) = LMG 27499(T)) as the type strain. Although this novel taxon could not be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of C. fetus.

PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation to potato diseases.

PubMed Central

Darrasse, A; Priou, S; Kotoujansky, A; Bertheau, Y

1994-01-01

Using a sequenced pectate lyase-encoding gene (pel gene), we developed a PCR test for Erwinia carotovora. A set of primers allowed the amplification of a 434-bp fragment in E. carotovora strains. Among the 89 E. carotovora strains tested, only the Erwinia carotovora subsp. betavasculorum strains were not detected. A restriction fragment length polymorphism (RFLP) study was undertaken on the amplified fragment with seven endonucleases. The Sau3AI digestion pattern specifically identified the Erwinia carotovora subsp. atroseptica strains, and the whole set of data identified the Erwinia carotovora subsp. wasabiae strains. However, Erwinia carotovora subsp. carotovora and Erwinia carotovora subsp. odorifera could not be separated. Phenetic and phylogenic analyses of RFLP results showed E. carotovora subsp. atroseptica as a homogeneous group while E. carotovora subsp. carotovora and E. carotovora subsp. odorifera strains exhibited a genetic diversity that may result from a nonmonophyletic origin. The use of RFLP on amplified fragments in epidemiology and for diagnosis is discussed. Images PMID:7912502

[Resistance of Lactobacillus casei subsp. casei SY13 and Lactobacillus delbrueckii subsp. bulgaricus LJJ to reactive oxygen species].

PubMed

Zhang, Shuwen; Lv, Jiaping; Menghe, Bilige; Zhang, Heping; Zhang, Liyu; Song, Jinhui; Wang, Zhifei

2009-02-01

We evaluated antioxidative effect of two antioxidative strains, isolated from the traditional fermented dairy products. Both intact cells and cell-free extract of Lactobacillus casei subsp. casei SY13 and Lactobacillus delbrueckii subsp. bulgaricus LJJ were used to study the inhibited effect of linoleic acid peroxidation, the ability of scavenging 1,1-diphenyl-2-picrylhydrazyl radical, hydroxyl radical, superoxide anion radical,the ability of tolerancing hydrogen peroxide and the chelating capacity of ferrous ion and reducting activity. Lactobacillus casei subsp. casei SY13 and Lactobacillus delbrueckii subsp. bulgaricus LJJ demonstrated highest inhibition on linoleic acid peroxidation by 62.95% and 66.16%, respectively. The cell-free extract showed excellent scavenging superoxide anion and hydroxyl radicals activity. However, the intact cells of Lactobacillus delbrueckii subsp. bulgaricus LJJ scavenging superoxide and hydroxyl radicals capacity were not detected. The intact cells of Lactobacillus casei subsp. casei SY13 and Lactobacillus delbrueckii subsp. bulgaricus LJJ on 1,1-diphenyl-2-picrylhydrazyl radical scavenging ability and chelating ferrous ion capacity were superior to cell-free extract. The highest reduced activety was equivalent to 305 micromol/L and 294 micromol/L L-cysteine. Two latobacilli strains had good antioxidant capacity. As potential probiotics, it can be used in future.

Genetic variation in Mediterranean Helichrysum italicum (Asteraceae; Gnaphalieae): do disjunct populations of subsp. microphyllum have a common origin?

PubMed

Galbany-Casals, M; Blanco-Moreno, J M; Garcia-Jacas, N; Breitwieser, I; Smissen, R D

2011-07-01

The yellow-flowered everlasting daisy Helichrysum italicum (Asteraceae, Gnaphalieae) is widely distributed in the Mediterranean basin, where it grows in continuous and widespread populations in diverse open habitats. Helichrysum italicum subsp. microphyllum has a disjunct distribution in the Balearic Islands (Majorca and Dragonera), Corsica, Sardinia, Crete and Cyprus. Numerous morphological intermediates between subsp. italicum and subsp. microphyllum are known from Corsica, where the two subspecies co-occur. The aims of the study were to investigate if subsp. microphyllum has a common origin, constituting an independent gene pool from subsp. italicum, or if the morphological differences between subsp. microphyllum and subsp. italicum have arisen independently in different locations from a common wider gene pool. Our analyses of AFLP, cpDNA sequences and morphological characters show that there is geographic structure to the genetic variation within H. italicum, with eastern and western Mediterranean groups, which do not correspond with the division into subsp. microphyllum and subsp. italicum as currently circumscribed. Local selection on quantitative trait loci provides sufficient explanation for the morphological divergence observed and is consistent with genetic data. Within the western Mediterranean group of the species we found considerable polymorphism in chloroplast DNA sequences among and within some populations. Comparison with chloroplast DNA sequences from other Helichrysum species showed that some chloroplast haplotypes are shared across species. © 2010 German Botanical Society and The Royal Botanical Society of the Netherlands.

Homologous Recombination and Xylella fastidiosa Host-Pathogen Associations in South America.

PubMed

Coletta-Filho, Helvécio D; Francisco, Carolina S; Lopes, João R S; Muller, Christiane; Almeida, Rodrigo P P

2017-03-01

Homologous recombination affects the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity. Multilocus sequence typing (MLST) has previously identified six sequence types (ST) among plant samples collected in Brazil (both subsp. pauca and multiplex). Here, we report on a survey of X. fastidiosa genetic diversity (MLST based) performed in six regions in Brazil and two in Argentina, by sampling five different plant species. In addition to the six previously reported ST, seven new subsp. pauca and two new subsp. multiplex ST were identified. The presence of subsp. multiplex in South America is considered to be the consequence of a single introduction from its native range in North America more than 80 years ago. Different phylogenetic approaches clustered the South American ST into four groups, with strains infecting citrus (subsp. pauca); coffee and olive (subsp. pauca); coffee, hibiscus, and plum (subsp. pauca); and plum (subsp. multiplex). In areas where these different genetic clusters occurred sympatrically, we found evidence of homologous recombination in the form of bidirectional allelic exchange between subspp. pauca and multiplex. In fact, the only strain of subsp. pauca isolated from a plum host had an allele that originated from subsp. multiplex. These signatures of bidirectional homologous recombination between endemic and introduced ST indicate that gene flow occurs in short evolutionary time frames in X. fastidiosa, despite the ecological isolation (i.e., host plant species) of genotypes.

Relationship between presence of cows with milk positive for Mycobacterium avium subsp. paratuberculosis-specific antibody by enzyme-linked immunosorbent assay and viable M. avium subsp. paratuberculosis in dust in cattle barns.

PubMed

Eisenberg, Susanne W F; Chuchaisangrat, Ruj; Nielen, Mirjam; Koets, Ad P

2013-09-01

Paratuberculosis, or Johne's disease, in cattle is caused by Mycobacterium avium subsp. paratuberculosis, which has recently been suspected to be transmitted through dust. This longitudinal study on eight commercial M. avium subsp. paratuberculosis-positive dairy farms studied the relationship between the number of cows with M. avium subsp. paratuberculosis antibody-positive milk and the presence of viable M. avium subsp. paratuberculosis in settled-dust samples, including their temporal relationship. Milk and dust samples were collected in parallel monthly for 2 years. M. avium subsp. paratuberculosis antibodies in milk were measured by enzyme-linked immunosorbent assay (ELISA) and used as a proxy for M. avium subsp. paratuberculosis shedding. Settled-dust samples were collected by using electrostatic dust collectors (EDCs) at six locations in housing for dairy cattle and young stock. The presence of viable M. avium subsp. paratuberculosis was identified by liquid culture and PCR. The results showed a positive relationship (odds ratio [OR], 1.2) between the number of cows with ELISA-positive milk and the odds of having positive EDCs in the same airspace as the adult dairy cattle. Moreover, the total number of lactating cows also showed an OR slightly above 1. This relationship remained the same for settled-dust samples collected up to 2 months before or after the time of milk sampling. The results suggest that removal of adult cows with milk positive for M. avium subsp. paratuberculosis-specific antibody by ELISA might result in a decrease in the presence of viable M. avium subsp. paratuberculosis in dust and therefore in the environment. However, this decrease is likely delayed by several weeks at least. In addition, the data support the notion that M. avium subsp. paratuberculosis exposure of young stock is reduced by separate housing.

Relationship between Presence of Cows with Milk Positive for Mycobacterium avium subsp. paratuberculosis-Specific Antibody by Enzyme-Linked Immunosorbent Assay and Viable M. avium subsp. paratuberculosis in Dust in Cattle Barns

PubMed Central

Chuchaisangrat, Ruj; Nielen, Mirjam; Koets, Ad P.

2013-01-01

Paratuberculosis, or Johne's disease, in cattle is caused by Mycobacterium avium subsp. paratuberculosis, which has recently been suspected to be transmitted through dust. This longitudinal study on eight commercial M. avium subsp. paratuberculosis-positive dairy farms studied the relationship between the number of cows with M. avium subsp. paratuberculosis antibody-positive milk and the presence of viable M. avium subsp. paratuberculosis in settled-dust samples, including their temporal relationship. Milk and dust samples were collected in parallel monthly for 2 years. M. avium subsp. paratuberculosis antibodies in milk were measured by enzyme-linked immunosorbent assay (ELISA) and used as a proxy for M. avium subsp. paratuberculosis shedding. Settled-dust samples were collected by using electrostatic dust collectors (EDCs) at six locations in housing for dairy cattle and young stock. The presence of viable M. avium subsp. paratuberculosis was identified by liquid culture and PCR. The results showed a positive relationship (odds ratio [OR], 1.2) between the number of cows with ELISA-positive milk and the odds of having positive EDCs in the same airspace as the adult dairy cattle. Moreover, the total number of lactating cows also showed an OR slightly above 1. This relationship remained the same for settled-dust samples collected up to 2 months before or after the time of milk sampling. The results suggest that removal of adult cows with milk positive for M. avium subsp. paratuberculosis-specific antibody by ELISA might result in a decrease in the presence of viable M. avium subsp. paratuberculosis in dust and therefore in the environment. However, this decrease is likely delayed by several weeks at least. In addition, the data support the notion that M. avium subsp. paratuberculosis exposure of young stock is reduced by separate housing. PMID:23793639

Could behaviour and not physiological thermal tolerance determine winter survival of aphids in cereal fields?

PubMed

Alford, Lucy; Andrade, Thiago Oliveira; Georges, Romain; Burel, Françoise; van Baaren, Joan

2014-01-01

Traits of physiological thermotolerance are commonly measured in the laboratory as predictors of the field success of ectotherms at unfavourable temperatures (e.g. during harsh winters, heatwaves, or under conditions of predicted global warming). Due to being more complicated to measure, behavioural thermoregulation is less commonly studied, although both physiology and behaviour interact to explain the survival of ectotherms. The aphids Metopolophium dirhodum, Rhopalosiphum padi and Sitobion avenae are commercially important pests of temperate cereal crops. Although coexisting, these species markedly differ in winter success, with R. padi being the most abundant species during cold winters, followed by S. avenae and lastly M. dirhodum. To better understand the thermal physiology and behavioural factors contributing to differential winter success, the lethal temperature (physiological thermotolerance) and the behaviour of aphids in a declining temperature regime (behavioural thermotolerance) of these three species were investigated. Physiological thermotolerance significantly differed between the three species, with R. padi consistently the least cold tolerant and S. avenae the most cold tolerant. However, although the least cold tolerant of the study species, significantly more R. padi remained attached to the host plant at extreme sub-zero temperatures than S. avenae and M. dirhodum. Given the success of anholocyclic R. padi in harsh winters compared to its anholocyclic counterparts, this study illustrates that behavioural differences could be more important than physiological thermotolerance in explaining resistance to extreme temperatures. Furthermore it highlights that there is a danger to studying physiological thermotolerance in isolation when ascertaining risks of ectotherm invasions, the establishment potential of exotic species in glasshouses, or predicting species impacts under climate change scenarios.

A Novel Enzyme-Linked Immunosorbent Assay for Diagnosis of Mycobacterium avium subsp. paratuberculosis Infections (Johne's Disease) in Cattle

PubMed Central

Speer, C. A.; Scott, M. Cathy; Bannantine, John P.; Waters, W. Ray; Mori, Yasuyuki; Whitlock, Robert H.; Eda, Shigetoshi

2006-01-01

Enzyme-linked immunosorbent assays (ELISAs) for the diagnosis of Johne's disease (JD), caused by Mycobacterium avium subsp. paratuberculosis, were developed using whole bacilli treated with formaldehyde (called WELISA) or surface antigens obtained by treatment of M. avium subsp. paratuberculosis bacilli with formaldehyde and then brief sonication (called SELISA). ELISA plates were coated with either whole bacilli or sonicated antigens and tested for reactivity against serum obtained from JD-positive and JD-negative cattle or from calves experimentally inoculated with M. avium subsp. paratuberculosis, Mycobacterium avium subsp. avium, or Mycobacterium bovis. Because the initial results obtained from the WELISA and SELISA were similar, most of the subsequent experiments reported herein were performed using the SELISA method. To optimize the SELISA test, various concentrations (3.7 to 37%) of formaldehyde and intervals of sonication (2 to 300 s) were tested. With an increase in formaldehyde concentration and a decreased interval of sonication, there was a concomitant decrease in nonspecific binding by the SELISA. SELISAs prepared by treating M. avium subsp. paratuberculosis with 37% formaldehyde and then a 2-s burst of sonication produced the greatest difference (7×) between M. avium subsp. paratuberculosis-negative and M. avium subsp. paratuberculosis-positive serum samples. The diagnostic sensitivity and specificity for JD by the SELISA were greater than 95%. The SELISA showed subspecies-specific detection of M. avium subsp. paratuberculosis infections in calves experimentally inoculated with M. avium subsp. paratuberculosis or other mycobacteria. Based on diagnostic sensitivity and specificity, the SELISA appears superior to the commercial ELISAs routinely used for the diagnosis of JD. PMID:16682472

Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages

PubMed Central

Gilbert, Maarten J.; Miller, William G.; Yee, Emma; Zomer, Aldert L.; van der Graaf-van Bloois, Linda; Fitzgerald, Collette; Forbes, Ken J.; Méric, Guillaume; Sheppard, Samuel K.; Wagenaar, Jaap A.; Duim, Birgitta

2016-01-01

Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies. PMID:27333878

Xylella fastidiosa Isolates from Both subsp. multiplex and fastidiosa Cause Disease on Southern Highbush Blueberry (Vaccinium sp.) Under Greenhouse Conditions.

PubMed

Oliver, J E; Cobine, P A; De La Fuente, L

2015-07-01

Xylella fastidiosa is a xylem-limited gram-negative plant pathogen that affects numerous crop species, including grape, citrus, peach, pecan, and almond. Recently, X. fastidiosa has also been found to be the cause of bacterial leaf scorch on blueberry in the southeastern United States. Thus far, all X. fastidiosa isolates obtained from infected blueberry have been classified as X. fastidiosa subsp. multiplex; however, X. fastidiosa subsp. fastidiosa isolates are also present in the southeastern United States and commonly cause Pierce's disease of grapevines. In this study, seven southeastern U.S. isolates of X. fastidiosa, including three X. fastidiosa subsp. fastidiosa isolates from grape, one X. fastidiosa subsp. fastidiosa isolate from elderberry, and three X. fastidiosa subsp. multiplex isolates from blueberry, were used to infect the southern highbush blueberry 'Rebel'. Following inoculation, all isolates colonized blueberry, and isolates from both X. fastidiosa subsp. multiplex and X. fastidiosa subsp. fastidiosa caused symptoms, including characteristic stem yellowing and leaf scorch symptoms as well as dieback of the stem tips. Two X. fastidiosa subsp. multiplex isolates from blueberry caused more severe symptoms than the other isolates examined, and infection with these two isolates also had a significant impact on host mineral nutrient content in sap and leaves. These findings have potential implications for understanding X. fastidiosa host adaptation and expansion and the development of emerging diseases caused by this bacterium.

Disparate host immunity to Mycobacterium avium subsp. paratuberculosis antigens in calves inoculated with M. avium subsp. paratuberculosis, M. avium subsp. avium, M. kansasii and M. bovis

USDA-ARS?s Scientific Manuscript database

Cross-reactivity of mycobacterial antigens in immune-based diagnostic assays has been a major concern and criticism of current tests for the detection of paratuberculosis. In the present study, host immune responses to antigen preparations of Mycobacterium avium subsp. paratuberculosis (MAP), consis...

Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material.

PubMed

Švec, Pavel; De Bel, Annelies; Sedláček, Ivo; Petráš, Petr; Gelbíčová, Tereza; Černohlávková, Jitka; Mašlanˇová, Ivana; Cnockaert, Margo; Varbanovová, Ivana; Echahidi, Fedoua; Vandamme, Peter; Pantuček, Roman

2015-07-01

Seven coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococci assigned tentatively as Staphylococcus petrasii were investigated in this study in order to elucidate their taxonomic position. All strains were initially shown to form a genetically homogeneous group separated from remaining species of the genus Staphylococcus by using a repetitive sequence-based PCR fingerprinting with the (GTG)5 primer. Phylogenetic analysis based on 16S rRNA gene, hsp60, rpoB, dnaJ, gap and tuf sequences showed that the group is closely related to Staphylococcus petrasii but separated from the three hitherto known subspecies, S. petrasii subsp. petrasii, S. petrasii subsp. croceilyticus and S. petrasii subsp. jettensis. Further investigation using automated ribotyping, MALDI-TOF mass spectrometry, fatty acid methyl ester analysis, DNA-DNA hybridization and extensive biotyping confirmed that the analysed group represents a novel subspecies within S. petrasii, for which the name Staphylococcus petrasii subsp. pragensis subsp. nov. is proposed. The type strain is NRL/St 12/356(T) ( = CCM 8529(T) = LMG 28327(T)).

Quantification of the Sensitivity of Mycobacterium avium subsp paratuberculosis and Salmonella enterica subsp enterica to Low pH and High Organic Acids using Propidium Monoazide and Quantitative PCR

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp paratuberculosis (Map) and Salmonella enterica subsp enterica (S. enterica) are two pathogens that are a concern to food and animal safety due to their ability to withstand harsh conditions encountered in the natural environment and within the host during pathogenesis. Acid...

Detection and Verification of Mycobacterium avium subsp. paratuberculosis in Fresh Ileocolonic Mucosal Biopsy Specimens from Individuals with and without Crohn's Disease

PubMed Central

Bull, Tim J.; McMinn, Elizabeth J.; Sidi-Boumedine, Karim; Skull, Angela; Durkin, Damien; Neild, Penny; Rhodes, Glenn; Pickup, Roger; Hermon-Taylor, John

2003-01-01

Mycobacterium avium subsp. paratuberculosis is a robust and phenotypically versatile pathogen which causes chronic inflammation of the intestine in many species, including primates. M. avium subsp. paratuberculosis infection is widespread in domestic livestock and is present in retail pasteurized cows' milk in the United Kingdom and, potentially, elsewhere. Water supplies are also at risk. The involvement of M. avium subsp. paratuberculosis in Crohn's disease (CD) in humans has been uncertain because of the substantial difficulties in detecting this pathogen. In its Ziehl-Neelsen staining-negative form, M. avium subsp. paratuberculosis is highly resistant to chemical and enzymatic lysis. The present study describes the development of optimized sample processing and DNA extraction procedures with fresh human intestinal mucosal biopsy specimens which ensure access to M. avium subsp. paratuberculosis DNA and maximize detection of these low-abundance pathogens. Also described are two nested PCR methodologies targeted at IS900, designated IS900[L/AV] and IS900[TJ1-4], which are uniquely specific for IS900. Detection of M. avium subsp. paratuberculosis in mucosal biopsy specimens was also evaluated by using mycobacterial growth indicator tube (MGIT) cultures (Becton Dickinson). IS900[L/AV] PCR detected M. avium subsp. paratuberculosis in 34 of 37 (92%) patients with CD and in 9 of 34 (26%) controls without CD (noninflammatory bowel disease [nIBD] controls) (P = 0.0002; odds ratio = 3.47). M. avium subsp. paratuberculosis was detected by IS900[L/AV] PCR in MGIT cultures after 14 to 88 weeks of incubation in 14 of 33 (42%) CD patients and 3 of 33 (9%) nIBD controls (P = 0.0019; odds ratio = 4.66). Nine of 15 (60%) MGIT cultures of specimens from CD patients incubated for more than 38 weeks were positive for M. avium subsp. paratuberculosis. In each case the identity of IS900 from M. avium subsp. paratuberculosis was verified by amplicon sequencing. The rate of detection of M. avium subsp. paratuberculosis in individuals with CD is highly significant and implicates this chronic enteric pathogen in disease causation. PMID:12843021

Maternal effects of the English grain aphids feeding on the wheat varieties with different resistance traits.

PubMed

Hu, Xiang-Shun; Zhang, Zhan-Feng; Zhu, Tong-Yi; Song, Yue; Wu, Li-Juan; Liu, Xiao-Feng; Zhao, Hui-Yan; Liu, Tong-Xian

2018-05-09

The maternal effects of the English grain aphid, Sitobion avenae on offspring phenotypes and performance on wheat varieties with different resistance traits were examined. We found that both conditioning wheat varieties(the host plant for over 3 months) and transition wheat varieties affected the biological parameters of aphid offspring after they were transferred between wheat varieties with different resistance traits. The conditioning varieties affected weight gain, development time (DT), and the intrinsic rate of natural increase (r m ), whereas transition varieties affected the fecundity, r m , net reproductive rate, and fitness index. The conditioning and transition wheat varieties had significant interaction effects on the aphid offspring's DT, mean relative growth rate, and fecundity. Our results showed that there was obvious maternal effects on offspring when S. avenae transferred bwteen wheat varieties with different resistance level, and the resistance traits of wheat varieties could induce an interaction between the conditioning and transition wheat varieties to influence the growth, development, reproduction, and even population dynamics of S. avenae. The conditioning varieties affected life-history traits related to individual growth and development to a greater extent, whereas transition varieties affected fecundity and population parameters more.

Assessing the inactivation of Mycobacterium avium subsp. paratuberculosis during composting of livestock carcasses.

PubMed

Tkachuk, Victoria L; Krause, Denis O; McAllister, Tim A; Buckley, Katherine E; Reuter, Tim; Hendrick, Steve; Ominski, Kim H

2013-05-01

Mycobacterium avium subsp. paratuberculosis causes Johne's disease (JD) in ruminants, with substantial economic impacts on the cattle industry. Johne's disease is known for its long latency period, and difficulties in diagnosis are due to insensitivities of current detection methods. Eradication is challenging as M. avium subsp. paratuberculosis can survive for extended periods within the environment, resulting in new infections in naïve animals (W. Xu et al., J. Environ. Qual. 38:437-450, 2009). This study explored the use of a biosecure, static composting structure to inactivate M. avium subsp. paratuberculosis. Mycobacterium smegmatis was also assessed as a surrogate for M. avium subsp. paratuberculosis. Two structures were constructed to hold three cattle carcasses each. Naturally infected tissues and ground beef inoculated with laboratory-cultured M. avium subsp. paratuberculosis and M. smegmatis were placed in nylon and plastic bags to determine effects of temperature and compost environment on viability over 250 days. After removal, samples were cultured and growth of both organisms was assessed after 12 weeks. After 250 days, M. avium subsp. paratuberculosis was still detectable by PCR, while M. smegmatis was not detected after 67 days of composting. Furthermore, M. avium subsp. paratuberculosis remained viable in both implanted nylon and plastic bags over the composting period. As the compost never reached a homogenous thermophilic (55 to 65°C) state throughout each structure, an in vitro experiment was conducted to examine viability of M. avium subsp. paratuberculosis after exposure to 80°C for 90 days. Naturally infected lymph tissues were mixed with and without compost. After 90 days, M. avium subsp. paratuberculosis remained viable despite exposure to temperatures typically higher than that achieved in compost. In conclusion, it is unlikely composting can be used as a means of inactivating M. avium subsp. paratuberculosis associated with cattle mortalities.

Assessing the Inactivation of Mycobacterium avium subsp. paratuberculosis during Composting of Livestock Carcasses

PubMed Central

Tkachuk, Victoria L.; Krause, Denis O.; McAllister, Tim A.; Buckley, Katherine E.; Reuter, Tim; Hendrick, Steve

2013-01-01

Mycobacterium avium subsp. paratuberculosis causes Johne's disease (JD) in ruminants, with substantial economic impacts on the cattle industry. Johne's disease is known for its long latency period, and difficulties in diagnosis are due to insensitivities of current detection methods. Eradication is challenging as M. avium subsp. paratuberculosis can survive for extended periods within the environment, resulting in new infections in naïve animals (W. Xu et al., J. Environ. Qual. 38:437-450, 2009). This study explored the use of a biosecure, static composting structure to inactivate M. avium subsp. paratuberculosis. Mycobacterium smegmatis was also assessed as a surrogate for M. avium subsp. paratuberculosis. Two structures were constructed to hold three cattle carcasses each. Naturally infected tissues and ground beef inoculated with laboratory-cultured M. avium subsp. paratuberculosis and M. smegmatis were placed in nylon and plastic bags to determine effects of temperature and compost environment on viability over 250 days. After removal, samples were cultured and growth of both organisms was assessed after 12 weeks. After 250 days, M. avium subsp. paratuberculosis was still detectable by PCR, while M. smegmatis was not detected after 67 days of composting. Furthermore, M. avium subsp. paratuberculosis remained viable in both implanted nylon and plastic bags over the composting period. As the compost never reached a homogenous thermophilic (55 to 65°C) state throughout each structure, an in vitro experiment was conducted to examine viability of M. avium subsp. paratuberculosis after exposure to 80°C for 90 days. Naturally infected lymph tissues were mixed with and without compost. After 90 days, M. avium subsp. paratuberculosis remained viable despite exposure to temperatures typically higher than that achieved in compost. In conclusion, it is unlikely composting can be used as a means of inactivating M. avium subsp. paratuberculosis associated with cattle mortalities. PMID:23503307

Culture- and quantitative IS900 real-time PCR-based analysis of the persistence of Mycobacterium avium subsp. paratuberculosis in a controlled dairy cow farm environment.

PubMed

Moravkova, M; Babak, V; Kralova, A; Pavlik, I; Slana, I

2012-09-01

The aim of this study was to monitor the persistence of Mycobacterium avium subsp. paratuberculosis in environmental samples taken from a Holstein farm with a long history of clinical paratuberculosis. A herd of 606 head was eradicated, and mechanical cleaning and disinfection with chloramine B with ammonium (4%) was carried out on the farm; in the surrounding areas (on the field and field midden) lime was applied. Environmental samples were collected before and over a period of 24 months after destocking. Only one sample out of 48 (2%) examined on the farm (originating from a waste pit and collected before destocking) was positive for M. avium subsp. paratuberculosis by cultivation on solid medium (Herrold's egg yolk medium). The results using real-time quantitative PCR (qPCR) showed that a total of 81% of environmental samples with an average mean M. avium subsp. paratuberculosis cell number of 3.09 × 10(3) were positive for M. avium subsp. paratuberculosis before destocking compared to 43% with an average mean M. avium subsp. paratuberculosis cell number of 5.86 × 10(2) after 24 months. M. avium subsp. paratuberculosis-positive samples were detected in the cattle barn as well as in the calf barn and surrounding areas. M. avium subsp. paratuberculosis was detected from different matrices: floor and instrument scrapings, sediment, or scraping from watering troughs, waste pits, and cobwebs. M. avium subsp. paratuberculosis DNA was also detected in soil and plants collected on the field midden and the field 24 months after destocking. Although the proportion of positive samples decreased from 64% to 23% over time, the numbers of M. avium subsp. paratuberculosis cells were comparable.

Culture- and Quantitative IS900 Real-Time PCR-Based Analysis of the Persistence of Mycobacterium avium subsp. paratuberculosis in a Controlled Dairy Cow Farm Environment

PubMed Central

Moravkova, M.; Babak, V.; Kralova, A.; Pavlik, I.

2012-01-01

The aim of this study was to monitor the persistence of Mycobacterium avium subsp. paratuberculosis in environmental samples taken from a Holstein farm with a long history of clinical paratuberculosis. A herd of 606 head was eradicated, and mechanical cleaning and disinfection with chloramine B with ammonium (4%) was carried out on the farm; in the surrounding areas (on the field and field midden) lime was applied. Environmental samples were collected before and over a period of 24 months after destocking. Only one sample out of 48 (2%) examined on the farm (originating from a waste pit and collected before destocking) was positive for M. avium subsp. paratuberculosis by cultivation on solid medium (Herrold's egg yolk medium). The results using real-time quantitative PCR (qPCR) showed that a total of 81% of environmental samples with an average mean M. avium subsp. paratuberculosis cell number of 3.09 × 103 were positive for M. avium subsp. paratuberculosis before destocking compared to 43% with an average mean M. avium subsp. paratuberculosis cell number of 5.86 × 102 after 24 months. M. avium subsp. paratuberculosis-positive samples were detected in the cattle barn as well as in the calf barn and surrounding areas. M. avium subsp. paratuberculosis was detected from different matrices: floor and instrument scrapings, sediment, or scraping from watering troughs, waste pits, and cobwebs. M. avium subsp. paratuberculosis DNA was also detected in soil and plants collected on the field midden and the field 24 months after destocking. Although the proportion of positive samples decreased from 64% to 23% over time, the numbers of M. avium subsp. paratuberculosis cells were comparable. PMID:22773642

Bioluminescence imaging of Clavibacter michiganensis subsp. michiganensis infection of tomato seeds and plants.

PubMed

Xu, Xiulan; Miller, Sally A; Baysal-Gurel, Fulya; Gartemann, Karl-Heinz; Eichenlaub, Rudolf; Rajashekara, Gireesh

2010-06-01

Clavibacter michiganensis subsp. michiganensis is a Gram-positive bacterium that causes wilting and cankers, leading to severe economic losses in commercial tomato production worldwide. The disease is transmitted from infected seeds to seedlings and mechanically from plant to plant during seedling production, grafting, pruning, and harvesting. Because of the lack of tools for genetic manipulation, very little is known regarding the mechanisms of seed and seedling infection and movement of C. michiganensis subsp. michiganensis in grafted plants, two focal points for application of bacterial canker control measures in tomato. To facilitate studies on the C. michiganensis subsp. michiganensis movement in tomato seed and grafted plants, we isolated a bioluminescent C. michiganensis subsp. michiganensis strain using the modified Tn1409 containing a promoterless lux reporter. A total of 19 bioluminescent C. michiganensis subsp. michiganensis mutants were obtained. All mutants tested induced a hypersensitive response in Mirabilis jalapa and caused wilting of tomato plants. Real-time colonization studies of germinating seeds using a virulent, stable, constitutively bioluminescent strain, BL-Cmm17, showed that C. michiganensis subsp. michiganensis aggregated on hypocotyls and cotyledons at an early stage of germination. In grafted seedlings in which either the rootstock or scion was exposed to BL-Cmm17 via a contaminated grafting knife, bacteria were translocated in both directions from the graft union at higher inoculum doses. These results emphasize the use of bioluminescent C. michiganensis subsp. michiganensis to help better elucidate the C. michiganensis subsp. michiganensis-tomato plant interactions. Further, we demonstrated the broader applicability of this tool by successful transformation of C. michiganensis subsp. nebraskensis with Tn1409::lux. Thus, our approach would be highly useful to understand the pathogenesis of diseases caused by other subspecies of the agriculturally important C. michiganensis.

Bioluminescence Imaging of Clavibacter michiganensis subsp. michiganensis Infection of Tomato Seeds and Plants ▿

PubMed Central

Xu, Xiulan; Miller, Sally A.; Baysal-Gurel, Fulya; Gartemann, Karl-Heinz; Eichenlaub, Rudolf; Rajashekara, Gireesh

2010-01-01

Clavibacter michiganensis subsp. michiganensis is a Gram-positive bacterium that causes wilting and cankers, leading to severe economic losses in commercial tomato production worldwide. The disease is transmitted from infected seeds to seedlings and mechanically from plant to plant during seedling production, grafting, pruning, and harvesting. Because of the lack of tools for genetic manipulation, very little is known regarding the mechanisms of seed and seedling infection and movement of C. michiganensis subsp. michiganensis in grafted plants, two focal points for application of bacterial canker control measures in tomato. To facilitate studies on the C. michiganensis subsp. michiganensis movement in tomato seed and grafted plants, we isolated a bioluminescent C. michiganensis subsp. michiganensis strain using the modified Tn1409 containing a promoterless lux reporter. A total of 19 bioluminescent C. michiganensis subsp. michiganensis mutants were obtained. All mutants tested induced a hypersensitive response in Mirabilis jalapa and caused wilting of tomato plants. Real-time colonization studies of germinating seeds using a virulent, stable, constitutively bioluminescent strain, BL-Cmm17, showed that C. michiganensis subsp. michiganensis aggregated on hypocotyls and cotyledons at an early stage of germination. In grafted seedlings in which either the rootstock or scion was exposed to BL-Cmm17 via a contaminated grafting knife, bacteria were translocated in both directions from the graft union at higher inoculum doses. These results emphasize the use of bioluminescent C. michiganensis subsp. michiganensis to help better elucidate the C. michiganensis subsp. michiganensis-tomato plant interactions. Further, we demonstrated the broader applicability of this tool by successful transformation of C. michiganensis subsp. nebraskensis with Tn1409::lux. Thus, our approach would be highly useful to understand the pathogenesis of diseases caused by other subspecies of the agriculturally important C. michiganensis. PMID:20400561

Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages.

PubMed

Gilbert, Maarten J; Miller, William G; Yee, Emma; Zomer, Aldert L; van der Graaf-van Bloois, Linda; Fitzgerald, Collette; Forbes, Ken J; Méric, Guillaume; Sheppard, Samuel K; Wagenaar, Jaap A; Duim, Birgitta

2016-07-02

Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C fetus was performed. The genomes of C fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C fetus subspecies, but a clear distinction between mammal- and reptile-associated C fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C fetus subsp. testudinum strains. Within C fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C fetus Overall, this study shows that reptile-associated C fetus subsp. testudinum is genetically divergent from mammal-associated C fetus subspecies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Diversity Analysis of Dairy and Nondairy Lactococcus lactis Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)5-PCR Fingerprinting▿

PubMed Central

Rademaker, Jan L. W.; Herbet, Hélène; Starrenburg, Marjo J. C.; Naser, Sabri M.; Gevers, Dirk; Kelly, William J.; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E. T.

2007-01-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)5-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene. PMID:17890345

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting.

PubMed

Rademaker, Jan L W; Herbet, Hélène; Starrenburg, Marjo J C; Naser, Sabri M; Gevers, Dirk; Kelly, William J; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E T

2007-11-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)(5)-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene.

Distribution of Bacillus thuringiensis subsp. israelensis in Soil of a Swiss Wetland Reserve after 22 Years of Mosquito Control▿†

PubMed Central

Guidi, Valeria; Patocchi, Nicola; Lüthy, Peter; Tonolla, Mauro

2011-01-01

Recurrent treatments with Bacillus thuringiensis subsp. israelensis are required to control the floodwater mosquito Aedes vexans that breeds in large numbers in the wetlands of the Bolle di Magadino Reserve in Canton Ticino, Switzerland. Interventions have been carried out since 1988. In the present study, the spatial distribution of resting B. thuringiensis subsp. israelensis spores in the soil was measured. The B. thuringiensis subsp. israelensis concentration was determined in soil samples collected along six transects covering different elevations within the periodically flooded zones. A total of 258 samples were processed and analyzed by quantitative PCR that targeted an identical fragment of 159 bp for the B. thuringiensis subsp. israelensis cry4Aa and cry4Ba genes. B. thuringiensis subsp. israelensis spores were found to persist in soils of the wetland reserve at concentrations of up to 6.8 log per gram of soil. Continuous accumulation due to regular treatments could be excluded, as the decrease in spores amounted to 95.8% (95% confidence interval, 93.9 to 97.7%). The distribution of spores was correlated to the number of B. thuringiensis subsp. israelensis treatments, the elevation of the sampling point, and the duration of the flooding periods. The number of B. thuringiensis subsp. israelensis treatments was the major factor influencing the distribution of spores in the different topographic zones (P < 0.0001). These findings indicated that B. thuringiensis subsp. israelensis spores are rather immobile after their introduction into the environment. PMID:21498758

Multilocus sequence typing of Xylella fastidiosa causing Pierce's disease and oleander leaf scorch in the United States.

PubMed

Yuan, Xiaoli; Morano, Lisa; Bromley, Robin; Spring-Pearson, Senanu; Stouthamer, Richard; Nunney, Leonard

2010-06-01

Using a modified multilocus sequence typing (MLST) scheme for the bacterial plant pathogen Xylella fastidiosa based on the same seven housekeeping genes employed in a previously published MLST, we studied the genetic diversity of two subspecies, X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. sandyi, which cause Pierce's disease and oleander leaf scorch, respectively. Typing of 85 U.S. isolates (plus one from northern Mexico) of X. fastidiosa subsp. fastidiosa from 15 different plant hosts and 21 isolates of X. fastidiosa subsp. sandyi from 4 different hosts in California and Texas supported their subspecific status. Analysis using the MLST genes plus one cell-surface gene showed no significant genetic differentiation based on geography or host plant within either subspecies. Two cases of homologous recombination (with X. fastidiosa subsp. multiplex, the third U.S. subspecies) were detected in X. fastidiosa subsp. fastidiosa. Excluding recombination, MLST site polymorphism in X. fastidiosa subsp. fastidiosa (0.048%) and X. fastidiosa subsp. sandyi (0.000%) was substantially lower than in X. fastidiosa subsp. multiplex (0.240%), consistent with the hypothesis that X. fastidiosa subspp. fastidiosa and sandyi were introduced into the United States (probably just prior to 1880 and 1980, respectively). Using whole-genome analysis, we showed that MLST is more effective at genetic discrimination at the specific and subspecific level than other typing methods applied to X. fastidiosa. Moreover, MLST is the only technique effective in detecting recombination.

Regulation and Adaptive Evolution of Lactose Operon Expression in Lactobacillus delbrueckii

PubMed Central

Lapierre, Luciane; Mollet, Beat; Germond, Jacques-Edouard

2002-01-01

Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis are both used in the dairy industry as homofermentative lactic acid bacteria in the production of fermented milk products. After selective pressure for the fast fermentation of milk in the manufacture of yogurts, L. delbrueckii subsp. bulgaricus loses its ability to regulate lac operon expression. A series of mutations led to the constitutive expression of the lac genes. A complex of insertion sequence (IS) elements (ISL4 inside ISL5), inserted at the border of the lac promoter, induced the loss of the palindromic structure of one of the operators likely involved in the binding of regulatory factors. A lac repressor gene was discovered downstream of the β-galactosidase gene of L. delbrueckii subsp. lactis and was shown to be inactivated by several mutations in L. delbrueckii subsp. bulgaricus. Regulatory mechanisms of the lac gene expression of L. delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis were compared by heterologous expression in Lactococcus lactis of the two lac promoters in front of a reporter gene (β-glucuronidase) in the presence or absence of the lac repressor gene. Insertion of the complex of IS elements in the lac promoter of L. delbrueckii subsp. bulgaricus increased the promoter's activity but did not prevent repressor binding; rather, it increased the affinity of the repressor for the promoter. Inactivation of the lac repressor by mutations was then necessary to induce the constitutive expression of the lac genes in L. delbrueckii subsp. bulgaricus. PMID:11807052

Establishment of Three Francisella Infections in Zebrafish Embryos at Different Temperatures

PubMed Central

Brudal, Espen; Ulanova, Lilia S.; O. Lampe, Elisabeth; Rishovd, Anne-Lise; Winther-Larsen, Hanne C.

2014-01-01

Francisella spp. are facultative intracellular pathogens identified in increasingly diverse hosts, including mammals. F. noatunensis subsp. orientalis and F. noatunensis subsp. noatunensis infect fish inhabiting warm and cold waters, respectively, while F. tularensis subsp. novicida is highly infectious for mice and has been widely used as a model for the human pathogen F. tularensis. Here, we established zebrafish embryo infection models of fluorescently labeled F. noatunensis subsp. noatunensis, F. noatunensis subsp. orientalis, and F. tularensis subsp. novicida at 22, 28, and 32°C, respectively. All infections led to significant bacterial growth, as shown by reverse transcription-quantitative PCR (RT-qPCR), and to a robust proinflammatory immune response, dominated by increased transcription of tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β). F. noatunensis subsp. orientalis was the most virulent, F. noatunensis subsp. noatunensis caused chronic infection, and F. tularensis subsp. novicida showed moderate virulence and led to formation of relatively small granuloma-like structures. The use of transgenic zebrafish strains with enhanced green fluorescent protein (EGFP)-labeled immune cells revealed their detailed interactions with Francisella species. All three strains entered preferentially into macrophages, which eventually assembled into granuloma-like structures. Entry into neutrophils was also observed, though the efficiency of this event depended on the route of infection. The results demonstrate the usefulness of the zebrafish embryo model for studying infections caused by different Francisella species at a wide range of temperatures and highlight their interactions with immune cells. PMID:24614659

Distribution of Bacillus thuringiensis subsp. israelensis in Soil of a Swiss Wetland reserve after 22 years of mosquito control.

PubMed

Guidi, Valeria; Patocchi, Nicola; Lüthy, Peter; Tonolla, Mauro

2011-06-01

Recurrent treatments with Bacillus thuringiensis subsp. israelensis are required to control the floodwater mosquito Aedes vexans that breeds in large numbers in the wetlands of the Bolle di Magadino Reserve in Canton Ticino, Switzerland. Interventions have been carried out since 1988. In the present study, the spatial distribution of resting B. thuringiensis subsp. israelensis spores in the soil was measured. The B. thuringiensis subsp. israelensis concentration was determined in soil samples collected along six transects covering different elevations within the periodically flooded zones. A total of 258 samples were processed and analyzed by quantitative PCR that targeted an identical fragment of 159 bp for the B. thuringiensis subsp. israelensis cry4Aa and cry4Ba genes. B. thuringiensis subsp. israelensis spores were found to persist in soils of the wetland reserve at concentrations of up to 6.8 log per gram of soil. Continuous accumulation due to regular treatments could be excluded, as the decrease in spores amounted to 95.8% (95% confidence interval, 93.9 to 97.7%). The distribution of spores was correlated to the number of B. thuringiensis subsp. israelensis treatments, the elevation of the sampling point, and the duration of the flooding periods. The number of B. thuringiensis subsp. israelensis treatments was the major factor influencing the distribution of spores in the different topographic zones (P < 0.0001). These findings indicated that B. thuringiensis subsp. israelensis spores are rather immobile after their introduction into the environment.

Nested PCR for ultrasensitive detection of the potato ring rot bacterium, Clavibacter michiganensis subsp. sepedonicus.

PubMed

Lee, I M; Bartoszyk, I M; Gundersen, D E; Mogen, B; Davis, R E

1997-07-01

Oligonucleotide primers derived from sequences of the 16S rRNA gene (CMR16F1, CMR16R1, CMR16F2, and CMR16R2) and insertion element IS1121 of Clavibacter michiganensis subsp. sepedonicus (CMSIF1, CMSIR1, CMSIF2, and CMISR2) were used in nested PCR to detect the potato ring rot bacterium C. michiganensis subsp. sepedonicus. Nested PCR with primer pair CMSIF1-CMSIR1 followed by primer pair CMSIF2-CMSIR2 specifically detected C. michiganensis subsp. sepedonicus, while nested PCR with CMR16F1-CMR16R1 followed by CMR16F2-CMR16R2 detected C. michiganensis subsp. sepedonicus and the other C. michiganensis subspecies. In the latter case, C. michiganensis subsp. sepedonicus can be differentiated from the other subspecies by restriction fragment length polymorphism (RFLP) analyses of the nested PCR products (16S rDNA sequences). The nested PCR assays developed in this work allow ultrasensitive detection of very low titers of C. michiganensis subsp. sepedonicus which may be present in symptomiess potato plants or tubers and which cannot be readily detected by direct PCR (single PCR amplification). RFLP analysis of PCR products provides for an unambiguous confirmation of the identify of C. michiganensis subsp. sepedonicus.

Systematics of Juniperus section Juniperus based on leaf essential oils and random amplified polymorphic DNAs (RAPDs).

PubMed

Adams

2000-07-01

The composition of the leaf essential oils of all the species of Juniperus in sect. Juniperus (=sect. Oxycedrus) are reported and compared (J. brevifolia, J. cedrus, J. communis, J. c. var. saxatilis, J. c. var. oblonga, J. formosana, J. oxycedrus, J. o. subsp. badia, J. o. subsp. macrocarpa, J. o. subsp. transtagana, J. rigida, J. r. subsp. conferta, J. sibirica, J. taxifolia and J. t. var. lutchuensis). In addition, DNA fingerprinting by RAPDs was utilized. Based on these data, several taxa remained at the same taxonomic level: J. brevifolia, J. cedrus, J. communis, J. c. var. saxatilis, J. formosana, J. oxycedrus, J. rigida, J. r. var. conferta, and J. taxifolia. However, several taxa exhibited considerable differentiation that warranted their recognition at the specific level: J. oblonga M.-Bieb. (=J. communis var. oblonga), J. badia H. Gay (=J. oxycedrus subsp. badia), J. macrocarpa Sibth. and Sm. (=J. oxycedrus subsp. macrocarpa), J. navicularis Gand. (=J. oxycedrus subsp. transtagana), J. sibirica Brugsd. (=J. communis var. saxatilis in part), and J. lutchuensis Koidz. (= J. taxifolia var. lutchuensis).

Specific 16S ribosomal RNA targeted oligonucleotide probe against Clavibacter michiganensis subsp. sepedonicus.

PubMed

Mirza, M S; Rademaker, J L; Janse, J D; Akkermans, A D

1993-11-01

In this article we report on the polymerase chain reaction amplification of a partial 16S rRNA gene from the plant pathogenic bacterium Clavibacter michiganensis subsp. sepedonicus. A partial sequence (about 400 base pairs) of the gene was determined that covered two variable regions important for oligonucleotide probe development. A specific 24mer oligonucleotide probe targeted against the V6 region of 16S rRNA was designed. Specificity of the probe was determined using dot blot hybridization. Under stringent conditions (60 degrees C), the probe hybridized with all 16 Cl. michiganensis subsp. sepedonicus strains tested. Hybridization did not occur with 32 plant pathogenic and saprophytic bacteria used as controls under the same conditions. Under less stringent conditions (55 degrees C) the related Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. nebraskensis, and Clavibacter michiganensis subsp. tesselarius also showed hybridization. At even lower stringency (40 degrees C), all Cl. michiganensis subspecies tested including Clavibacter michiganensis subsp. michiganensis showed hybridization signal, suggesting that under these conditions the probe may be used as a species-specific probe for Cl. michiganensis.

[Identification and phylogenetic analysis of one strain of Lactobacillus delbrueckii subsp. bulgaricus separated from yoghourt].

PubMed

Wang, Chuan; Zhang, Chaowu; Pei, Xiaofang; Liu, Hengchuan

2007-11-01

For being further applied and studied, one strain of Lactobacillus delbrueckii subsp. bulgaricus (wch9901) separated from yoghourt which had been identified by phenotype characteristic analysis was identified by 16S rDNA and phylogenetic analyzed. The 16S rDNA of wch9901 was amplified with the genomic DNA of wch9901 as template, and the conservative sequences of the 16S rDNA as primers. Inserted 16S rDNA amplified into clonal vector pGEM-T under the function of T4 DNA ligase to construct recombined plasmid pGEM-wch9901 16S rDNA. The recombined plasmid was identified by restriction enzyme digestion, and the eligible plasmid was presented to sequencing company for DNA sequencing. Nucleic acid sequence was blast in GenBank and phylogenetic tree was constructed using neighbor-joining method of distance methods by Mega3.1 soft. Results of blastn showed that the homology of 16S rDNA of wch9901 with the 16S rDNA of Lactobacillus delbrueckii subsp. bulgaricus strains was higher than 96%. On the phylogenetic tree, wch9901 formed a separate branch and located between Lactobacillus delbrueckii subsp. bulgaricus LGM2 evolution branch and another evolution branch which was composed of Lactobacillus delbrueckii subsp. bulgaricus DL2 evolution cluster and Lactobacillus delbrueckii subsp. bulgaricus JSQ evolution cluster. The distance between wch9901 evolution branch and Lactobacillus delbrueckii subsp. bulgaricus LGM2 evolution branch was the closest. wch9901 belonged to Lactobacillus delbrueckii subsp. bulgaricus. wch9901 showed the closest evolution relationship to Lactobacillus delbrueckii subsp. bulgaricus LGM2.

Taxonomic Subgroups of Pasteurella multocida Correlate with Clinical Presentation

PubMed Central

Chen, Henry I.; Hulten, Kristina; Clarridge III, Jill E.

2002-01-01

Pasteurella multocida is a small nonmotile gram-negative coccobacillus that is found in the nasopharynx and gastrointestinal tract of many wild and domesticated animals. In humans it most commonly causes cellulitis and localized superficial skin abscesses following an animal bite or scratch. The respiratory tract is the second most common site of infection for Pasteurella. Of the more than 17 species of Pasteurella known, Pasteurella multocida subsp. multocida and Pasteurella multocida subsp. septica are among the most common pathogens in humans. With the use of molecular techniques, distinction between different subspecies of P. multocida can be made more easily and accurately. We used the sequence of the 16S ribosomal DNA (rDNA) and repetitive extragenic palindromic sequence-PCR (REP-PCR) to characterize 20 strains (14 of P. multocida subsp. multocida and 6 of P. multocida subsp. septica; the 16S rDNA is identical for P. multocida subsp. multocida and Pasteurella multocida subsp. gallicida but differs from that of P. multocida subsp. septica) isolated from various anatomic sites. We found excellent correlation between the 16S rDNA sequence (a marker for a small conserved region of the genome), REP-PCR (a marker for a large portion of the genome), and biochemical tests (trehalose and sorbitol). We also found a correlation between the clinical presentation and the taxonomic group, with P. multocida subsp. septica more often associated with wounds than with respiratory infections (67 versus 17%, respectively) (P < 0.05, Z test) and P. multocida subsp. multocida more often associated with respiratory infections than with wounds (71 versus 14%, respectively) (P < 0.05, Z test). PMID:12202590

Rapid and sensitive method to identify Mycobacterium avium subsp. paratuberculosis in cow's milk by DNA methylase genotyping.

PubMed

Mundo, Silvia Leonor; Gilardoni, Liliana Rosa; Hoffman, Federico José; Lopez, Osvaldo Jorge

2013-03-01

Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants, caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily through feces of infected cows but can be also excreted in colostrum and milk and might survive pasteurization. Since an association of genomic sequences of M. avium subsp. paratuberculosis in patients with Crohn's disease has been described; it is of interest to rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion is used as a target for PCR amplification to identify the presence of M. avium subsp. paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and digested with restriction enzymes to confirm their identity. The methylated amplicons from 100 CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp. paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation and thus multiple samples can be tested at the same time.

Rapid and Sensitive Method To Identify Mycobacterium avium subsp. paratuberculosis in Cow's Milk by DNA Methylase Genotyping

PubMed Central

Mundo, Silvia Leonor; Gilardoni, Liliana Rosa; Hoffman, Federico José

2013-01-01

Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants, caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily through feces of infected cows but can be also excreted in colostrum and milk and might survive pasteurization. Since an association of genomic sequences of M. avium subsp. paratuberculosis in patients with Crohn's disease has been described; it is of interest to rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion is used as a target for PCR amplification to identify the presence of M. avium subsp. paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and digested with restriction enzymes to confirm their identity. The methylated amplicons from 100 CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp. paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation and thus multiple samples can be tested at the same time. PMID:23275511

Identification and characterization of lactic acid bacteria isolated from mixed pasture of timothy and orchardgrass, and its badly preserved silage.

PubMed

Tohno, Masanori; Kobayashi, Hisami; Nomura, Masaru; Uegaki, Ryuichi; Cai, Yimin

2012-04-01

In order to understand the relationship between lactic acid bacteria (LAB) species and silage fermentation, a total of 65 LAB strains isolated from mixed pasture of timothy (Phleum pratense L.) and orchardgrass (Dactylis glomerata L.), and its badly preserved silages were subjected to phenotypic and genetic analysis. According to these analyses, the isolates were divided into 13 groups, including Enterococcus gallinarum, Lactobacillus acidipiscis, L. coryniformis subsp. coryniformis, L. coryniformis subsp. torquens, L. curvatus, L. paraplantarum, L. plantarum subsp. argentoratensis, L. plantarum subsp. plantarum, L. sakei subsp. carnosus, Lactococcus garvieae, Lactococcus lactis subsp. cremoris, Leuconostoc pseudomesenteroides, Pediococcus acidilactici, Pediococcus pentosaceus, Weissella hellenica, Weissella paramesenteroides and Carnobacterium divergens. This is the first report to document that C. divergens, L. acidipiscis, L. sakei subsp. carnosus, L. garvieae, phenotypically novel L. lactis subsp. cremoris, E. gallinarum and W. hellenica are present in vegetative forage crops. L. plantarum group strains were most frequently isolated from the badly preserved silages. Some isolates showed a wide range of growth preferences for carbohydrate utilization, optimal growth pH and temperature in vitro, indicating that they have a high growth potential. These results are useful in understanding the diversity of LAB associated with decayed silage of timothy and orchardgrass. © 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

An Ecological Study of Lactococci Isolated from Raw Milk in the Camembert Cheese Registered Designation of Origin Area

PubMed Central

Corroler, D.; Mangin, I.; Desmasures, N.; Gueguen, M.

1998-01-01

The genetic diversity of lactococci isolated from raw milk in the Camembert cheese Registered Designation of Origin area was studied. Two seasonal samples (winter and summer) of raw milk were obtained from six farms in two areas (Bessin and Bocage Falaisien) of Normandy. All of the strains analyzed had a Lactococcus lactis subsp. lactis phenotype, whereas the randomly amplified polymorphic DNA (RAPD) technique genotypically identified the strains as members of L. lactis subsp. lactis or L. lactis subsp. cremoris. The genotypes were confirmed by performing standard PCR with primers corresponding to a region of the histidine biosynthesis operon. The geographic distribution of each subspecies of L. lactis was determined; 80% of the Bocage Falaisien strains were members of L. lactis subsp. lactis, and 30.5% of the Bessin strains were members of L. lactis subsp. lactis. A dendrogram was produced from a computer analysis of the RAPD profiles in order to evaluate the diversity of the lactococci below the subspecies level. The coefficient of similarity for 117 of the 139 strains identified as members of L. lactis subsp. cremoris was as high as 66%. The L. lactis subsp. lactis strains were more heterogeneous and formed 10 separate clusters (the level of similarity among the clusters was 18%). Reference strains of L. lactis subsp. lactis fell into 2 of these 10 clusters, demonstrating that lactococcal isolates are clearly different. As determined by the RAPD profiles, some L. lactis subsp. lactis strains were specific to the farms from which they originated and were recovered throughout the year (in both summer and winter). Therefore, the typicality of L. lactis subsp. lactis strains was linked to the farm of origin rather than the area. These findings emphasize the significance of designation of origin and the specificity of “Camembert de Normandie” cheese. PMID:9835555

An ecological study of lactococci isolated from raw milk in the camembert cheese registered designation of origin area.

PubMed

Corroler, D; Mangin, I; Desmasures, N; Gueguen, M

1998-12-01

The genetic diversity of lactococci isolated from raw milk in the Camembert cheese Registered Designation of Origin area was studied. Two seasonal samples (winter and summer) of raw milk were obtained from six farms in two areas (Bessin and Bocage Falaisien) of Normandy. All of the strains analyzed had a Lactococcus lactis subsp. lactis phenotype, whereas the randomly amplified polymorphic DNA (RAPD) technique genotypically identified the strains as members of L. lactis subsp. lactis or L. lactis subsp. cremoris. The genotypes were confirmed by performing standard PCR with primers corresponding to a region of the histidine biosynthesis operon. The geographic distribution of each subspecies of L. lactis was determined; 80% of the Bocage Falaisien strains were members of L. lactis subsp. lactis, and 30.5% of the Bessin strains were members of L. lactis subsp. lactis. A dendrogram was produced from a computer analysis of the RAPD profiles in order to evaluate the diversity of the lactococci below the subspecies level. The coefficient of similarity for 117 of the 139 strains identified as members of L. lactis subsp. cremoris was as high as 66%. The L. lactis subsp. lactis strains were more heterogeneous and formed 10 separate clusters (the level of similarity among the clusters was 18%). Reference strains of L. lactis subsp. lactis fell into 2 of these 10 clusters, demonstrating that lactococcal isolates are clearly different. As determined by the RAPD profiles, some L. lactis subsp. lactis strains were specific to the farms from which they originated and were recovered throughout the year (in both summer and winter). Therefore, the typicality of L. lactis subsp. lactis strains was linked to the farm of origin rather than the area. These findings emphasize the significance of designation of origin and the specificity of "Camembert de Normandie" cheese.

Polyploidisation and Geographic Differentiation Drive Diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae)

PubMed Central

Pachschwöll, Clemens; Escobar García, Pedro; Winkler, Manuela; Schneeweiss, Gerald M.; Schönswetter, Peter

2015-01-01

Range shifts (especially during the Pleistocene), polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum) are differentiated geographically, ecologically (basiphilous versus silicicolous) and/or via their ploidy levels (diploid versus tetraploid). Here, we use DNA sequences (three plastid and one nuclear spacer) and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids—whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates—and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii) silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp. calcareum (northeastern Alps); each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale subsp. glaciale originated from D. glaciale subsp. calcareum, which is restricted to a prominent Pleistocene refugium previously identified in other alpine plant species. PMID:25749621

Chemical decontamination with N-acetyl-L-cysteine-sodium hydroxide improves recovery of viable Mycobacterium avium subsp. paratuberculosis organisms from cultured milk.

PubMed

Bradner, L; Robbe-Austerman, S; Beitz, D C; Stabel, J R

2013-07-01

Mycobacterium avium subsp. paratuberculosis is shed into the milk and feces of cows with advanced Johne's disease, allowing the transmission of M. avium subsp. paratuberculosis between animals. The objective of this study was to formulate an optimized protocol for the isolation of M. avium subsp. paratuberculosis in milk. The parameters investigated included chemical decontamination with N-acetyl-l-cysteine-sodium hydroxide (NALC-NaOH), alone and in combination with antibiotics (vancomycin, amphotericin B, and nalidixic acid), and the efficacy of solid (Herrold's egg yolk medium [HEY]) and liquid (Bactec 12B and para-JEM) culture media. For each experiment, raw milk samples from a known noninfected cow were inoculated with 10(2) to 10(8) CFU/ml of live M. avium subsp. paratuberculosis organisms. The results indicate that an increased length of exposure to NALC-NaOH from 5 to 30 min and an increased concentration of NaOH from 0.5 to 2.0% did not affect the viability of M. avium subsp. paratuberculosis. Additional treatment of milk samples with the antibiotics following NALC-NaOH treatment decreased the recovery of viable M. avium subsp. paratuberculosis cells more than treatment with NALC-NaOH alone. The Bactec 12B medium was the superior medium of the three evaluated for the isolation of M. avium subsp. paratuberculosis from milk, as it achieved the lowest threshold of detection. The optimal conditions for NALC-NaOH decontamination were determined to be exposure to 1.50% NaOH for 15 min followed by culture in Bactec 12B medium. This study demonstrates that chemical decontamination with NALC-NaOH resulted in a greater recovery of viable M. avium subsp. paratuberculosis cells from milk than from samples treated with hexadecylpyridinium chloride (HPC). Therefore, it is important to optimize milk decontamination protocols to ensure that low concentrations of M. avium subsp. paratuberculosis can be detected.

Effect of Three Factors in Cheese Production (pH, Salt, and Heat) on Mycobacterium avium subsp. paratuberculosis Viability

PubMed Central

Sung, Nackmoon; Collins, Michael T.

2000-01-01

Low pH and salt are two factors contributing to the inactivation of bacterial pathogens during a 60-day curing period for cheese. The kinetics of inactivation for Mycobacterium avium subsp. paratuberculosis strains ATCC 19698 and Dominic were measured at 20°C under different pH and NaCl conditions commonly used in processing cheese. The corresponding D values (decimal reduction times; the time required to kill 1 log10 concentration of bacteria) were measured. Also measured were the D values for heat-treated and nonheated M. avium subsp. paratuberculosis in 50 mM acetate buffer (pH 5.0, 2% [wt/vol] NaCl) and a soft white Hispanic-style cheese (pH 6.0, 2% [wt/vol] NaCl). Samples were removed at various intervals until no viable cells were detected using the radiometric culture method (BACTEC) for enumeration of M. avium subsp. paratuberculosis. NaCl had little or no effect on the inactivation of M. avium subsp. paratuberculosis, and increasing NaCl concentrations were not associated with decreasing D values (faster killing) in the acetate buffer. Lower pHs, however, were significantly correlated with decreasing D values of M. avium subsp. paratuberculosis in the acetate buffer. The D values for heat-treated M. avium subsp. paratuberculosis ATCC 19698 in the cheese were higher than those predicted by studies done in acetate buffer. The heat-treated M. avium subsp. paratuberculosis strains had lower D values than the nonheated cells (faster killing) both in the acetate buffer (pH 5, 2% [wt/vol] NaCl) and in the soft white cheese. The D value for heat-treated M. avium subsp. paratuberculosis ATCC 19698 in the cheese (36.5 days) suggests that heat treatment of raw milk coupled with a 60-day curing period will inactivate about 103 cells of M. avium subsp. paratuberculosis per ml. PMID:10742208

Mycobacterium avium biofilm attenuates mononuclear phagocyte function by triggering hyperstimulation and apoptosis during early infection.

PubMed

Rose, Sasha J; Bermudez, Luiz E

2014-01-01

Mycobacterium avium subsp. hominissuis is an opportunistic human pathogen that has been shown to form biofilm in vitro and in vivo. Biofilm formation in vivo appears to be associated with infections in the respiratory tract of the host. The reasoning behind how M. avium subsp. hominissuis biofilm is allowed to establish and persist without being cleared by the innate immune system is currently unknown. To identify the mechanism responsible for this, we developed an in vitro model using THP-1 human mononuclear phagocytes cocultured with established M. avium subsp. hominissuis biofilm and surveyed various aspects of the interaction, including phagocyte stimulation and response, bacterial killing, and apoptosis. M. avium subsp. hominissuis biofilm triggered robust tumor necrosis factor alpha (TNF-α) release from THP-1 cells as well as superoxide and nitric oxide production. Surprisingly, the hyperstimulated phagocytes did not effectively eliminate the cells of the biofilm, even when prestimulated with gamma interferon (IFN-γ) or TNF-α or cocultured with natural killer cells (which have been shown to induce anti-M. avium subsp. hominissuis activity when added to THP-1 cells infected with planktonic M. avium subsp. hominissuis). Time-lapse microscopy and the TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) assay determined that contact with the M. avium subsp. hominissuis biofilm led to early, widespread onset of apoptosis, which is not seen until much later in planktonic M. avium subsp. hominissuis infection. Blocking TNF-α or TNF-R1 during interaction with the biofilm significantly reduced THP-1 apoptosis but did not lead to elimination of M. avium subsp. hominissuis. Our data collectively indicate that M. avium subsp. hominissuis biofilm induces TNF-α-driven hyperstimulation and apoptosis of surveilling phagocytes, which prevents clearance of the biofilm by cells of the innate immune system and allows the biofilm-associated infection to persist.

Tomato fruit and seed colonization by Clavibacter michiganensis subsp. michiganensis through external and internal routes.

PubMed

Tancos, Matthew A; Chalupowicz, Laura; Barash, Isaac; Manulis-Sasson, Shulamit; Smart, Christine D

2013-11-01

The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial wilt and canker of tomato, is an economically devastating pathogen that inflicts considerable damage throughout all major tomato-producing regions. Annual outbreaks continue to occur in New York, where C. michiganensis subsp. michiganensis spreads via infected transplants, trellising stakes, tools, and/or soil. Globally, new outbreaks can be accompanied by the introduction of contaminated seed stock; however, the route of seed infection, especially the role of fruit lesions, remains undefined. In order to investigate the modes of seed infection, New York C. michiganensis subsp. michiganensis field strains were stably transformed with a gene encoding enhanced green fluorescent protein (eGFP). A constitutively eGFP-expressing virulent C. michiganensis subsp. michiganensis isolate, GCMM-22, was used to demonstrate that C. michiganensis subsp. michiganensis could not only access seeds systemically through the xylem but also externally through tomato fruit lesions, which harbored high intra- and intercellular populations. Active movement and expansion of bacteria into the fruit mesocarp and nearby xylem vessels followed, once the fruits began to ripen. These results highlight the ability of C. michiganensis subsp. michiganensis to invade tomato fruits and seeds through multiple entry routes.

Tomato Fruit and Seed Colonization by Clavibacter michiganensis subsp. michiganensis through External and Internal Routes

PubMed Central

Tancos, Matthew A.; Chalupowicz, Laura; Barash, Isaac; Manulis-Sasson, Shulamit

2013-01-01

The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial wilt and canker of tomato, is an economically devastating pathogen that inflicts considerable damage throughout all major tomato-producing regions. Annual outbreaks continue to occur in New York, where C. michiganensis subsp. michiganensis spreads via infected transplants, trellising stakes, tools, and/or soil. Globally, new outbreaks can be accompanied by the introduction of contaminated seed stock; however, the route of seed infection, especially the role of fruit lesions, remains undefined. In order to investigate the modes of seed infection, New York C. michiganensis subsp. michiganensis field strains were stably transformed with a gene encoding enhanced green fluorescent protein (eGFP). A constitutively eGFP-expressing virulent C. michiganensis subsp. michiganensis isolate, GCMM-22, was used to demonstrate that C. michiganensis subsp. michiganensis could not only access seeds systemically through the xylem but also externally through tomato fruit lesions, which harbored high intra- and intercellular populations. Active movement and expansion of bacteria into the fruit mesocarp and nearby xylem vessels followed, once the fruits began to ripen. These results highlight the ability of C. michiganensis subsp. michiganensis to invade tomato fruits and seeds through multiple entry routes. PMID:24014525

Screening of the antioxidative properties and total phenolic contents of three endemic Tanacetum subspecies from Turkish flora.

PubMed

Tepe, Bektas; Sokmen, Atalay

2007-11-01

Methanolic extracts of three different Tanacetum subspecies [Tanacetum densum (Lab.) Schultz Bip. subsp. sivasicum Hub-Mor and Grierson, Tanacetum densum (Lab.) Schultz Bip. subsp. eginense Heywood and Tanacetum densum (Lab.) Schultz Bip. subsp. amani Heywood] which are endemic to Turkish flora were screened for their possible antioxidant activities by two complementary test systems namely DPPH free radical scavenging and beta-carotene/linoleic acid. In DPPH system, the most active plant was T. densum subsp. amani with an IC(50) value of 69.30+/-0.37 microg/ml. On the other hand, T. densum subsp. sivasicum exerted greater antioxidant activity than those of other subspecies in beta-carotene/linoleic acid system (79.10%+/-1.83). Antioxidant activities of BHT, curcumine and ascorbic acid were also determined as positive controls in parallel experiments. Total phenolic constituents of the extracts of Tanacetum subspecies were performed employing the literature methods involving Folin-Ciocalteu reagent and gallic acid as standard. The amount of total phenolics was highest in subsp. sivasicum (162.33+/-3.57 microg/mg), followed by subsp. amani (158.44+/-2.17 microg/mg). Especially, a positive correlation was observed between total phenolic content and antioxidant activity of the extracts.

Loop-mediated amplification of the Clavibacter michiganensis subsp. michiganensis micA gene is highly specific.

PubMed

Yasuhara-Bell, Jarred; Kubota, Ryo; Jenkins, Daniel M; Alvarez, Anne M

2013-12-01

Loop-mediated amplification (LAMP) was used to specifically identify Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial canker of tomato. LAMP primers were developed to detect micA, a chromosomally stable gene that encodes a type II lantibiotic, michiganin A, which inhibits growth of other C. michiganensis subspecies. In all, 409 bacterial strains (351 C. michiganensis subsp. michiganensis and 58 non-C. michiganensis subsp. michiganensis) from a worldwide collection were tested with LAMP to determine its specificity. LAMP results were compared with genetic profiles established using polymerase chain reaction (PCR) amplification of seven genes (dnaA, ppaJ, pat-1, chpC, tomA, ppaA, and ppaC). C. michiganensis subsp. michiganensis strains produced eight distinct profiles. The LAMP reaction identified all C. michiganensis subsp. michiganensis strains and discriminated them from other C. michiganensis subspecies and non-Clavibacter bacteria. LAMP has advantages over immunodiagnostic and other molecular detection methods because of its specificity and isothermal nature, which allows for easy field application. The LAMP reaction is also not affected by as many inhibitors as PCR. This diagnostic tool has potential to provide an easy, one-step test for rapid identification of C. michiganensis subsp. michiganensis.

Environmental Mycobacterium avium subsp. paratuberculosis hosted by free-living amoebae

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis is responsible for paratuberculosis in animals. This disease, leading to an inflammation of the gastrointestinal tract, has a high impact on animal health and an important economic burden. The environmental life cycle of Mycobacterium avium subsp. paratube...

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CRL871, a Folate-Producing Strain Isolated from a Northwestern Argentinian Yogurt.

PubMed

Laiño, Jonathan Emiliano; Hebert, Elvira María; Savoy de Giori, Graciela; LeBlanc, Jean Guy

2015-06-25

Lactobacillus delbrueckii subsp. bulgaricus CRL871 is the first strain of L. delbrueckii subsp. bulgaricus reported as a folate-producing strain. We report the draft genome sequence of L. delbrueckii subsp. bulgaricus CRL871 (2,063,981 bp, G+C content of 49.1%). This strain is of great biotechnological importance to the dairy industry because it constitutes an alternative to folic acid fortification. Copyright © 2015 Laiño et al.

Seed-associated subspecies of the genus Clavibacter are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis.

PubMed

Yasuhara-Bell, Jarred; Alvarez, Anne M

2015-03-01

The genus Clavibacter contains one recognized species, Clavibacter michiganensis. Clavibacter michiganensis is subdivided into subspecies based on host specificity and bacteriological characteristics, with Clavibacter michiganensis subsp. michiganensis causing bacterial canker of tomato. Clavibacter michiganensis subsp. michiganensis is often spread through contaminated seed leading to outbreaks of bacterial canker in tomato production areas worldwide. The frequent occurrence of non-pathogenic Clavibacter michiganensis subsp. michiganensis-like bacteria (CMB) is a concern for seed producers because Clavibacter michiganensis subsp. michiganensis is a quarantine organism and detection of a non-pathogenic variant may result in destruction of an otherwise healthy seed lot. A thorough biological and genetic characterization of these seed-associated CMB strains was performed using standard biochemical tests, cell wall analyses, metabolic profiling using Biolog, and single-gene and multilocus sequence analyses. Combined, these tests revealed two distinct populations of seed-associated members of the genus Clavibacter that differed from each other, as well as from all other described subspecies of Clavibacter michiganensis. DNA-DNA hybridization values are 70 % or higher, justifying placement into the single recognized species, C. michiganensis, but other analyses justify separate subspecies designations. Additionally, strains belonging to the genus Clavibacter isolated from pepper also represent a distinct population and warrant separate subspecies designation. On the basis of these data we propose subspecies designations for separate non-pathogenic subpopulations of Clavibacter michiganensis: Clavibacter michiganensis subsp. californiensis subsp. nov. and Clavibacter michiganensis subsp. chilensis subsp. nov. for seed-associated strains represented by C55(T) ( = ATCC BAA-2691(T) = CFBP 8216(T)) and ZUM3936(T) ( = ATCC BAA-2690(T) = CFBP 8217(T)), respectively. Recognition of separate subspecies is essential for improved international seed testing operations. © 2015 IUMS.

Efficacy of various pasteurization time-temperature conditions in combination with homogenization on inactivation of Mycobacterium avium subsp. paratuberculosis in milk.

PubMed

Grant, Irene R; Williams, Alan G; Rowe, Michael T; Muir, D Donald

2005-06-01

The effect of various pasteurization time-temperature conditions with and without homogenization on the viability of Mycobacterium avium subsp. paratuberculosis was investigated using a pilot-scale commercial high-temperature, short-time (HTST) pasteurizer and raw milk spiked with 10(1) to 10(5) M. avium subsp. paratuberculosis cells/ml. Viable M. avium subsp. paratuberculosis was cultured from 27 (3.3%) of 816 pasteurized milk samples overall, 5 on Herrold's egg yolk medium and 22 by BACTEC culture. Therefore, in 96.7% of samples, M. avium subsp. paratuberculosis had been completely inactivated by HTST pasteurization, alone or in combination with homogenization. Heat treatments incorporating homogenization at 2,500 lb/in2, applied upstream (as a separate process) or in hold (at the start of a holding section), resulted in significantly fewer culture-positive samples than pasteurization treatments without homogenization (P < 0.001 for those in hold and P < 0.05 for those upstream). Where colony counts were obtained, the number of surviving M. avium subsp. paratuberculosis cells was estimated to be 10 to 20 CFU/150 ml, and the reduction in numbers achieved by HTST pasteurization with or without homogenization was estimated to be 4.0 to 5.2 log10. The impact of homogenization on clump size distribution in M. avium subsp. paratuberculosis broth suspensions was subsequently assessed using a Mastersizer X spectrometer. These experiments demonstrated that large clumps of M. avium subsp. paratuberculosis cells were reduced to single-cell or "miniclump" status by homogenization at 2,500 lb/in2. Consequently, when HTST pasteurization was being applied to homogenized milk, the M. avium subsp. paratuberculosis cells would have been present as predominantly declumped cells, which may possibly explain the greater inactivation achieved by the combination of pasteurization and homogenization.

Efficacy of Various Pasteurization Time-Temperature Conditions in Combination with Homogenization on Inactivation of Mycobacterium avium subsp. paratuberculosis in Milk

PubMed Central

Grant, Irene R.; Williams, Alan G.; Rowe, Michael T.; Muir, D. Donald

2005-01-01

The effect of various pasteurization time-temperature conditions with and without homogenization on the viability of Mycobacterium avium subsp. paratuberculosis was investigated using a pilot-scale commercial high-temperature, short-time (HTST) pasteurizer and raw milk spiked with 101 to 105 M. avium subsp. paratuberculosis cells/ml. Viable M. avium subsp. paratuberculosis was cultured from 27 (3.3%) of 816 pasteurized milk samples overall, 5 on Herrold's egg yolk medium and 22 by BACTEC culture. Therefore, in 96.7% of samples, M. avium subsp. paratuberculosis had been completely inactivated by HTST pasteurization, alone or in combination with homogenization. Heat treatments incorporating homogenization at 2,500 lb/in2, applied upstream (as a separate process) or in hold (at the start of a holding section), resulted in significantly fewer culture-positive samples than pasteurization treatments without homogenization (P < 0.001 for those in hold and P < 0.05 for those upstream). Where colony counts were obtained, the number of surviving M. avium subsp. paratuberculosis cells was estimated to be 10 to 20 CFU/150 ml, and the reduction in numbers achieved by HTST pasteurization with or without homogenization was estimated to be 4.0 to 5.2 log10. The impact of homogenization on clump size distribution in M. avium subsp. paratuberculosis broth suspensions was subsequently assessed using a Mastersizer X spectrometer. These experiments demonstrated that large clumps of M. avium subsp. paratuberculosis cells were reduced to single-cell or “miniclump” status by homogenization at 2,500 lb/in2. Consequently, when HTST pasteurization was being applied to homogenized milk, the M. avium subsp. paratuberculosis cells would have been present as predominantly declumped cells, which may possibly explain the greater inactivation achieved by the combination of pasteurization and homogenization. PMID:15932977

Emendation of Propionibacterium acnes subsp. acnes (Deiko et al. 2015) and proposal of Propionibacterium acnes type II as Propionibacterium acnes subsp. defendens subsp. nov.

PubMed

McDowell, Andrew; Barnard, Emma; Liu, Jared; Li, Huiying; Patrick, Sheila

2016-12-01

Recently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnessubsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnessubsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA-DNA similarity values also fall within the 70-80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for β-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnessubsp. acnes subsp. nov., and type II as P. acnessubsp. defendens subsp. nov. The type strain of P. acnessubsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnessubsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).

Use of inter-simple sequence repeats and amplified fragment length polymorphisms to analyze genetic relationships among small grain-infecting species of ustilago.

PubMed

Menzies, J G; Bakkeren, G; Matheson, F; Procunier, J D; Woods, S

2003-02-01

ABSTRACT In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

Population biology of Avena : IX. Gene flow and neighborhood size in relation to microgeographic variation in Avena barbata.

PubMed

Rai, Kedar N; Jain, Subodh K

1982-06-01

Pollen and seed dispersal patterns were analyzed in both natural and experimental populations of Avena barbata. Localized estimates of gene flow rates and plant densities gave estimates of neighborhood size in the range of 40 to 400 plants; the estimates of mean rate and distance of gene flow seemed to vary widely due to variable wind direction, rodent activity, microsite heterogeneity, etc. The relative sizes of neighborhoods in several populations were correlated with the patchy distribution of different genotypes (scored for lemma color and leaf sheath hairiness) within short distances, but patch sizes had a wide range among different sites. Highly localized gene flow patterns seemed to account for the observed pattern of highly patchy variation even when the dispersal curves for both pollen and seed were platykurtic in many cases. Measures of the stability of patches in terms of their size, dispersion in space and genetic structure in time are needed in order to sort out the relative roles of founder effects, random drift (due to small neighborhood size), and highly localized selection. However, our observations suggest that many variables and stochastic processes are involved in such studies so as to allow only weak inference about the underlying role of natural selection, drift and factors of population regulatien.

Elongation growth of the leaf sheath base of Avena sativa seedlings: regulation by hormones and sucrose

NASA Technical Reports Server (NTRS)

Brock, T. G.; Kaufman, P. B.

1991-01-01

The leaf sheath base of the seedling of Avena sativa was characterized for growth response to hormones and sucrose. Six day old plants, raised under a 10:14 hr light:dark cycle, were excised at the coleoptilar node and 1 cm above the node for treatment. The growth of the leaf sheath base was promoted by gibberellic acid (GA3) and this response was dose dependent. The lag to response initiation was approximately 4 hr. Growth with or without GA3 (10 micromoles) was transient, diminishing appreciably after 48 hr. The addition of 10 mM sucrose greatly prolonged growth; the effect of GA3 and sucrose was additive. Neither indole-3-acetic acid (IAA) nor the cytokinin N6-benzyladenine (BA), alone or in combination, promoted the growth of leaf sheath bases. However, both significantly inhibited the action of GA3. The inhibitory effect of IAA was dose dependent and was not affected by the addition of BA or sucrose. These results indicate that the growth of leaf sheath bases of Avena sativa is promoted specifically by gibberellin, that this action depends on the availability of carbohydrates from outside of the leaf sheath base, and that the promotional effect of GA3 can be modified by either auxins or cytokinins.

Spatio-temporal distribution and environmental drivers of Barley yellow dwarf virus and vector abundance in Kansas.

PubMed

Enders, Laramy; Hefley, Trevor; Girvin, John; Whitworth, Robert; Smith, Charles

2018-05-11

Several aphid species transmit barley yellow dwarf, a globally destructive disease caused by viruses that infect cereal grain crops. Data from >400 samples collected across Kansas wheat fields in 2014 and 2015 were used to develop spatio-temporal models predicting the extent to which landcover, temperature and precipitation affect spring aphid vector abundance and presence of individuals carrying Barley yellow dwarf virus (BYDV). The distribution of Rhopalosiphum padi abundance was not correlated with climate or landcover, but Sitobion avenae abundance was positively correlated to fall temperature and negatively correlated to spring temperature and precipitation. The abundance of Schizaphis graminum was negatively correlated with fall precipitation and winter temperature. The incidence of viruliferous (+BYDV) R. padi was positively correlated with fall precipitation but negatively correlated with winter precipitation. In contrast, the probability of +BYDV S. avenae was unaffected by precipitation but was positively correlated with average fall temperatures and distance to nearest forest or shrubland. R. padi and S. avenae were more prevalent at Eastern sample sites where ground cover is more grassland than cropland, suggesting that grassland may provide over-summering sites for vectors and pose a risk as potential BYDV reservoirs. Nevertheless, land cover patterns were not strongly associated with differences in abundance or probability that viruliferous aphids were present.

Horizontal transfer of facultative endosymbionts is limited by host relatedness.

PubMed

Łukasik, Piotr; Guo, Huifang; van Asch, Margriet; Henry, Lee M; Godfray, H Charles J; Ferrari, Julia

2015-10-01

Heritable microbial symbionts can have important effects on many aspects of their hosts' biology. Acquisition of a novel symbiont strain can provide fitness benefits to the host, with significant ecological and evolutionary consequences. We measured barriers to horizontal transmission by artificially transferring facultative symbionts from the grain aphid, Sitobion avenae, and five other aphid species into two clonal genotypes of S. avenae. We found the symbiont Hamiltonella defensa establishes infections more easily following a transfer from the same host species and that such infections are more stable. Infection success was also higher when the introduced symbiont strain was more closely related to the strain that was originally present in the host (but which had previously been removed). There were no differences among successfully established symbiont strains in their effect on aphid fecundity. Hamiltonella defensa did not confer protection against parasitoids in our S. avenae clones, although it often does in other aphid hosts. However, strains of the symbiont Regiella insecticola originating from two host species protected grain aphids against the pathogenic fungus Pandora neoaphidis. This study helps describe the extent to which facultative symbionts can act as a pool of adaptations that can be sampled by their eukaryote hosts. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Chemical composition and antimicrobial activity of the essential oils of some species of Anthemis sect. Anthemis (Asteraceae) from Sicily.

PubMed

Riccobono, Luana; Maggio, Antonella; Bruno, Maurizio; Spadaro, Vivienne; Raimondo, Francesco Maria

2017-12-01

The chemical composition of the essential oils isolated from the aerial parts of Anthemis arvensis L. subsp. arvensis, Anthemis cretica subsp. messanensis (Brullo) Giardina & Raimondo and from flowers and leaves of Anthemis cretica subsp. columnae (Ten.) Frezén were determinated by GC-FID and GC-MS analyses. Torreyol (85.4%) was recognised as the main constituent of the Anthemis arvensis subsp. arvensis essential oil, while in the essential oils of Anthemis cretica subsp. messanensis, collected on the rock and cultivated in Hortus Botanicus Panormitanus, (E)-chrysanthenyl acetate (28.8 and 24.2% resp.), 14-hydroxy-α-humulene (8.1 and 5.3% resp.), santolina triene (8 and 5.8% resp.) and α-pinene (6.7 and 5.4% resp.) prevailed. 18-cineole (13.3 and 12.2% resp.), was the main component of both flower and leaf oils of Anthemis cretica subsp. columnae together with δ-cadinene (9.0 and 8.2% resp.) and (E)-caryophyllene (8.3 and 5.6% resp.).

Comparison of 16S ribosomal RNA genes in Clavibacter michiganensis subspecies with other coryneform bacteria.

PubMed

Li, X; De Boer, S H

1995-10-01

Nearly complete sequences (97-99%) of the 16S rRNA genes were determined for type strains of Clavibacter michiganensis subsp. michiganensis, Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. sepedonicus, and Clavibacter michiganensis subsp. nebraskensis. The four subspecies had less than 1% dissimilarity in their 16S rRNA genes. Comparative studies indicated that the C. michiganensis subsp. shared relatively high homology with the 16S rRNA gene of Clavibacter xyli. Further comparison with representatives of other Gram-positive coryneform and related bacteria with high G+C% values showed that this group of bacteria was subdivided into three clusters. One cluster consisted of the Clavibacter michiganensis subsp., Clavibacter xyli, Arthrobacter globiformis, Arthrobacter simplex, and Frankia sp.; another cluster consisted of members of the corynebacteria-mycobacteria-nocardia (CMN) group of Mycobacteriaceae including Tsukamurella paurometabolum; and Propionibacterium freudenreichii alone formed a unique cluster, which was remote from other coryneform bacteria analyzed. The three clusters may reflect a systematic rank higher than the genus level among these bacteria.

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing

PubMed Central

Ortiz-Martínez, Sebastían; Silva, Andrea X.; Lavandero, Blas

2018-01-01

Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected. We discuss these results in relation to the bacterial endosymbiont diversity found in other regions of the native and introduced range of S. avenae and R. padi. A similar endosymbiont diversity has been reported for both aphid species in their native range. However, variation in the secondary endosymbiont infection could be observed among the introduced and native populations of the aphid S. avenae, indicating that aphid-endosymbiont associations can vary across the geographic range of an aphid species. In addition, we discuss the potential role of aphids as vectors and/or alternative hosts of phytopathogenic bacteria. PMID:29761046

Persistence of Mycobacterium avium subsp. paratuberculosis at a Farm-Scale Biogas Plant Supplied with Manure from Paratuberculosis-Affected Dairy Cattle▿

PubMed Central

Slana, I.; Pribylova, R.; Kralova, A.; Pavlik, I.

2011-01-01

In this study, products from all steps of anaerobic digestion at a farm-scale biogas plant supplied with manure from paratuberculosis-affected dairy cattle were examined and quantified for the presence of the causal agent of paratuberculosis, Mycobacterium avium subsp. paratuberculosis, using culture and quantitative real-time PCR (qPCR). Viable M. avium subsp. paratuberculosis cells were detected using culture in fermentors for up to 2 months; the presence of M. avium subsp. paratuberculosis DNA (101 cells/g) was demonstrated in all anaerobic fermentors and digestate 16 months after initiation of work at a biogas plant, using IS900 qPCR. F57 qPCR was able to detect M. avium subsp. paratuberculosis DNA (102 cells/g) at up to 12 months. According to these results, a fermentation process that extended beyond 2 months removed all viable M. avium subsp. paratuberculosis cells and therefore rendered its product M. avium subsp. paratuberculosis free. However, M. avium subsp. paratuberculosis DNA was found during all the examined periods (more than 1 year), which could be explained by either residual DNA being released from dead cells or by the presence of viable cells whose amount was under the limit of cultivability. As the latter hypothesis cannot be excluded, the safety of the final products of digestion used for fertilization or animal bedding cannot be defined, and further investigation is necessary to confirm or refute this risk. PMID:21398476

Specific Detection of Clavibacter michiganensis subsp. sepedonicus by Amplification of Three Unique DNA Sequences Isolated by Subtraction Hybridization.

PubMed

Mills, D; Russell, B W; Hanus, J W

1997-08-01

ABSTRACT Three single-copy, unique DNA fragments, designated Cms50, Cms72, and Cms85, were isolated from strain CS3 of Clavibacter michiganensis subsp. sepedonicus by subtraction hybridization using driver DNA from C. michiganensis subsp. insidiosus, C. michiganensis subsp. michiganensis, and Rhodococcus facians. Radio-labeled probes made of these fragments and used in Southern blot analysis revealed each to be absolutely specific to all North American C. michiganensis subsp. sepedonicus strains tested, including plasmidless and nonmucoid strains. The probes have no homology with genomic DNA from related C. michiganensis subspecies insidiosus, michiganensis, and tessellarius, nor with DNA from 11 additional bacterial species and three unidentified strains, some of which have been previously reported to display cross-reactivity with C. michiganensis subsp. sepedonicus-specific antisera. The three fragments shared no homology, and they appeared to be separated from each other by at least 20 kbp in the CS3 genome. Internal primer sets permitted amplification of each fragment by the polymerase chain reaction (PCR) only from C. michiganensis subsp. sepedonicus DNA. In a PCR-based sensitivity assay using a primer set that amplifies Cms85, the lowest level of detection of C. michiganensis subsp. sepedonicus was 100 CFU per milliliter when cells were added to potato core fluid. Erroneous results that may arise from PCR artifacts and mutational events are, therefore, minimized by the redundancy of the primer sets, and the products should be verifiable with unique capture probes in sequence-based detection systems.

Complete genome sequence of Mycobacterium avium subsp. paratuberculosis, isolated from human breast milk

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp paratuberculosis is the etiologic agent of Johne’s disease. We report the draft genome sequences of six M. avium subsp paratuberculosis isolates obtained from diverse hosts including bison, cattle and sheep. These sequences will deepen our understanding of host association ...

Draft Genome Sequences of Three Pectobacterium Strains Causing Blackleg of Potato: P. carotovorum subsp. brasiliensis ICMP 19477, P. atrosepticum ICMP 1526, and P. carotovorum subsp. carotovorum UGC32

PubMed Central

Fiers, Mark W. E. J.; Lu, Ashley; Armstrong, Karen F.

2015-01-01

Blackleg is a disease caused by several species of Pectobacterium that results in losses to potato crops worldwide. Here, we report the draft genomes of three taxonomically and geographically distinct blackleg-causing strains of Pectobacterium: P. carotovorum subsp. brasiliensis ICMP 19477, P. atrosepticum ICMP 1526, and P. carotovorum subsp. carotovorum UGC32. Comparison of these genomes will support the identification of common traits associated with their capacity to cause blackleg. PMID:26251497

Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows.

PubMed

Kaevska, Marija; Videnska, Petra; Sedlar, Karel; Bartejsova, Iva; Kralova, Alena; Slana, Iva

2016-06-01

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne's disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

The in vitro effect of six antimicrobials against Mycoplasma putrefaciens, Mycoplasma mycoides subsp. mycoides LC and Mycoplasma capricolum subsp. capricolum isolated from sheep and goats in Jordan.

PubMed

Al-Momani, W; Nicholas, R A J; Janakat, S; Abu-Basha, E; Ayling, R D

2006-01-01

Respiratory disease in sheep and goats is a major problem in Jordan and is often associated with Mycoplasma species. Without effective vaccines, control is mainly by chemotherapy, but the uncontrolled use of antimicrobials has led to concerns about the potential development of antimicrobial resistance. The in vitro effect of chloramphenicol, florfenicol, enrofloxacin, tylosin, erythromycin and oxytetracycline was determined against 32 isolates of Mycoplasma species-M. mycoides subsp. mycoides LC (6), M. capricolum subsp. capricolum (8) and M. putrefaciens (18), all isolated from either nasal swabs or milk, from sheep and goats in different regions of Jordan. The antimicrobial susceptibility showed some Mycoplasma species-specific differences, with M. capricolum subsp. capricolum being more susceptible to tylosin and erythromycin. Chloramphenicol and florfenicol were the least effective for all three Mycoplasma species. No trends or significant differences in antimicrobial susceptibilities were observed between sheep and goat isolates, between milk or nasal swab isolates, or between isolates from different regions of Jordan. Some isolates of M. capricolum subsp. capricolum and M. putrefaciens showed higher MIC levels with oxytetracycline, as did two isolates of M. mycoides subsp. mycoides LC with tylosin, possibly indicating signs of development of antimicrobial resistance.

Effects of six substances on the growth and freeze-drying of Lactobacillus delbrueckii subsp. bulgaricus.

PubMed

Chen, He; Huang, Jie; Shi, Xiaoyu; Li, Yichao; Liu, Yu

2017-01-01

The efficacy of Lactobacillus delbrueckii subsp. bulgaricus as starter cultures for the dairy industry depends largely on the number of viable and active cells. Freeze-drying is the most convenient and successful method to preserve the bacterial cells. However, not all strains survived during freeze-drying. The effects of six substances including NaCl, sorbitol, mannitol, mannose, sodium glutamate, betaine added to the MRS medium on the growth and freeze-drying survival rate and viable counts of Lb. delbrueckii subsp. bulgaricus were studied through a single-factor test and Plackett-Burman design. Subsequently, the optimum freeze-drying conditions of Lb. delbrueckii subsp. bulgaricus were determined. Lb. delbrueckii subsp. bulgaricus survival rates were up to the maximum of 42.7%, 45.4%, 23.6%, while the concentrations of NaCl, sorbitol, sodium glutamate were 0.6%, 0.15%, 0.09%, respectively. In the optimum concentration, the viable counts in broth is 6.1, 6.9, 5.13 (×108 CFU/mL), respectively; the viable counts in freeze-drying power are 3.09, 5.2, 2.7 (×1010 CFU/g), respectively. Three antifreeze factors including NaCl, sorbitol, sodium glutamate have a positive effect on the growth and freeze-drying of Lb. delbrueckii subsp. bulgaricus. The results are beneficial for developing Lb. delbrueckii subsp. bulgaricus.

Derivation of Mutants of Erwinia carotovora subsp. betavasculorum Deficient in Export of Pectolytic Enzymes with Potential for Biological Control of Potato Soft Rot

PubMed Central

Costa, José M.; Loper, Joyce E.

1994-01-01

Erwinia carotovora subsp. betavasculorum Ecb168 produces an antibiotic(s) that suppresses growth of the related bacterium Erwinia carotovora subsp. carotovora in culture and in wounds of potato tubers. Strain Ecb168 also produces and secretes pectolytic enzymes and causes a vascular necrosis and root rot of sugar beet. Genes (out) involved in secretion of pectolytic enzymes by Ecb168 were localized to two HindIII fragments (8.5 and 10.5 kb) of Ecb168 genomic DNA by hybridization to the cloned out region of E. carotovora subsp. carotovora and by complementation of Out- mutants of E. carotovora subsp. carotovora. Out- mutants of Ecb168, which did not secrete pectate lyase into the culture medium, were obtained when deletions internal to either HindIII fragment were introduced into the genome of Ecb168 through marker exchange mutagenesis. Out- mutants of Ecb168 were complemented to the Out+ phenotype by introduction of the corresponding cloned HindIII fragment. Out- mutants of Ecb168 were less virulent than the Out+ parental strain on potato tubers. Strain Ecb168 and Out- derivatives inhibited the growth of E. carotovora subsp. carotovora in culture, indicating that the uncharacterized antibiotic(s) responsible for antagonism was exported through an out-independent mechanism. Strain Ecb168 and Out- derivatives reduced the establishment of large populations of E. carotovora subsp. carotovora in wounds of potato tubers and suppressed tuber soft rot caused by E. carotovora subsp. carotovora. PMID:16349316

Isolation of Bartonella vinsonii subsp. berkhoffii Genotype II from a Boy with Epithelioid Hemangioendothelioma and a Dog with Hemangiopericytoma▿

PubMed Central

Breitschwerdt, Edward B.; Maggi, Ricardo G.; Varanat, Mrudula; Linder, Keith E.; Weinberg, Guy

2009-01-01

In this report, we describe isolation of Bartonella vinsonii subsp. berkhoffii genotype II from a boy with epithelioid hemangioendothelioma and a dog with hemangiopericytoma. These results suggest that B. vinsonii subsp. berkhoffii may cause vasoproliferative lesions in both humans and dogs. PMID:19369441

Isolation of Bartonella vinsonii subsp. berkhoffii genotype II from a boy with epithelioid hemangioendothelioma and a dog with hemangiopericytoma.

PubMed

Breitschwerdt, Edward B; Maggi, Ricardo G; Varanat, Mrudula; Linder, Keith E; Weinberg, Guy

2009-06-01

In this report, we describe isolation of Bartonella vinsonii subsp. berkhoffii genotype II from a boy with epithelioid hemangioendothelioma and a dog with hemangiopericytoma. These results suggest that B. vinsonii subsp. berkhoffii may cause vasoproliferative lesions in both humans and dogs.

Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures

PubMed Central

Yin, Xiaochen; Salemi, Michelle R.; Phinney, Brett S.; Gotcheva, Velitchka; Angelov, Angel

2017-01-01

ABSTRACT We identified the proteins synthesized by Lactobacillus delbrueckii subsp. bulgaricus strain LBB.B5 in laboratory culture medium (MRS) at 37°C and milk at 37 and 4°C. Cell-associated proteins were measured by gel-free, shotgun proteomics using high-performance liquid chromatography coupled with tandem mass spectrophotometry. A total of 635 proteins were recovered from all cultures, among which 72 proteins were milk associated (unique or significantly more abundant in milk). LBB.B5 responded to milk by increasing the production of proteins required for purine biosynthesis, carbohydrate metabolism (LacZ and ManM), energy metabolism (TpiA, PgK, Eno, SdhA, and GapN), amino acid synthesis (MetE, CysK, LBU0412, and AspC) and transport (GlnM and GlnP), and stress response (Trx, MsrA, MecA, and SmpB). The requirement for purines was confirmed by the significantly improved cell yields of L. delbrueckii subsp. bulgaricus when incubated in milk supplemented with adenine and guanine. The L. delbrueckii subsp. bulgaricus-expressed proteome in milk changed upon incubation at 4°C for 5 days and included increased levels of 17 proteins, several of which confer functions in stress tolerance (AddB, UvrC, RecA, and DnaJ). However, even with the activation of stress responses in either milk or MRS, L. delbrueckii subsp. bulgaricus did not survive passage through the murine digestive tract. These findings inform efforts to understand how L. delbrueckii subsp. bulgaricus is adapted to the dairy environment and its implications for its health-benefiting properties in the human digestive tract. IMPORTANCE Lactobacillus delbrueckii subsp. bulgaricus has a long history of use in yogurt production. Although commonly cocultured with Streptococcus salivarius subsp. thermophilus in milk, fundamental knowledge of the adaptive responses of L. delbrueckii subsp. bulgaricus to the dairy environment and the consequences of those responses on the use of L. delbrueckii subsp. bulgaricus as a probiotic remain to be elucidated. In this study, we identified proteins of L. delbrueckii subsp. bulgaricus LBB.B5 that are synthesized in higher quantities in milk at growth-conducive and non-growth-conductive (refrigeration) temperatures compared to laboratory culture medium and further examined whether those L. delbrueckii subsp. bulgaricus cultures were affected differently in their capacity to survive transit through the murine digestive tract. This work provides novel insight into how a major, food-adapted microbe responds to its primary habitat. Such knowledge can be applied to improve starter culture and yogurt production and to elucidate matrix effects on probiotic performance. PMID:28951887

Salmonella enterica suppresses Pectobacterium carotovorum subsp. carotovorum population and soft rot progression by acidifying the microaerophilic environment.

PubMed

Kwan, Grace; Charkowski, Amy O; Barak, Jeri D

2013-02-12

Although enteric human pathogens are usually studied in the context of their animal hosts, a significant portion of their life cycle occurs on plants. Plant disease alters the phyllosphere, leading to enhanced growth of human pathogens; however, the impact of human pathogens on phytopathogen biology and plant health is largely unknown. To characterize the interaction between human pathogens and phytobacterial pathogens in the phyllosphere, we examined the interactions between Pectobacterium carotovorum subsp. carotovorum and Salmonella enterica or Escherichia coli O157:H7 with regard to bacterial populations, soft rot progression, and changes in local pH. The presence of P. carotovorum subsp. carotovorum enhanced the growth of both S. enterica and E. coli O157:H7 on leaves. However, in a microaerophilic environment, S. enterica reduced P. carotovorum subsp. carotovorum populations and soft rot progression by moderating local environmental pH. Reduced soft rot was not due to S. enterica proteolytic activity. Limitations on P. carotovorum subsp. carotovorum growth, disease progression, and pH elevation were not observed on leaves coinoculated with E. coli O157:H7 or when leaves were coinoculated with S. enterica in an aerobic environment. S. enterica also severely undermined the relationship between the phytobacterial population and disease progression of a P. carotovorum subsp. carotovorum budB mutant defective in the 2,3-butanediol pathway for acid neutralization. Our results show that S. enterica and E. coli O157:H7 interact differently with the enteric phytobacterial pathogen P. carotovorum subsp. carotovorum. S. enterica inhibition of soft rot progression may conceal a rapidly growing human pathogen population. Whereas soft rotted produce can alert consumers to the possibility of food-borne pathogens, healthy-looking produce may entice consumption of contaminated vegetables. Salmonella enterica and Escherichia coli O157:H7 may use plants to move between animal and human hosts. Their populations are higher on plants cocolonized with the common bacterial soft rot pathogen Pectobacterium carotovorum subsp. carotovorum, turning edible plants into a risk factor for human disease. We inoculated leaves with P. carotovorum subsp. carotovorum and S. enterica or E. coli O157:H7 to study the interactions between these bacteria. While P. carotovorum subsp. carotovorum enhanced the growth of both S. enterica and E. coli O157:H7, these human pathogens affected P. carotovorum subsp. carotovorum fundamentally differently. S. enterica reduced P. carotovorum subsp. carotovorum growth and acidified the environment, leading to less soft rot on leaves; E. coli O157:H7 had no such effects. As soft rot signals a food safety risk, the reduction of soft rot symptoms in the presence of S. enterica may lead consumers to eat healthy-looking but S. enterica-contaminated produce.

Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures.

PubMed

Yin, Xiaochen; Salemi, Michelle R; Phinney, Brett S; Gotcheva, Velitchka; Angelov, Angel; Marco, Maria L

2017-01-01

We identified the proteins synthesized by Lactobacillus delbrueckii subsp. bulgaricus strain LBB.B5 in laboratory culture medium (MRS) at 37°C and milk at 37 and 4°C. Cell-associated proteins were measured by gel-free, shotgun proteomics using high-performance liquid chromatography coupled with tandem mass spectrophotometry. A total of 635 proteins were recovered from all cultures, among which 72 proteins were milk associated (unique or significantly more abundant in milk). LBB.B5 responded to milk by increasing the production of proteins required for purine biosynthesis, carbohydrate metabolism (LacZ and ManM), energy metabolism (TpiA, PgK, Eno, SdhA, and GapN), amino acid synthesis (MetE, CysK, LBU0412, and AspC) and transport (GlnM and GlnP), and stress response (Trx, MsrA, MecA, and SmpB). The requirement for purines was confirmed by the significantly improved cell yields of L. delbrueckii subsp. bulgaricus when incubated in milk supplemented with adenine and guanine. The L. delbrueckii subsp. bulgaricus -expressed proteome in milk changed upon incubation at 4°C for 5 days and included increased levels of 17 proteins, several of which confer functions in stress tolerance (AddB, UvrC, RecA, and DnaJ). However, even with the activation of stress responses in either milk or MRS, L. delbrueckii subsp. bulgaricus did not survive passage through the murine digestive tract. These findings inform efforts to understand how L. delbrueckii subsp. bulgaricus is adapted to the dairy environment and its implications for its health-benefiting properties in the human digestive tract. IMPORTANCE Lactobacillus delbrueckii subsp. bulgaricus has a long history of use in yogurt production. Although commonly cocultured with Streptococcus salivarius subsp. thermophilus in milk, fundamental knowledge of the adaptive responses of L. delbrueckii subsp. bulgaricus to the dairy environment and the consequences of those responses on the use of L. delbrueckii subsp. bulgaricus as a probiotic remain to be elucidated. In this study, we identified proteins of L. delbrueckii subsp. bulgaricus LBB.B5 that are synthesized in higher quantities in milk at growth-conducive and non-growth-conductive (refrigeration) temperatures compared to laboratory culture medium and further examined whether those L. delbrueckii subsp. bulgaricus cultures were affected differently in their capacity to survive transit through the murine digestive tract. This work provides novel insight into how a major, food-adapted microbe responds to its primary habitat. Such knowledge can be applied to improve starter culture and yogurt production and to elucidate matrix effects on probiotic performance.

Pork Meat as a Potential Source of Salmonella enterica subsp. arizonae Infection in Humans

PubMed Central

Kritas, Spyridon; Govaris, Alexander; Burriel, Angeliki R.

2014-01-01

Salmonella enterica subsp. arizonae was isolated from 13 of 123 slaughtered pigs in central Greece. The samples cultured were feces, ileum tissue, mesenteric lymph nodes, and gallbladder swabs. A total of 74 isolates from 492 samples were identified as Salmonella spp. by use of standard laboratory culture media and two commercial micromethods and by use of a polyvalent slide agglutination test for the detection of O and H antigens. Among them were 19 (25.68%) suspected to be S. enterica subsp. arizonae according to analysis with standard laboratory culture media. Of those, 14 were identified as S. enterica subsp. arizonae by the API 20E (bioMérieux, France) and the Microgen GnA+B-ID (Microgen Bioproducts, Ltd., United Kingdom) identification systems. All the isolates were tested for resistance to 23 antimicrobials. Strains identified as S. enterica subsp. arizonae were resistant to 17 (70.8%) antibiotics. The highest proportions of resistance were observed for sulfamethoxazole-trimethoprim (71.4%), tetracycline (71.4%), ampicillin (64.3%), and amoxicillin (57.1%). Two isolates were resistant to aztreonam (7.1%) and tigecycline (7.1%), used only for the treatment of humans. Thus, pork meat may play a role in the transmission of antibiotic-resistant S. enterica subsp. arizonae to human consumers. This is the first report of S. enterica subsp. arizonae isolation from pigs. PMID:24335956

Pork meat as a potential source of Salmonella enterica subsp. arizonae infection in humans.

PubMed

Evangelopoulou, Grammato; Kritas, Spyridon; Govaris, Alexander; Burriel, Angeliki R

2014-03-01

Salmonella enterica subsp. arizonae was isolated from 13 of 123 slaughtered pigs in central Greece. The samples cultured were feces, ileum tissue, mesenteric lymph nodes, and gallbladder swabs. A total of 74 isolates from 492 samples were identified as Salmonella spp. by use of standard laboratory culture media and two commercial micromethods and by use of a polyvalent slide agglutination test for the detection of O and H antigens. Among them were 19 (25.68%) suspected to be S. enterica subsp. arizonae according to analysis with standard laboratory culture media. Of those, 14 were identified as S. enterica subsp. arizonae by the API 20E (bioMérieux, France) and the Microgen GnA+B-ID (Microgen Bioproducts, Ltd., United Kingdom) identification systems. All the isolates were tested for resistance to 23 antimicrobials. Strains identified as S. enterica subsp. arizonae were resistant to 17 (70.8%) antibiotics. The highest proportions of resistance were observed for sulfamethoxazole-trimethoprim (71.4%), tetracycline (71.4%), ampicillin (64.3%), and amoxicillin (57.1%). Two isolates were resistant to aztreonam (7.1%) and tigecycline (7.1%), used only for the treatment of humans. Thus, pork meat may play a role in the transmission of antibiotic-resistant S. enterica subsp. arizonae to human consumers. This is the first report of S. enterica subsp. arizonae isolation from pigs.

Response to low-dose herbicide selection in self-pollinated Avena fatua.

PubMed

Busi, Roberto; Girotto, Marcelo; Powles, Stephen B

2016-03-01

When applied at the correct plant stage and dose, herbicides are highly toxic to plants. At reduced, low herbicide doses (below the recommended dose) plants can survive and display continuous and quantitative variation in dose-survival responses. Recurrent (directional) selection studies can reveal whether such a phenotypic variation in plant survival response to low herbicide dose is heritable and leads to herbicide resistance. In a common experimental garden study, we have subjected a susceptible population of self-pollinated hexaploid Avena fatua to low-dose recurrent selection with the ACCase-inhibiting herbicide diclofop-methyl for three consecutive generations. Significant differences in response to low-dose diclofop-methyl selection were observed between the selected progenies and parent plants, with a twofold diclofop-methyl resistance and cross-resistance to ALS-inhibiting herbicides. Thus, the capacity of self-pollinated A. fatua to respond to low-dose herbicide selection is marginal, and it is much lower than in cross-pollinated L. rigidum. Lolium rigidum in the same experiment evolved 40-fold diclofop-methyl resistance by progressive enrichment of quantitative resistance-endowing traits. Cross-pollination rate, genetic variation and ploidy levels are identified as possible drivers affecting the contrasting capacity of Avena versus Lolium plants to respond to herbicide selection and the subsequent likelihood of resistance evolution at low herbicide dose usage. © 2015 Society of Chemical Industry.

Bacterial symbionts, Buchnera, and starvation on wing dimorphism in English grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae)

PubMed Central

Zhang, Fangmei; Li, Xiangrui; Zhang, Yunhui; Coates, Brad; Zhou, Xuguo “Joe”; Cheng, Dengfa

2015-01-01

Wing dimorphism in aphids can be affected by multiple cues, including both biotic (nutrition, crowding, interspecific interactions, the presence of natural enemies, maternal and transgenerational effects, and alarm pheromone) and abiotic factors (temperature, humidity, and photoperiod). The majority of the phloem-feeding aphids carry Buchnera, an obligate symbiotic proteobacteria. Buchnera has a highly reduced genome size, but encode key enzymes in the tryptophan biosynthetic pathway and is crucial for nutritional balance, development and reproduction in aphids. In this study, we investigated the impact of two nutritional-based biotic factors, symbionts and starvation, on the wing dimorphism in the English grain aphid, Sitobion avenae, a devastating insect pest of cereal crops (e.g., wheat) worldwide. Elimination of Buchnera using the antibiotic rifampicin significantly reduced the formation of winged morphs, body mass, and fecundity in S. avenae. Furthermore, the absence of this primary endosymbiont may disrupt the nutrient acquisition in aphids and alter transgenerational phenotypic expression. Similarly, both survival rate and the formation of winged morphs were substantially reduced after neonatal (<24 h old) offspring were starved for a period of time. The combined results shed light on the impact of two nutritional-based biotic factors on the phenotypic plasticity in aphids. A better understanding of the wing dimorphism in aphids will provide the theoretical basis for the prediction and integrated management of these phloem-feeding insect pests. PMID:26042046

Interaction between 2,4-Diacetylphloroglucinol- and Hydrogen Cyanide-Producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the Tomato Rhizosphere

PubMed Central

Paulin, Mélanie M.; Novinscak, Amy; Lanteigne, Carine; Gadkar, Vijay J.

2017-01-01

ABSTRACT We have previously demonstrated that inoculation of tomato plants with 2,4-diacetylphloroglucinol (DAPG)- and hydrogen cyanide (HCN)-producing Pseudomonas brassicacearum LBUM300 could significantly reduce bacterial canker symptoms caused by Clavibacter michiganensis subsp. michiganensis. In this study, in order to better characterize the population dynamics of LBUM300 in the rhizosphere of tomato plants, we characterized the role played by DAPG and HCN production by LBUM300 on rhizosphere colonization of healthy and C. michiganensis subsp. michiganensis-infected tomato plants. The impact of C. michiganensis subsp. michiganensis presence on the expression of DAPG and HCN biosynthetic genes in the rhizosphere was also examined. In planta assays were performed using combinations of C. michiganensis subsp. michiganensis and wild-type LBUM300 or DAPG (LBUM300ΔphlD) or HCN (LBUM300ΔhcnC) isogenic mutant strains. Populations of LBUM300 and phlD and hcnC gene expression levels were quantified in rhizosphere soil at several time points up to 264 h postinoculation using culture-independent quantitative PCR (qPCR) and reverse transcriptase quantitative PCR (RT-qPCR) TaqMan assays, respectively. The presence of C. michiganensis subsp. michiganensis significantly increased rhizospheric populations of LBUM300. In C. michiganensis subsp. michiganensis-infected tomato rhizospheres, the populations of wild-type LBUM300 and strain LBUM300ΔhcnC, both producing DAPG, were significantly higher than the population of strain LBUM300ΔphlD. A significant upregulation of phlD expression was observed in the presence of C. michiganensis subsp. michiganensis, while hcnC expression was only slightly increased in the mutant strain LBUM300ΔphlD when C. michiganensis subsp. michiganensis was present. Additionally, biofilm production was found to be significantly reduced in strain LBUM300ΔphlD compared to the wild-type and LBUM300ΔhcnC strains. IMPORTANCE The results of this study suggest that C. michiganensis subsp. michiganensis infection of tomato plants contributes to increasing rhizospheric populations of LBUM300, a biocontrol agent, as well as the overexpression of the DAPG biosynthetic operon in this bacterium. The increasing rhizospheric populations of LBUM300 represent one of the key factors in controlling C. michiganensis subsp. michiganensis in tomato plants, as DAPG-producing bacteria have shown the ability to decrease bacterial canker symptoms in tomato plants. PMID:28432096

A foundation monograph of Convolvulus L. (Convolvulaceae)

PubMed Central

Wood, John R.I.; Williams, Bethany R.M.; Mitchell, Thomas C.; Carine, Mark A.; Harris, David J.; Scotland, Robert W.

2015-01-01

Abstract A global revision of Convolvulus L. is presented, Calystegia R.Br. being excluded on pragmatic grounds. One hundred and ninety species are recognised with the greatest diversity in the Irano-Turanian region. All recognised species are described and the majority are illustrated. Distribution details, keys to species identification and taxonomic notes are provided. Four new species, Convolvulus austroafricanus J.R.I.Wood & R.W.Scotland, sp. nov., Convolvulus iranicus J.R.I.Wood & R.W.Scotland, sp. nov., Convolvulus peninsularis J.R.I.Wood & R.W.Scotland, sp. nov. and Convolvulus xanthopotamicus J.R.I.Wood & R.W.Scotland, sp. nov., one new subspecies Convolvulus chinensis subsp. triangularis J.R.I.Wood & R.W.Scotland, subsp. nov., and two new varieties Convolvulus equitans var. lindheimeri J.R.I.Wood & R.W.Scotland, var. nov., Convolvulus glomeratus var. sachalitarum J.R.I.Wood & R.W.Scotland, var. nov. are described. Convolvulus incisodentatus J.R.I.Wood & R.W.Scotland, nom. nov., is provided as a replacement name for the illegitimate Convolvulus incisus Choisy. Several species treated as synonyms of other species in recent publications are reinstated including Convolvulus chinensis Ker-Gawl., Convolvulus spinifer M.Popov., Convolvulus randii Rendle and Convolvulus aschersonii Engl. Ten taxa are given new status and recognised at new ranks: Convolvulus namaquensis (Schltr. ex. A.Meeuse) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus hermanniae subsp. erosus (Desr.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus crenatifolius subsp. montevidensis (Spreng.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus fruticulosus subsp. glandulosus (Webb) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus capituliferus subsp. foliaceus (Verdc.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus hystrix subsp. ruspolii (Dammer ex Hallier f.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus hystrix subsp. inermis (Chiov.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus rottlerianus subsp. stocksii (Boiss.) J.R.I.Wood & R.W.Scotland, comb. et stat. nov., Convolvulus calvertii subsp. ruprechtii (Boiss.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus cephalopodus subsp. bushiricus (Bornm.) J.R.I.Wood & R.W.Scotland, stat. nov. The status of various infraspecific taxa is clarified and numerous taxa are lectotypified. This account represents a new initiative in terms of taxonomic monography, being an attempt to bring together the global approach of the traditional monograph with the more pragmatic and identification-focussed approach of most current floras while at the same time being informed by insights from molecular systematics. PMID:26140023

Identification of Novel Seroreactive Antigens in Johne's Disease Cattle by Using the Mycobacterium tuberculosis Protein Array

PubMed Central

Campo, Joseph J.; Li, Lingling; Randall, Arlo; Pablo, Jozelyn; Praul, Craig A.; Raygoza Garay, Juan Antonio; Stabel, Judith R.

2017-01-01

ABSTRACT Johne's disease, a chronic gastrointestinal inflammatory disease caused by Mycobacterium avium subspecies paratuberculosis, is endemic in dairy cattle and other ruminants worldwide and remains a challenge to diagnose using traditional serological methods. Given the close phylogenetic relationship between M. avium subsp. paratuberculosis and the human pathogen Mycobacterium tuberculosis, here, we applied a whole-proteome M. tuberculosis protein array to identify seroreactive and diagnostic M. avium subsp. paratuberculosis antigens. A genome-scale pairwise analysis of amino acid identity levels between orthologous proteins in M. avium subsp. paratuberculosis and M. tuberculosis showed an average of 62% identity, with more than half the orthologous proteins sharing >75% identity. Analysis of the M. tuberculosis protein array probed with sera from M. avium subsp. paratuberculosis-infected cattle showed antibody binding to 729 M. tuberculosis proteins, with 58% of them having ≥70% identity to M. avium subsp. paratuberculosis orthologs. The results showed that only 4 of the top 40 seroreactive M. tuberculosis antigens were orthologs of previously reported M. avium subsp. paratuberculosis antigens, revealing the existence of a large number of previously unrecognized candidate diagnostic antigens. Enzyme-linked immunosorbent assay (ELISA) testing of 20 M. avium subsp. paratuberculosis recombinant proteins, representing reactive and nonreactive M. tuberculosis orthologs, further confirmed that the M. tuberculosis array has utility as a screening tool for identifying candidate antigens for Johne's disease diagnostics. Additional ELISA testing of field serum samples collected from dairy herds around the United States revealed that MAP2942c had the strongest seroreactivity with Johne's disease-positive samples. Collectively, our studies have considerably expanded the number of candidate M. avium subsp. paratuberculosis proteins with potential utility in the next generation of rationally designed Johne's disease diagnostic assays. PMID:28515134

Identification of Novel Seroreactive Antigens in Johne's Disease Cattle by Using the Mycobacterium tuberculosis Protein Array.

PubMed

Bannantine, John P; Campo, Joseph J; Li, Lingling; Randall, Arlo; Pablo, Jozelyn; Praul, Craig A; Raygoza Garay, Juan Antonio; Stabel, Judith R; Kapur, Vivek

2017-07-01

Johne's disease, a chronic gastrointestinal inflammatory disease caused by Mycobacterium avium subspecies paratuberculosis , is endemic in dairy cattle and other ruminants worldwide and remains a challenge to diagnose using traditional serological methods. Given the close phylogenetic relationship between M. avium subsp. paratuberculosis and the human pathogen Mycobacterium tuberculosis , here, we applied a whole-proteome M. tuberculosis protein array to identify seroreactive and diagnostic M. avium subsp. paratuberculosis antigens. A genome-scale pairwise analysis of amino acid identity levels between orthologous proteins in M. avium subsp. paratuberculosis and M. tuberculosis showed an average of 62% identity, with more than half the orthologous proteins sharing >75% identity. Analysis of the M. tuberculosis protein array probed with sera from M. avium subsp. paratuberculosis -infected cattle showed antibody binding to 729 M. tuberculosis proteins, with 58% of them having ≥70% identity to M. avium subsp. paratuberculosis orthologs. The results showed that only 4 of the top 40 seroreactive M. tuberculosis antigens were orthologs of previously reported M. avium subsp. paratuberculosis antigens, revealing the existence of a large number of previously unrecognized candidate diagnostic antigens. Enzyme-linked immunosorbent assay (ELISA) testing of 20 M. avium subsp. paratuberculosis recombinant proteins, representing reactive and nonreactive M. tuberculosis orthologs, further confirmed that the M. tuberculosis array has utility as a screening tool for identifying candidate antigens for Johne's disease diagnostics. Additional ELISA testing of field serum samples collected from dairy herds around the United States revealed that MAP2942c had the strongest seroreactivity with Johne's disease-positive samples. Collectively, our studies have considerably expanded the number of candidate M. avium subsp. paratuberculosis proteins with potential utility in the next generation of rationally designed Johne's disease diagnostic assays. Copyright © 2017 American Society for Microbiology.

Effects of Pistacia atlantica subsp. kurdica on Growth and Aflatoxin Production by Aspergillus parasiticus

PubMed Central

Khodavaisy, Sadegh; Rezaie, Sassan; Noorbakhsh, Fatemeh; Baghdadi, Elham; Sharifynia, Somayeh; Aala, Farzad

2016-01-01

Background Aflatoxins are highly toxic secondary metabolites mainly produced by Aspergillus parasiticus. This species can contaminate a wide range of agricultural commodities, including cereals, peanuts, and crops in the field. In recent years, research on medicinal herbs, such as Pistacia atlantica subsp. kurdica, have led to reduced microbial growth, and these herbs also have a particular effect on the production of aflatoxins as carcinogenic compounds. Objectives In this study, we to examine P. atlantica subsp. kurdica as a natural compound used to inhibit the growth of A. parasiticus and to act as an anti-mycotoxin. Materials and Methods In vitro antifungal susceptibility testing of P. atlantica subsp. kurdica for A. parasiticus was performed according to CLSI document M38-A2. The rate of aflatoxin production was determined using the HPLC technique after exposure to different concentrations (62.5 - 125 mg/mL) of the gum. The changes in expression levels of the aflR gene were analyzed with a quantitative real-time PCR assay. Results The results showed that P. atlantica subsp. kurdica can inhibit A. parasiticus growth at a concentration of 125 mg/mL. HPLC results revealed a significant decrease in aflatoxin production with 125 mg/mL of P. atlantica subsp. kurdica, and AFL-B1 production was entirely inhibited. Based on quantitative real-time PCR results, the rate of aflR gene expression was significantly decreased after treatment with P. atlantica subsp. kurdica. Conclusions Pistacia atlantica subsp. kurdica has anti-toxic properties in addition to an inhibitory effect on A. parasiticus growth, and is able to decrease aflatoxin production effectively in a dose-dependent manner. Therefore, this herbal extract maybe considered a potential anti-mycotoxin agent in medicine or industrial agriculture. PMID:27800127

Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

PubMed Central

Loquasto, Joseph R.; Barrangou, Rodolphe; Dudley, Edward G.; Stahl, Buffy; Chen, Chun

2013-01-01

Many strains of Bifidobacterium animalis subsp. lactis are considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes of B. animalis subsp. lactis have revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey of Bifidobacterium, it was revealed that B. animalis subsp. lactis ATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes of B. animalis subsp. lactis and B. animalis subsp. animalis. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G+C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-cas system differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system in B. animalis subsp. lactis. This study revealed that ATCC 27673 is a strain of B. animalis subsp. lactis with novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains. PMID:23995933

The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity▿ †

PubMed Central

Gartemann, Karl-Heinz; Abt, Birte; Bekel, Thomas; Burger, Annette; Engemann, Jutta; Flügel, Monika; Gaigalat, Lars; Goesmann, Alexander; Gräfen, Ines; Kalinowski, Jörn; Kaup, Olaf; Kirchner, Oliver; Krause, Lutz; Linke, Burkhard; McHardy, Alice; Meyer, Folker; Pohle, Sandra; Rückert, Christian; Schneiker, Susanne; Zellermann, Eva-Maria; Pühler, Alfred; Eichenlaub, Rudolf; Kaiser, Olaf; Bartels, Daniela

2008-01-01

Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil. PMID:18192381

Improvement of DNA transfer frequency and transposon mutagenesis of Erwinia carotovora subsp. betavasculorum.

PubMed Central

Rella, M; Axelrood, P E; Weinhold, A R; Schroth, M N

1989-01-01

The production of antibiotics and their role in microbial competition under natural conditions can be readily studied by the use of transposon mutants. Several antibiotic-producing strains of Erwinia carotovora subsp. betavasculorum were unable to accept foreign DNA. A plasmid delivery system was developed, using ethyl methanesulfonate mutagenesis, which entailed isolating E. carotovora subsp. betavasculorum mutants able to accept foreign DNA and transfer it to other strains. This enabled transposon mutagenesis of a wild-type antibiotic-producing strain of E. carotovora subsp. betavasculorum. Twelve antibiotic-negative mutants were isolated, and one of these showed a reduction in antibiotic production in vitro. Many of these mutants also showed a reduction in their ability to macerate potato tissue. The mutants were classified into four genetic groups on the basis of their genetic and phenotypic characteristics, indicating that several genes are involved in antibiotic biosynthesis by E. carotovora subsp. betavasculorum. PMID:2543291

Complete Genome Sequence of Campylobacter fetus subsp. venerealis Biovar Intermedius, Isolated from the Prepuce of a Bull

PubMed Central

Iraola, Gregorio; Pérez, Ruben; Naya, Hugo; Paolicchi, Fernando; Harris, David; Lawley, Trevor D.; Rego, Natalia; Hernández, Martín; Calleros, Lucía; Carretto, Luis; Velilla, Alejandra; Morsella, Claudia; Méndez, Alejandra

2013-01-01

Campylobacter fetus subsp. venerealis is the causative agent of bovine genital campylobacteriosis, a sexually transmitted disease distributed worldwide. Campylobacter fetus subsp. venerealis biovar Intermedius strains differ in their biochemical behavior and are prevalent in some countries. We report the first genome sequence for this biovar, isolated from bull prepuce. PMID:23908278

Potato (Solanum tuberosum L.).

PubMed

Chetty, Venkateswari J; Narváez-Vásquez, Javier; Orozco-Cárdenas, Martha L

2015-01-01

Agrobacterium-mediated transformation is the most common method for the incorporation of foreign genes into the genome of potato as well as many other species in the Solanaceae family. This chapter describes protocols for the genetic transformation of three species of potato: Solanum tuberosum subsp. tuberosum (Desiréé), S. tuberosum subsp. andigenum (Blue potato), and S. tuberosum subsp. andigena using internodal segments as explants.

Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production

USDA-ARS?s Scientific Manuscript database

Campylobacter fetus can cause disease in both humans and animals. C. fetus has been divided into three subspecies: C. fetus subsp. fetus (Cff), C. fetus subsp. venerealis (Cfv) and C. fetus subsp. testudinum. Subspecies identification of C. fetus strains is crucial in the control of Bovine Genital C...

Local genetic diversity of Xanthomonas citri subsp. citri in citrus orchards in northwest Paraná state, Brazil

USDA-ARS?s Scientific Manuscript database

Xanthomonas citri subsp. citri, causal agent of Asiatic citrus canker, is an important pathogen of citrus in Brazil and elsewhere. The genetic diversity of X. citri subsp. citri pathtype ‘A’ has not been studied in Brazil at a local scale (up to 300 km). A total of 40 isolates were collected from le...

Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87.

PubMed

Alexandraki, Voula; Kazou, Maria; Pot, Bruno; Tsakalidou, Effie; Papadimitriou, Konstantinos

2017-08-24

Lactobacillus delbrueckii subsp. bulgaricus is widely used in the production of yogurt and cheese. In this study, we present the complete genome sequence of L. delbrueckii subsp. bulgaricus ACA-DC 87 isolated from traditional Greek yogurt. Whole-genome analysis may reveal desirable technological traits of the strain for dairy fermentations. Copyright © 2017 Alexandraki et al.

Quick detection of Leifsonia xyli subsp. xyli by PCR and necleotide sequence analysis of PCR amplicons from Chinese Leifsonia xyli subsp. xyli isolates

USDA-ARS?s Scientific Manuscript database

A quick polymerase chain reaction (PCR) assay was developed for the detection of Leifsonia xyli subsp. xyli (Lxx), the bacterial causal agent of ratoon stunting disease (RSD) of sugarcane, in crude juice samples from stalks. After removal of abiotic impurities and large molecular weight microorgani...

Characterization of a novel bacteriophage, Phda1, infecting the histamine-producing Photobacterium damselae subsp. damselae.

PubMed

Yamaki, S; Kawai, Y; Yamazaki, K

2015-06-01

Photobacterium damselae subsp. damselae is a potent histamine-producing micro-organism. The aim of this study was to isolate and characterize a bacteriophage Phda1 that infected P. damselae subsp. damselae to inhibit its growth and histamine accumulation. Phda1 was isolated from a raw oyster, and the host range, morphology and the bacteriophage genome size were analysed. Phda1 formed a clear plaque only against P. damselae subsp. damselae JCM8969 among five Gram-positive and 32 Gram-negative bacterial strains tested. Phda1 belongs to the family Myoviridae, and its genome size was estimated as 35·2-39·5 kb. According to the one-step growth curve analysis, the latent period, rise period and burst size of Phda1 were 60 min, 50 min and 19 plaque-forming units per infected cell, respectively. Divalent cations, especially Ca(2+) and Mg(2+) , strongly improved Phda1 adsorption to the host cells and its propagation. Phda1 treatment delayed the growth and histamine production of P. damselae subsp. damselae in an in vitro challenge test. The bacteriophage Phda1 might serve as a potential antimicrobial agent to inhibit the histamine poisoning caused by P. damselae subsp. damselae. This is the first description of a bacteriophage specifically infecting P. damselae subsp. damselae and its potential applications. Bacteriophage therapy could prove useful in the prevention of histamine poisoning. © 2015 The Society for Applied Microbiology.

Detection of Goss's Wilt Pathogen Clavibacter michiganensis subsp. nebraskensis in Maize by Loop-Mediated Amplification.

PubMed

Yasuhara-Bell, Jarred; de Silva, Asoka; Heuchelin, Scott A; Chaky, Jennifer L; Alvarez, Anne M

2016-03-01

The Goss's wilt pathogen, Clavibacter michiganensis subsp. nebraskensis, can cause considerable losses in maize (Zea mays) production. Diagnosis of Goss's wilt currently is based on symptomology and identification of C. michiganensis subsp. nebraskensis, following isolation on a semiselective medium and/or serological testing. In an effort to provide a more efficient identification method, a loop-mediated amplification (LAMP) assay was developed to detect the tripartite ATP-independent periplasmic (TRAP)-type C4-dicarboxylate transport system large permease component and tested using strains of C. michiganensis subsp. nebraskensis, all other C. michiganensis subspecies and several genera of nontarget bacteria. Only strains of C. michiganensis subsp. nebraskensis reacted positively with the LAMP assay. The LAMP assay was then used to identify bacterial isolates from diseased maize. 16S rDNA and dnaA sequence analyses were used to confirm the identity of the maize isolates and validate assay specificity. The Cmm ImmunoStrip assay was included as a presumptive identification test of C. michiganensis subsp. nebraskensis at the species level. The Cmn-LAMP assay was further tested using symptomatic leaf tissue. The Cmn-LAMP assay was run in a hand-held real-time monitoring device (SMART-DART) and performed equally to in-lab quantitative polymerase chain reaction equipment. The Cmn-LAMP assay accurately identified C. michiganensis subsp. nebraskensis and has potential as a field test. The targeted sequence also has potential application in other molecular detection platforms.

A quantitative and direct PCR assay for the subspecies-specific detection of Clavibacter michiganensis subsp. michiganensis based on a ferredoxin reductase gene.

PubMed

Cho, Min Seok; Lee, Jang Ha; Her, Nam Han; Kim, Changkug; Seol, Young-Joo; Hahn, Jang Ho; Baeg, Ji Hyoun; Kim, Hong Gi; Park, Dong Suk

2012-06-01

The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is the causal agent of canker disease in tomato. Because it is very important to control newly introduced inoculum sources from commercial materials, the specific detection of this pathogen in seeds and seedlings is essential for effective disease control. In this study, a novel and efficient assay for the detection and quantitation of C. michiganensis subsp. michiganensis in symptomless tomato and red pepper seeds was developed. A pair of polymerase chain reaction (PCR) primers (Cmm141F/R) was designed to amplify a specific 141 bp fragment on the basis of a ferredoxin reductase gene of C. michiganensis subsp. michiganensis NCPPB 382. The specificity of the primer set was evaluated using purified DNA from 16 isolates of five C. michiganensis subspecies, one other Clavibacter species, and 17 other reference bacteria. The primer set amplified a single band of expected size from the genomic DNA obtained from the C. michiganensis subsp. michiganensis strains but not from the other C. michiganensis subspecies or from other Clavibacter species. The detection limit was a single cloned copy of the ferredoxin reductase gene of C. michiganensis subsp. michiganensis. In conclusion, this quantitative direct PCR assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of seeds and seedlings with a low level or latent infection of C. michiganensis subsp. michiganensis.

Regulation of the production of extracellular pectinase, cellulase, and protease in the soft rot bacterium Erwinia carotovora subsp. carotovora: evidence that aepH of E. carotovora subsp. carotovora 71 activates gene expression in E. carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Escherichia coli.

PubMed Central

Murata, H; Chatterjee, A; Liu, Y; Chatterjee, A K

1994-01-01

The production of pectolytic enzymes (pectate lyase [Pel] and polygalacturonase [Peh]), cellulase (Cel), and protease (Prt) is activated in the soft rot bacterium Erwinia carotovora subsp. carotovora by aepA (activator of extracellular protein production) and celery extract (Y. Liu, H. Murata, A. Chatterjee, and A. K. Chatterjee, Mol. Plant-Microbe Interact. 6:299-308, 1993). We recently isolated a new class of mutants of strain E. carotovora subsp. carotovora 71 which overproduces Pel, Peh, Cel, and Prt. From the overproducing strain AC5034, we identified an activator locus, designated aepH*, which stimulated Pel, Peh, Cel, and Prt production in E. carotovora subsp. carotovora 71 or its derivatives. The nucleotide sequence of the aepH* DNA segment revealed an open reading frame of 141 bp that could encode a small (5.45-kDa) highly basic (pI 11.7) protein of 47 amino acid residues. Analyses of deletions and MudI insertions indicated that the activator function required the 508-bp DNA segment which contains this open reading frame. The wild-type locus, aepH+, is localized within a DNA segment upstream of aepA. An AepH- strain constructed by exchanging aepH+ with aepH*::MudI was deficient in Pel, Peh, Cel, and Prt production; exoenzyme production was restored upon the introduction of a plasmid carrying aepH+ or aepH*. Plasmids carrying either aepH+ or aepH* activated the production of Pel-1, Peh-1, and Cel in Escherichia coli HB101 carrying the cognate genes. The aepH effect in E. coli was due to the activation of transcription, as indicated by assays of pel-1 and peh-1 mRNAs. The aepH+ and aepH* plasmids also stimulated Pel, Peh, Cel, and Prt production in other wild-type E. carotovora subsp. carotovora strains as well as in E. carotovora subsp. atroseptica. Although the stimulatory effect was generally more pronounced with aepH* than with aepH+, the extent of activation in the wild-type strains depended upon the bacterial strain and the growth medium. Southern blot hybridization revealed the presence of aepH homologs in E. carotovora subsp. carotovora and E. carotovora subsp. atroseptica, and provided physical evidence for linkage between aepA and aepH homologs in genomes of these bacteria. We conclude that aepH-mediated activation of exoprotein gene expression is a feature common to most strains of E. carotovora. Images PMID:7944360

Molecular discrimination of lactobacilli used as starter and probiotic cultures by amplified ribosomal DNA restriction analysis.

PubMed

Roy, D; Sirois, S; Vincent, D

2001-04-01

Lactic acid bacteria such as Lactobacillus helveticus, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. lactis, L. delbrueckii subsp. bulgaricus, L. acidophilus, and L. casei related taxa which are widely used as starter or probiotic cultures can be identified by amplified ribosomal DNA restriction analysis (ARDRA). The genetic discrimination of the related species belonging to these groups was first obtained by PCR amplifications by using group-specific or species-specific 16S rDNA primers. The numerical analysis of the ARDRA patterns obtained by using CfoI, HinfI, Tru9I, and ScrFI was an efficient typing tool for identification of species of the L. acidophilus and L. casei complex. ARDRA by using CfoI was a reliable method for differentiation of L. delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. Finally, strains ATCC 393 and ATCC 15820 exhibited unique ARDRA patterns with CfoI and Tru9I restriction enzymes as compared with the other strains of L. casei, L. paracasei, and L. rhamnosus.

A new methodology for rapid detection of Lactobacillus delbrueckii subsp. bulgaricus based on multiplex PCR.

PubMed

Nikolaou, Anastasios; Saxami, Georgia; Kourkoutas, Yiannis; Galanis, Alex

2011-02-01

In this study we present a novel multiplex PCR assay for rapid and efficient detection of Lactobacillus delbrueckii subsp. bulgaricus. The accuracy of our method was confirmed by the successful identification of L. delbrueckii subsp. bulgaricus in commercial yoghurts and food supplements and it may be readily applied to the food industry. Copyright © 2010 Elsevier B.V. All rights reserved.

Development of a pentaplex PCR assay for the simultaneous detection of Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. helveticus, L. fermentum in whey starter for Grana Padano cheese.

PubMed

Cremonesi, Paola; Vanoni, Laura; Morandi, Stefano; Silvetti, Tiziana; Castiglioni, Bianca; Brasca, Milena

2011-03-30

A pentaplex PCR assay for the rapid, selective and simultaneous detection of Lactobacillus helveticus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and L. fermentum, was developed. The target sequences were a group of genes coding for beta-galactosidase production (S. thermophilus and L. delbrueckii subsp. bulgaricus), for cell-enveloped associated proteinase synthesis (L. helveticus), for dipeptide transport system production (L. delbrueckii subsp. lactis) and for arginine-ornithine antiporter protein production (L. fermentum). The analytical specificity of the assay was evaluated with 5 reference strains and 140 lactic acid bacterial strains derived from raw milk cheeses and belonging to the Lactobacillus, Streptococcus, Lactococcus and Enterococcus genera. The identification limit for each target strain was 10(3)CFU/ml. This new molecular assay was used to investigate the LAB population by direct extraction of DNA from the 12 whey cultures for Grana Padano. The pentaplex PCR assay revealed a good correspondence with microbiological analyses and allowed to identify even minor LAB community members which, can be out-competed in vitro by numerically more abundant microbial species. Copyright © 2011 Elsevier B.V. All rights reserved.

Fate of Mycobacterium avium subsp. paratuberculosis in Swiss hard and semihard cheese manufactured from raw milk.

PubMed

Spahr, U; Schafroth, K

2001-09-01

Raw milk was artificially contaminated with declumped cells of Mycobacterium avium subsp. paratuberculosis at a concentration of 10(4) to 10(5) CFU/ml and was used to manufacture model hard (Swiss Emmentaler) and semihard (Swiss Tisliter) cheese. Two different strains of M. avium subsp. paratuberculosis were tested, and for each strain, two model hard and semihard cheeses were produced. The survival of M. avium subsp. paratuberculosis cells was monitored over a ripening period of 120 days by plating out homogenized cheese samples onto 7H10-PANTA agar. In both the hard and the semihard cheeses, counts decreased steadily but slowly during cheese ripening. Nevertheless, viable cells could still be detected in 120-day cheese. D values were calculated at 27.8 days for hard and 45.5 days for semihard cheese. The most important factors responsible for the death of M. avium subsp. paratuberculosis in cheese were the temperatures applied during cheese manufacture and the low pH at the early stages of cheese ripening. Since the ripening period for these raw milk cheeses lasts at least 90 to 120 days, the D values found indicate that 10(3) to 10(4) cells of M. avium subsp. paratuberculosis per g will be inactivated.

Phenotypic variation in Lactococcus lactis subsp. lactis isolates derived from intestinal tracts of marine and freshwater fish.

PubMed

Itoi, S; Yuasa, K; Washio, S; Abe, T; Ikuno, E; Sugita, H

2009-09-01

We compared phenotypic characteristics of Lactococcus lactis subsp. lactis derived from different sources including the intestinal tract of marine fish and freshwater fish, and cheese starter culture. In the phylogenetic analysis based on partial 16S rRNA gene nucleotide sequences (1371 bp), freshwater fish-, marine fish- and cheese starter culture-derived strains were identical to that of L. lactis subsp. lactis previously reported. Fermentation profiles determined using the API 50 CH system were similar except for fermentation of several sugars including l-arabinose, mannitol, amygdalin, saccharose, trehalose, inulin and gluconate. The strains did have distinct levels of halotolerance: marine fish-derived strains > cheese starter-derived strain > freshwater fish-derived isolate. Lactococcus lactis subsp. lactis showed extensive diversity in phenotypic adaptation to various environments. The phenotypic properties of these strains suggested that L. lactis subsp. lactis strains from fish intestine have additional functions compared with the cheese starter-derived strain that has previously described. The unique phenotypic traits of the fish intestinal tract-derived L. lactis subsp. lactis might make them useful as a probiotics in aquaculture, and contribute to the development of functional foods and novel food additives, since the strains derived from fish intestines might have additional functions such as antibacterial activity.

Fate of Mycobacterium avium subsp. paratuberculosis in Swiss Hard and Semihard Cheese Manufactured from Raw Milk

PubMed Central

Spahr, U.; Schafroth, K.

2001-01-01

Raw milk was artificially contaminated with declumped cells of Mycobacterium avium subsp. paratuberculosis at a concentration of 104 to 105 CFU/ml and was used to manufacture model hard (Swiss Emmentaler) and semihard (Swiss Tisliter) cheese. Two different strains of M. avium subsp. paratuberculosis were tested, and for each strain, two model hard and semihard cheeses were produced. The survival of M. avium subsp. paratuberculosis cells was monitored over a ripening period of 120 days by plating out homogenized cheese samples onto 7H10-PANTA agar. In both the hard and the semihard cheeses, counts decreased steadily but slowly during cheese ripening. Nevertheless, viable cells could still be detected in 120-day cheese. D values were calculated at 27.8 days for hard and 45.5 days for semihard cheese. The most important factors responsible for the death of M. avium subsp. paratuberculosis in cheese were the temperatures applied during cheese manufacture and the low pH at the early stages of cheese ripening. Since the ripening period for these raw milk cheeses lasts at least 90 to 120 days, the D values found indicate that 103 to 104 cells of M. avium subsp. paratuberculosis per g will be inactivated. PMID:11526024

Transcriptome-Based Characterization of Interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in Lactose-Grown Chemostat Cocultures

PubMed Central

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J. H.; Luttik, Marijke A. H.; Pronk, Jack T.; Smid, Eddy J.; Bron, Peter A.

2013-01-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations. PMID:23872557

Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures.

PubMed

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J H; Luttik, Marijke A H; Pronk, Jack T; Smid, Eddy J; Bron, Peter A; Daran-Lapujade, Pascale

2013-10-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations.

Persistence and Decontamination of Bacillus atrophaeus subsp. globigii Spores on Corroded Iron in a Model Drinking Water System▿

PubMed Central

Szabo, Jeffrey G.; Rice, Eugene W.; Bishop, Paul L.

2007-01-01

Persistence of Bacillus atrophaeus subsp. globigii spores on corroded iron coupons in drinking water was studied using a biofilm annular reactor. Spores were inoculated at 106 CFU/ml in the dechlorinated reactor bulk water. The dechlorination allowed for observation of the effects of hydraulic shear and biofilm sloughing on persistence. Approximately 50% of the spores initially adhered to the corroded iron surface were not detected after 1 month. Addition of a stable 10 mg/liter free chlorine residual after 1 month led to a 2-log10 reduction of adhered B. atrophaeus subsp. globigii, but levels on the coupons quickly stabilized thereafter. Increasing the free chlorine concentration to 25 or 70 mg/liter had no additional effect on inactivation. B. atrophaeus subsp. globigii spores injected in the presence of a typical distribution system chlorine residual (∼0.75 mg/liter) resulted in a steady reduction of adhered B. atrophaeus subsp. globigii over 1 month, but levels on the coupons eventually stabilized. Adding elevated chlorine levels (10, 25, and 70 mg/liter) after 1 month had no effect on the rate of inactivation. Decontamination with elevated free chlorine levels immediately after spore injection resulted in a 3-log10 reduction within 2 weeks, but the rate of inactivation leveled off afterward. This indicates that free chlorine did not reach portions of the corroded iron surface where B. atrophaeus subsp. globigii spores had adhered. B. atrophaeus subsp. globigii spores are capable of persisting for an extended time in the presence of high levels of free chlorine. PMID:17308186

Description of Mycobacterium chelonae subsp. bovis subsp. nov., isolated from cattle (Bos taurus coreanae), emended description of Mycobacterium chelonae and creation of Mycobacterium chelonae subsp. chelonae subsp. nov.

PubMed

Kim, Byoung-Jun; Kim, Ga-Na; Kim, Bo-Ram; Jeon, Che Ok; Jeong, Joseph; Lee, Seon Ho; Lim, Ji-Hun; Lee, Seung-Heon; Kim, Chang Ki; Kook, Yoon-Hoh; Kim, Bum-Joon

2017-10-01

Three rapidly growing mycobacterial strains, QIA-37 T , QIA-40 and QIA-41, were isolated from the lymph nodes of three separate Korean native cattle, Hanwoo (Bos taurus coreanae). These strains were previously shown to be phylogenetically distinct but closely related to Mycobacterium chelonae ATCC 35752 T by taxonomic approaches targeting three genes (16S rRNA, hsp6 and rpoB) and were further characterized using a polyphasic approach in this study. The 16S rRNA gene sequences of all three strains showed 99.7 % sequence similarity with that of the M. chelonae type strain. A multilocus sequence typing analysis targeting 10 housekeeping genes, including hsp65 and rpoB, revealed a phylogenetic cluster of these strains with M. chelonae. DNA-DNA hybridization values of 78.2 % between QIA-37 T and M. chelonae indicated that it belongs to M. chelonae but is a novel subspecies distinct from M. chelonae. Phylogenetic analysis based on whole-genome sequences revealed a 95.44±0.06 % average nucleotide identity (ANI) value with M. chelonae, slightly higher than the 95.0 % ANI criterion for determining a novel species. In addition, distinct phenotypic characteristics such as positive growth at 37 °C, at which temperature M. chelonae does not grow, further support the taxonomic status of these strains as representatives of a novel subspecies of M. chelonae. Therefore, we propose an emended description of Mycobacterium chelonae, and descriptions of M. chelonae subsp. chelonae subsp. nov. and M. chelonae subsp. bovis subsp. nov. are presented; strains ATCC 35752 T (=CCUG 47445 T =CIP 104535 T =DSM 43804 T =JCM 6388 T =NCTC 946 T ) and QIA-37 T (=KCTC 39630 T =JCM 30986 T ) are the type strains of the two novel subspecies.

Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae).

PubMed

Zhang, Chong-Xing; Yang, Shou-Yun; Xu, Ming-Xu; Sun, Jie; Liu, Huan; Liu, Jing-Rui; Liu, Hui; Kan, Fei; Sun, Jing; Lai, Ren; Zhang, Ke-Yun

2009-07-01

A novel red-pigmented, Gram-negative, motile, fluorescent, rod-shaped strain, DZ0503SBS1(T), with a single lateral flagellum, was isolated from the intestine of the nematode Heterorhabditidoides chongmingensis. Comparative 16S rRNA gene sequence analysis indicated that the strain is a member of the genus Serratia, sharing highest sequence similarities with Serratia marcescens subsp. sakuensis JCM 11315(T) (99.8 %), S. marcescens subsp. marcescens DSM 30121(T) (99.5 %) and Serratia ureilytica LMG 22860(T) (98.3 %). Similarities between the rpoB gene sequence of strain DZ0503SBS1(T) and those of S. marcescens subsp. sakuensis JCM 11315(T), S. marcescens subsp. marcescens DSM 30121(T) and S. ureilytica LMG 22860(T) were 98.0, 97.4 and 98.3 %, respectively. DNA-DNA hybridization values of strain DZ0503SBS1(T) with S. marcescens subsp. sakuensis JCM 11315(T), S. marcescens subsp. marcescens DSM 30121(T) and S. ureilytica LMG 22860(T) were 68.2, 65.1 and 53.0 %, respectively. The major isoprenoid quinone of strain DZ0503SBS1(T) was Q-8 and the predominant fatty acids were C(16 : 0) (34.76 %), cyclo-C(17 : 0) (20.03 %) and cyclo-C(19 : 0)omega8c (17.24 %). The cyclo-C(19 : 0)omega8c content (17.24 %) was significantly different from those found in S. marcescens subsp. sakuensis JCM 11315(T) and S. marcescens subsp. marcescens DSM 30121(T). Some characteristics of strain DZ0503SBS1(T), i.e. fluorescence and its symbiotic association with nematodes, have not been reported previously in any species of the genus Serratia. Phenotypic and biochemical characteristics and molecular data show that strain DZ0503SBS1(T) represents a novel species, for which the name Serratia nematodiphila sp. nov. is proposed; the type strain is DZ0503SBS1(T) (=KCTC 22130(T) =CGMCC 1.6853(T)).

Wound healing and anti-inflammatory activity of some Ononis taxons.

PubMed

Ergene Öz, Burçin; Saltan İşcan, Gülçin; Küpeli Akkol, Esra; Süntar, İpek; Keleş, Hikmet; Bahadır Acıkara, Özlem

2017-07-01

Ononis species are used for their laxative, diuretic, analgesic, anti-inflammatory, antiviral, cytotoxic and antifungal effects as well as against skin diseases for wound healing activity. In the light of this information n-hexane, ethylacetate and methanol extracts prepared from Ononis spinosa L. subsp. leiosperma (Boiss.) Sirj., Ononis variegata L., Ononis viscosa L. subsp. brevifolia (DC) Nym. and Ononis natrix L. subsp. natrix L. were tested for their wound healing, anti-inflammatory and antioxidant activities. Linear incision and circular excision wound models and hydroxypyroline estimation assay were used for the wound healing activity. For the assessment of chronic inflammation FCA-induced arthritis and for acute inflammation carrageenan-induced hind paw edema, TPA-induced ear edema and acetic acid-induced increase in capillary permeability tests were conducted. 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay, 2,2-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) scavenging activity assay, reducing power assay and hydroxyl radical (OH - ) scavenging assay were used for determining antioxidant activities of the extracts. Results showed that O. spinosa subsp. leiosperma roots ethyl acetate extract exhibited remarkable wound healing activity with the 42.6% tensile strength value on the linear incision wound model and 60.1% reduction of the wound area at the day 12 on the circular excision wound model. Hydroxyproline content of the tissue treated by O. spinosa subsp. leiosperma roots ethyl acetate extract was found to be 41.3μg/mg. Acetic acid induced increase in capillary permeability test results revealed that O. spinosa subsp. leiosperma roots ethyl acetate extract and O. spinosa subsp. leiosperma roots methanol extract inhibited inflammation by 40.4% and 35.4% values respectively. O. spinosa subsp. leiosperma roots ethyl acetate extract showed 21.2-27.2% inhibition in carrageenan-induced hind paw edema test while did not posses activity on TPA-induced ear edema and FCA-induced arthritis models. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Role of Ca++ in Shoot Gravitropism. [avena

NASA Technical Reports Server (NTRS)

Rayle, D. L.

1985-01-01

A cornerstone in the argument that Ca(2+) levels may regulate growth is the finding the EGTA promotes straight growth. The usual explanation for these results is that Ca(2+) chelation from cell walls results in wall loosening and thus accelerated straight growth. The ability of frozen-thawed Avena coleoptile tissue (subjected to 15g tension) to extend in response to EGTA and Quin II was examined. The EGTA when applied in weakly buffered (i.e., 0.1mM) neutral solutions initiates rapid extension. When the buffer strength is increased, similar concentrations of EGTA produce no growth response. This implies when EGTA liberated protons are released upon Ca(2+) chelation they can either initiate acid growth (low buffer conditions) or if consumed (high buffer conditions) have no effect. Thus Ca(2+) chelation in itself apparently does not result in straight growth.

QTLs for important breeding characteristics in the doubled haploid oat progeny.

PubMed

Tanhuanpää, Pirjo; Manninen, Outi; Kiviharju, Elina

2010-06-01

A homozygous mapping population, consisting of doubled haploid (DH) oat (Avena sativa L.) plants generated through anther culture of F1 plants from the cross between the Finnish cultivar 'Aslak' and the Swedish cultivar 'Matilda', was used to construct an oat linkage map. Ten agronomic and quality traits were analyzed in the DH plants from field trials in 2005 and 2006. Leaf blotch (caused by Pyrenophora avenae) resistance was also evaluated in a greenhouse test with 2 different isolates. One to 8 quantitative trait loci (QTLs) were found to be associated with each trait studied. Some chromosomal regions affected more than 1 trait; for example, 4 regions affected both protein and oil content. This study gives valuable information to oat breeders concerning the inheritance of important traits, and it provides potential tools to assist breeding.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

PubMed

Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Calixto, Edmundo P da R; Motta, Mariana R; Ballesteros, Helkin G F; Peixoto, Barbara; de Lima, Berenice N S; Vieira, Lucas M; Walter, Maria Emilia; de Armas, Elvismary M; Entenza, Júlio O P; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

2017-12-20

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae . Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae , while the siRNAs were repressed in the presence of A. avenae . Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

PubMed Central

Grativol, Clícia; Motta, Mariana R.; Ballesteros, Helkin G. F.; Peixoto, Barbara; Vieira, Lucas M.; Walter, Maria Emilia; de Armas, Elvismary M.; Entenza, Júlio O. P.; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S.

2017-01-01

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly. PMID:29657296

Sublethal effects of imidacloprid on the fecundity, longevity, and enzyme activity of Sitobion avenae (Fabricius) and Rhopalosiphum padi (Linnaeus).

PubMed

Lu, Y-H; Zheng, X-S; Gao, X-W

2016-08-01

The aphid species Sitobion avenae and Rhopalosiphum padi are the most important pests in wheat growing regions of many countries. In this study, we investigated the sublethal effects of imidacloprid on fecundity, longevity, and enzyme activity in both aphid species by comparing 3-h exposure for one or three generations. Our results indicated that 3-h exposure to sublethal doses of imidacloprid for one generation had no discernible effect on the survival, fecundity, longevity, or enzyme activity levels of aphids. However, when pulse exposures to imidacloprid were sustained over three generations, both fecundity and longevity were significantly decreased in both S. avenae and R. padi. Interestingly, the fecundity of R. padi had almost recovered by the F5 generation, but its longevity was still deleteriously affected. These results indicated that R. padi laid eggs in shorter time lags and has a more fast resilience. The change in reproduction behavior may be a phenomenon of R. padi to compensate its early death. If this is stable for the next generation, it means that the next generation is more competitive than unexposed populations, which could be the reason underlying population outbreaks that occur after longer-term exposure to an insecticide. This laboratory-based study highlights the sublethal effects of imidacloprid on the longevity and fecundity of descendants and provides an empirical basis from which to consider management decisions for chemical control in the field.

76 FR 63298 - Pesticide Products; Registration Applications

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

... thuringiensis subsp. kurstaki strain VBTS 2546 fermentation solids, spores, and insecticidal toxins at 67... ingredient: Bacillus thuringiensis subsp. kurstaki strain VBTS 2546 fermentation solids, spores, and...

tuf Gene Sequence Variation in Bifidobacterium longum subsp. infantis Detected in the Fecal Microbiota of Chinese Infants.

PubMed

Lawley, Blair; Centanni, Manuela; Watanabe, Jun; Sims, Ian; Carnachan, Susan; Broadbent, Roland; Lee, Pheng Soon; Wong, Khai Hong; Tannock, Gerald W

2018-07-01

Members of the bacterial genus Bifidobacterium generally dominate the fecal microbiota of infants. The species Bifidobacterium longum is prevalent, but the B. longum subsp. longum and B. longum subsp. infantis strains that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacities to metabolize human milk oligosaccharides (HMO) and may have different ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms. However, amplification targets in DNA extracted from samples need to be dependably differential. We evaluated the tuf gene sequence as a molecular target for quantitative PCR measurements of the abundances of B. longum subsp. infantis and B. longum subsp. longum in fecal microbiotas. This approach resulted in the detection of a tuf gene variant (operational taxonomic unit 49 [OTU49]) in Chinese infants that has sequence similarities to both B. longum subsp. infantis and B. longum subsp. longum We compared the genome sequence and growth and transcriptional characteristics of an OTU49 isolate cultured in HMO medium to those of other B. longum subsp. infantis cultures. We concluded from these studies that OTU49 belongs to B. longum subsp. infantis , that dependable quantitative PCR (qPCR) differentiation between the B. longum subspecies cannot be achieved by targeting tuf gene sequences, and that functional genes involved in carbohydrate metabolism might be better targets because they delineate ecological functions. IMPORTANCE High-throughput DNA sequencing methods and advanced bioinformatics analysis have revealed the composition and biochemical capacities of microbial communities (microbiota and microbiome), including those that inhabit the gut of human infants. However, the microbiology and function of natural ecosystems have received little attention in recent decades, so an appreciation of the dynamics of gut microbiota interactions is lacking. With respect to infants, rapid methodologies, such as quantitative PCR, are needed to determine the prevalences and proportions of different bifidobacterial species in observational and microcosm studies in order to obtain a better understanding of the dynamics of bifidobacterial nutrition and syntrophy, knowledge that might be used to manipulate the microbiota and perhaps ensure the better health of infants. Copyright © 2018 American Society for Microbiology.

High-Throughput Direct Fecal PCR Assay for Detection of Mycobacterium avium subsp. paratuberculosis in Sheep and Cattle

PubMed Central

Waldron, Anna M.; Galea, Francesca; Whittington, Ann-Michele; Saunders, Vanessa F.; Begg, Douglas J.; de Silva, Kumudika; Purdie, Auriol C.; Whittington, Richard J.

2014-01-01

Johne's disease (JD) is a chronic enteric disease caused by Mycobacterium avium subsp. paratuberculosis that affects ruminants. Transmission occurs by the fecal-oral route. A commonly used antemortem diagnostic test for the detection of M. avium subsp. paratuberculosis in feces is liquid culture; however, a major constraint is the 2- to 3-month incubation period needed for this method. Rapid methods for the detection of M. avium subsp. paratuberculosis based on PCR have been reported, but comprehensive validation data are lacking. We describe here a new test, the high-throughput-Johnes (HT-J), to detect M. avium subsp. paratuberculosis in feces. Its diagnostic accuracy was compared with that of liquid radiometric (Bactec) fecal culture using samples from cattle (1,330 samples from 23 herds) and sheep (596 samples from 16 flocks). The multistage protocol involves the recovery of M. avium subsp. paratuberculosis cells from a fecal suspension, cell rupture by bead beating, extraction of DNA using magnetic beads, and IS900 quantitative PCR. The limit of detection of the assay was 0.0005 pg, and the limit of quantification was 0.005 pg M. avium subsp. paratuberculosis genomic DNA. Only M. avium subsp. paratuberculosis was detected from a panel of 51 mycobacterial isolates, including 10 with IS900-like sequences. Of the 549 culture-negative fecal samples from unexposed herds and flocks, 99% were negative in the HT-J test, while 60% of the bovine- and 84% of the ovine-culture-positive samples were positive in the HT-J test. As similar total numbers of samples from M. avium subsp. paratuberculosis-exposed animals were positive in culture and HT-J tests in both species, and as the results of a McNemar's test were not significant, these methods probably have similar sensitivities, but the true diagnostic sensitivities of these tests are unknown. These validation data meet the consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis and the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (S. A. Bustin et al., Clin. Chem. 55:611–622, 2009, doi:10.1373/clinchem.2008.112797). The HT-J assay has been approved for use in JD control programs in Australia and New Zealand. PMID:24352996

Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

PubMed Central

Durand, Karine; Orgeur, Geoffrey; Balidas, Samuel; Fricot, Céline; Bonneau, Sophie; Quillévéré, Anne; Audusseau, Corinne; Olivier, Valérie; Grimault, Valérie; Mathis, René

2012-01-01

The genus Clavibacter comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose. Clavibacter michiganensis subsp. michiganensis is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of C. michiganensis subsp. michiganensis strains, relatives (strains from the four other C. michiganensis subspecies), and nonpathogenic Clavibacter-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (atpD, dnaK, gyrB, ppK, recA, and rpoB). We compared this “framework” with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main C. michiganensis subsp. michiganensis pathogenicity determinants. We showed that C. michiganensis subsp. michiganensis is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic Clavibacter-like strains were identified as C. michiganensis using 16S rRNA gene sequencing. These strains, while cross-reacting with C. michiganensis subsp. michiganensis identification tools, are phylogenetically distinct from the pathogenic strains but belong to the C. michiganensis clade. C. michiganensis subsp. michiganensis clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced. PMID:23001675

Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonella koehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats

PubMed Central

Chomel, Bruno B.; Molia, Sophie; Kasten, Rickie W.; Borgo, Gina M.; Stuckey, Matthew J.; Maruyama, Soichi; Chang, Chao-chin; Haddad, Nadia; Koehler, Jane E.

2016-01-01

Domestic cats are the natural reservoir of Bartonella henselae, B. clarridgeiae and B. koehlerae. To determine the role of wild felids in the epidemiology of Bartonella infections, blood was collected from 14 free-ranging California mountain lions (Puma concolor) and 19 bobcats (Lynx rufus). Bartonella spp. were isolated from four (29%) mountain lions and seven (37%) bobcats. These isolates were characterized using growth characteristics, biochemical reactions, molecular techniques, including PCR-RFLP of selected genes or interspacer region, pulsed-field gel electrophoresis (PFGE), partial sequencing of several genes, and DNA-DNA hybridization. Two isolates were identical to B. henselae genotype II. All other isolates were distinguished from B. henselae and B. koehlerae by PCR-RFLP of the gltA gene using endonucleases HhaI, TaqI and AciI, with the latter two discriminating between the mountain lion and the bobcat isolates. These two novel isolates displayed specific PFGE profiles distinct from B. henselae, B. koehlerae and B. clarridgeiae. Sequences of amplified gene fragments from the three mountain lion and six bobcat isolates were closely related to, but distinct from, B. henselae and B. koehlerae. Finally, DNA-DNA hybridization studies demonstrated that the mountain lion and bobcat strains are most closely related to B. koehlerae. We propose naming the mountain lion isolates B. koehlerae subsp. boulouisii subsp. nov. (type strain: L-42-94), and the bobcat isolates B. koehlerae subsp. bothieri subsp. nov. (type strain: L-17-96), and to emend B. koehlerae as B. koehlerae subsp. koehlerae. The mode of transmission and the zoonotic potential of these new Bartonella subspecies remain to be determined. PMID:26981874

Phylogenetic analysis and polyphasic characterization of Clavibacter michiganensis strains isolated from tomato seeds reveal that nonpathogenic strains are distinct from C. michiganensis subsp. michiganensis.

PubMed

Jacques, Marie-Agnès; Durand, Karine; Orgeur, Geoffrey; Balidas, Samuel; Fricot, Céline; Bonneau, Sophie; Quillévéré, Anne; Audusseau, Corinne; Olivier, Valérie; Grimault, Valérie; Mathis, René

2012-12-01

The genus Clavibacter comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose. Clavibacter michiganensis subsp. michiganensis is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of C. michiganensis subsp. michiganensis strains, relatives (strains from the four other C. michiganensis subspecies), and nonpathogenic Clavibacter-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (atpD, dnaK, gyrB, ppK, recA, and rpoB). We compared this "framework" with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main C. michiganensis subsp. michiganensis pathogenicity determinants. We showed that C. michiganensis subsp. michiganensis is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic Clavibacter-like strains were identified as C. michiganensis using 16S rRNA gene sequencing. These strains, while cross-reacting with C. michiganensis subsp. michiganensis identification tools, are phylogenetically distinct from the pathogenic strains but belong to the C. michiganensis clade. C. michiganensis subsp. michiganensis clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced.

Supplementation with fruit and okara soybean by-products and amaranth flour increases the folate production by starter and probiotic cultures.

PubMed

Albuquerque, Marcela Albuquerque Cavalcanti de; Bedani, Raquel; Vieira, Antônio Diogo Silva; LeBlanc, Jean Guy; Saad, Susana Marta Isay

2016-11-07

The ability of two starter cultures (Streptococcus (S.) thermophilus ST-M6 and St. thermophilus TA-40) and eleven probiotic cultures (St. thermophilus TH-4, Lactobacillus (Lb.) acidophilus LA-5, Lb. fermentum PCC, Lb. reuteri RC-14, Lb. paracasei subsp. paracasei, Lb. casei 431, Lb. paracasei subsp. paracasei F19, Lb. rhamnosus GR-1, and Lb. rhamnosus LGG, Bifidobacterium (B.) animalis subsp. lactis BB-12, B. longum subsp. longum BB-46, and B. longum subsp. infantis BB-02) to produce folate in a modified MRS broth (mMRS) supplemented with different fruit (passion fruit, acerola, orange, and mango) and okara soybean by-products and amaranth flour was investigated. Initially, the folate content of each vegetable substrate was determined: passion fruit by-product showed the lowest folate content (8±2ng/mL) and okara the highest (457±22ng/mL). When the orange by-product and amaranth flour were added to mMRS, all strains were able to increase folate production after 24h of fermentation. B. longum subsp infantis BB-02 produced the highest concentrations (1223±116ng/mL) in amaranth flour. Okara was the substrate that had the lowest impact on the folate production by all strains evaluated. Lb. acidophilus LA-5 (297±36ng/mL) and B. animalis subsp. lactis BB-12 (237±23ng/mL) were also able to produce folate after growth in mMRS containing acerola and orange by-products, respectively. The results of this study demonstrate that folate production is not only strain-dependent but also influenced by the addition of different substrates in the growth media. Copyright © 2016 Elsevier B.V. All rights reserved.

Aeromonas hydrophila subsp. dhakensis Isolated from Feces, Water and Fish in Mediterranean Spain

PubMed Central

Esteve, Consuelo; Alcaide, Elena; Blasco, María Dolores

2012-01-01

Eight Aeromonas hydrophila-like arabinose-negative isolates from diverse sources (i.e., river freshwater, cooling-system water pond, diseased wild European eels, and human stools) sampled in Valencia (Spain) during 2004–2005, were characterized by 16S rRNA gene sequencing and extensive biochemical testing along with reference strains of most Aeromonas species. These isolates and all reference strains of A. hydrophila subsp. dhakensis and A. aquariorum showed a 16S rRNA sequence similarity of 99.8–100%, and they all shared an identical phenotype. This matched exactly with that of A. hydrophila subsp. dhakensis since all strains displayed positive responses to the Voges-Prokauer test and to the use of dl-lactate. This is the first report of A. hydrophila subsp. dhakensis recovered from environmental samples, and further, from its original isolation in India during 1993–1994. This was accurately identified and segregated from other clinical aeromonads (A. hydrophila subsp. hydrophila, A. caviae, A. veronii biovars veronii and sobria, A. trota, A. schubertii and A. jandaei) by using biochemical key tests. The API 20 E profile for all strains included in A. hydrophila subsp. dhakensis was 7047125. The prevalence of this species in Spanish sources was higher for water (9.4%) than for feces (6%) or eels (1.3%). Isolates recovered as pure cultures from diseased eels were moderately virulent (LD50 of 3.3×106 CFU fish−1) to challenged eels in experimental trials. They were all resistant to ticarcillin, amoxicillin-clavuranic acid, cefoxitin, and imipenem, regardless of its source. Our data point to A. hydrophila subsp. dhakensis as an emerging pathogen for humans and fish in temperate countries. PMID:22472298

Unusual Outbreak of Clinical Mastitis in Dairy Sheep Caused by Streptococcus equi subsp. zooepidemicus

PubMed Central

Las Heras, Alfonso; Vela, Ana I.; Fernández, Elena; Legaz, Emilio; Domínguez, Lucas; Fernández-Garayzábal, Jose F.

2002-01-01

This work describes an outbreak of clinical mastitis affecting 13 of 58 lactating ewes due to Streptococcus equi subsp. zooepidemicus. S. equi subsp. zooepidemicus was isolated in pure culture from all milk samples. All the clinical isolates had identical biochemical profiles and antimicrobial susceptibility patterns and also exhibited indistinguishable macrorestriction patterns by pulsed-field gel electrophoresis, indicating that all cases of mastitis were produced by a single strain. PMID:11880454

Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii.

PubMed

Tanigawa, Kana; Watanabe, Koichi

2011-03-01

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080(T), was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.

Identification of the "A" genome of finger millet using chloroplast DNA.

PubMed

Hilu, K W

1988-01-01

Finger millet (Eleusine corocana subsp. coracana), an important cereal in East Africa and India, is a tetraploid species with unknown genomic components. A recent cytogenetic study confirmed the direct origin of this millet from the tetraploid E. coracana subsp. africana but questioned Eleusine indica as a genomic donor. Chloroplast (ct) DNA sequence analysis using restriction fragment pattern was used to examine the phylogenetic relationships between E. coracana subsp. coracana (domesticated finger millet), E. coracana subspecies africana (wild finger millet), and E. indica. Eleusine tristachya was included since it is the only other annual diploid species in the genus with a basic chromosome number of x = 9 like finger millet. Eight of the ten restriction endonucleases used had 16 to over 30 restriction sites per genome and were informative. E. coracana subsp. coracana and subsp. africana and E. indica were identical in all the restriction sites surveyed, while the ct genome of E, tristachya differed consistently by at least one mutational event for each restriction enzyme surveyed. This random survey of the ct genomes of these species points out E. indica as one of the genome donors (maternal genome donor) of domesticated finger millet contrary to a previous cytogenetic study. The data also substantiate E. coracana subsp. africana as the progenitor of domesticated finger millet. The disparity between the cytogenetic and the molecular approaches is discussed in light of the problems associated with chromosome pairing and polyploidy.

The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.

PubMed

Cho, Yong-Joon; Yi, Hana; Chun, Jongsik; Cho, Sang-Nae; Daley, Charles L; Koh, Won-Jung; Shin, Sung Jae

2013-01-01

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.

Antioxidant activity profiling by spectrophotometric methods of aqueous methanolic extracts of Helichrysum stoechas subsp. rupestre and Phagnalon saxatile subsp. saxatile.

PubMed

Haddouchi, Farah; Chaouche, Tarik Mohammed; Ksouri, Riadh; Medini, Faten; Sekkal, Fatima Zohra; Benmansour, Abdelhafid

2014-06-01

The aqueous methanolic extracts of two plants from Algeria, Helichrysum stoechas subsp. rupestre and Phagnalon saxatile subsp. saxatile, were investigated for their antioxidant activity. Total phenolics, flavonoids, and tannins were determined by spectrophotometric techniques. In vitro antioxidant and radical scavenging profiling was determined by spectrophotometric methods, through: Total antioxidant capacity, and radical scavenging effects by the DPPH and ABTS methods, reducing and chelating power, and blanching inhibition of the β-carotene. All of the extracts showed interesting antioxidant and radical scavenging activity. The highest contents in phenolics, tannins, and the highest total antioxidant capacity as gallic acid equivalents of 97.5 ± 0.33 mg GAE/g DW was obtained for the flowers of H. stoechas subsp. rupestre extract in the phosphomolybdenum assay. An extract of the leafy stems of P. saxatile subsp. saxatile revealed the highest content of flavonoids, and the highest antioxidant activity by the radical scavenging and β-carotene assays when compared with standards. The best activity was by the scavenging radical DPPH with an IC50 value of 5.65 ± 0.10 μg·mL(-1). The studied medicinal plants could provide scientific evidence for some traditional uses in the treatment of diseases related to the production of reactive oxygen species (ROS) and oxidative stress. Copyright © 2014 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

Molecular Characterization of Multiresistant d-Tartrate-Positive Salmonella enterica Serovar Paratyphi B Isolates

PubMed Central

Miko, Angelika; Guerra, Beatriz; Schroeter, Andreas; Dorn, Christina; Helmuth, Reiner

2002-01-01

Since 1996, the National Salmonella Reference Laboratory of Germany has received an increasing number of Salmonella enterica subsp. enterica serovar Paratyphi B isolates. Nearly all of these belonged to the dextrorotatory tartrate-positive variant (S. enterica subsp. enterica serovar Paratyphi B dT+), formerly called S. enterica subsp. enterica serovar Java. A total of 55 selected contemporary and older S. enterica subsp. enterica serovar Paratyphi B dT+ isolates were analyzed by plasmid profiling, antimicrobial resistance testing, pulsed-field gel electrophoresis, IS200 profiling, and PCR-based detection of integrons. The results showed a high genetic heterogeneity among 10 old strains obtained from 1960 to 1993. In the following years, however, new distinct multiresistant S. enterica subsp. enterica serovar Paratyphi B dT+ clones emerged, and one clonal lineage successfully displaced the older ones. Since 1994, 88% of the isolates investigated were multiple drug resistant. Today, a particular clone predominates in some German poultry production lines, poultry products, and various other sources. It was also detected in contemporary isolates from two neighboring countries as well. PMID:12202551

Biological suppression of potato ring rot by fluorescent pseudomonads.

PubMed Central

de la Cruz, A R; Poplawsky, A R; Wiese, M V

1992-01-01

Three strains of fluorescent pseudomonads (IS-1, IS-2, and IS-3) isolated from potato underground stems with roots showed in vitro antibiosis against 30 strains of the ring rot bacterium Clavibacter michiganensis subsp. sepedonicus. On the basis of morphological and biochemical tests and fatty acid analysis, IS-1 and IS-2 were identified as Pseudomonas aureofaciens and IS-3 was identified as P. fluorescens biovar III. IS-1 was the most inhibitory to C. michiganensis subsp. sepedonicus strains in vitro, followed by IS-3 and IS-2. Suppression of ring rot by these antagonists was demonstrated in greenhouse trials with stem-cultured potato (cv. Russet Burbank) seedlings. Although each antagonist significantly reduced C. michiganensis subsp. sepedonicus populations, only IS-1 reduced infection by C. michiganensis subsp. sepedonicus. In a second experiment, treatment with IS-1 (10(9) CFU/ml) significantly reduced ring rot infection by 23.4 to 26.7% after 5 to 8 weeks. The average C. michiganensis subsp. sepedonicus population was also significantly reduced by 50 to 52%. Application of different combinations of antagonist strains was not more effective than single-strain treatment. Images PMID:1622275

Lactococcus lactis subsp. cremoris strain JFR1 attenuates Salmonella adhesion to human intestinal cells in vitro.

PubMed

Zhang, Justina Su; Guri, Anilda; Corredig, Milena; Morales-Rayas, Rocio; Hassan, Ashraf; Griffiths, Mansel; LaPointe, Gisèle

2016-12-01

Lactococcus lactis subsp. cremoris JFR1 has been studied in reduced fat cheese due to its ability to produce exopolysaccharides (EPS) in situ, contributing to improved textural and organoleptic properties. In this study, the effect of strain JFR1 on virulence gene expression and attachment of Salmonella to HT-29 human colon carcinoma cells was investigated. Overnight cultures of L. lactis subsp. cremoris JFR1 containing EPS, grown in M17 media with 0.5% glucose supplementation, decreased attachment as well as down regulated virulence gene expression in Salmonella enterica subsp. enterica when tested on HT-29 cells. However, EPS isolated from milk fermented with L. lactis subsp. cremoris JFR1 did not affect Salmonella virulence gene expression or attachment to HT-29 cells. These results suggest that EPS does not contribute to the attachment of Salmonella to human intestinal cells. However, the possibility that the isolation process may have affected the structural features of EPS cannot be ruled out. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Proteomic Study of Clavibacter Michiganensis Subsp. Michiganensis Culture Supernatants

PubMed Central

Hiery, Eva; Poetsch, Ansgar; Moosbauer, Tanja; Amin, Bushra; Hofmann, Jörg; Burkovski, Andreas

2015-01-01

Clavibacter michiganensis, subsp. michiganensis is a Gram-positive plant pathogen infecting tomato (Solanum lycopersicum). Despite a considerable economic importance due to significant losses of infected plants and fruits, knowledge about virulence factors of C. michiganensis subsp. michiganensis and host-pathogen interactions on a molecular level are rather limited. In the study presented here, the proteome of culture supernatants from C. michiganensis subsp. michiganensis NCPPB382 was analyzed. In total, 1872 proteins were identified in M9 and 1766 proteins in xylem mimicking medium. Filtration of supernatants before protein precipitation reduced these to 1276 proteins in M9 and 976 proteins in the xylem mimicking medium culture filtrate. The results obtained indicate that C. michiganensis subsp. michiganensis reacts to a sucrose- and glucose-depleted medium similar to the xylem sap by utilizing amino acids and host cell polymers as well as their degradation products, mainly peptides, amino acids and various C5 and C6 sugars. Interestingly, the bacterium expresses the previously described virulence factors Pat-1 and CelA not exclusively after host cell contact in planta but already in M9 minimal and xylem mimicking medium. PMID:28248277

Understanding the ontogeny and succession of Bacillus velezensis and B. subtilis subsp. subtilis by focusing on kimchi fermentation.

PubMed

Cho, Min Seok; Jin, Yong Ju; Kang, Bo Kyoung; Park, Yu Kyoung; Kim, ChangKug; Park, Dong Suk

2018-05-04

Bacillus subtilis and B. velezensis are frequently isolated from various niches, including fermented foods, water, and soil. Within the Bacillus subtilis group, B. velezensis and B. subtilis subsp. subtilis have received significant attention as biological resources for biotechnology-associated industries. Nevertheless, radical solutions are urgently needed to identify microbes during their ecological succession to accurately confirm their action at the species or subspecies level in diverse environments, such as fermented materials. Thus, in this study, previously published genome data of the B. subtilis group were compared to exploit species- or subspecies-specific genes for use as improved qPCR targets to detect B. velezensis and B. subtilis subsp. subtilis in kimchi samples. In silico analyses of the selected genes and designed primer sequences, in conjunction with SYBR Green real-time PCR, confirmed the robustness of this newly developed assay. Consequently, this study will allow for new insights into the ontogeny and succession of B. velezensis and B. subtilis subsp. subtilis in various niches. Interestingly, in white kimchi without red pepper powder, neither B. subtilis subsp. subtilis nor B. velezensis was detected.

Molecular Differentiation of Treponema pallidum Subspecies in Skin Ulceration Clinically Suspected as Yaws in Vanuatu Using Real-Time Multiplex PCR and Serological Methods

PubMed Central

Chi, Kai-Hua; Danavall, Damien; Taleo, Fasihah; Pillay, Allan; Ye, Tun; Nachamkin, Eli; Kool, Jacob L.; Fegan, David; Asiedu, Kingsley; Vestergaard, Lasse S.; Ballard, Ronald C.; Chen, Cheng-Yen

2015-01-01

We developed a TaqMan-based real-time quadriplex polymerase chain reaction (PCR) to simultaneously detect Treponema pallidum subspecies pallidum, T. pallidum subsp. pertenue, and T. pallidum subsp. endemicum, the causative agents of venereal syphilis, yaws, and bejel, respectively. The PCR assay was applied to samples from skin ulcerations of clinically presumptive yaws cases among children on Tanna Island, Vanuatu. Another real-time triplex PCR was used to screen for the point mutations in the 23S rRNA genes that have previously been associated with azithromycin resistance in T. pallidum subsp. pallidum strains. Seropositivity by the classical syphilis serological tests was 35.5% among children with skin ulcerations clinically suspected with yaws, whereas the presence of T. pallidum subsp. pertenue DNA was only found in lesions from 15.5% of children. No evidence of T. pallidum subsp. pertenue infection, by either PCR or serology was found in ∼59% of cases indicating alternative causes of yaws-like lesions in this endemic area. PMID:25404075

Comparative sensitivity to UV-B radiation of two Bacillus thuringiensis subspecies and other Bacillus sp.

PubMed

Myasnik, M; Manasherob, R; Ben-Dov, E; Zaritsky, A; Margalith, Y; Barak, Z

2001-08-01

Susceptibility of Bacillus thuringiensis spores and toxins to the UV-B range (280--330 nm) of the solar spectrum reaching Earth's surface may be responsible for its inactivation and low persistence in nature. Spores of the mosquito larvicidal B. thuringiensis subsp. israelensis were significantly more resistant to UV-B than spores of the lepidopteran-active subsp. kurstaki. Spores of subsp. israelensis were as resistant to UV-B as spores of B. subtilis and more resistant than spores of the closely related B. cereus and another mosquito larvicidal species B. sphaericus. Sensitivity of B. thuringiensis subsp. israelensis spores to UV-B radiation depended upon their culture age; 24-h cultures, approaching maximal larvicidal activity, were still sensitive. Maximal resistance to UV-B was achieved only at 48 h.

Lactic Acid Bacteria from Kefir Increase Cytotoxicity of Natural Killer Cells to Tumor Cells.

PubMed

Yamane, Takuya; Sakamoto, Tatsuji; Nakagaki, Takenori; Nakano, Yoshihisa

2018-03-27

The Japanese fermented beverage, homemade kefir, contains six lactic acid bacteria: Lactococcus. lactis subsp. Lactis , Lactococcus . lactis subsp. Cremoris , Lactococcus. Lactis subsp. Lactis biovar diacetylactis , Lactobacillus plantarum , Leuconostoc meseuteroides subsp. Cremoris and Lactobacillus casei . In this study, we found that a mixture of the six lactic acid bacteria from kefir increased the cytotoxicity of human natural killer KHYG-1 cells to human chronic myelogenous leukemia K562 cells and colorectal tumor HCT116 cells. Furthermore, levels of mRNA expression and secretion of IFN-γ (interferon gamma) increased in KHYG-1 cells that had been treated with the six lactic acid bacteria mixture from kefir. The results suggest that the six lactic acid bacteria mixture from kefir has strong effects on natural immunity and tumor cell cytotoxicity.

Lactic Acid Bacteria from Kefir Increase Cytotoxicity of Natural Killer Cells to Tumor Cells

PubMed Central

Yamane, Takuya; Sakamoto, Tatsuji; Nakagaki, Takenori; Nakano, Yoshihisa

2018-01-01

The Japanese fermented beverage, homemade kefir, contains six lactic acid bacteria: Lactococcus. lactis subsp. Lactis, Lactococcus. lactis subsp. Cremoris, Lactococcus. Lactis subsp. Lactis biovar diacetylactis, Lactobacillus plantarum, Leuconostoc meseuteroides subsp. Cremoris and Lactobacillus casei. In this study, we found that a mixture of the six lactic acid bacteria from kefir increased the cytotoxicity of human natural killer KHYG-1 cells to human chronic myelogenous leukemia K562 cells and colorectal tumor HCT116 cells. Furthermore, levels of mRNA expression and secretion of IFN-γ (interferon gamma) increased in KHYG-1 cells that had been treated with the six lactic acid bacteria mixture from kefir. The results suggest that the six lactic acid bacteria mixture from kefir has strong effects on natural immunity and tumor cell cytotoxicity. PMID:29584690

Subspecific variation in the widespread burl-forming Arctostaphylos glandulosa

USGS Publications Warehouse

Keeley, Jon E.; Vasey, Michael C.; Parker, V. Thomas

2007-01-01

The genus Arctostaphylos consists mostly of chaparral shrubs known by the common name manzanita, and one of the widest ranging of these is A. glandulosa Eastw., distributed from Baja California to Oregon. Particularly in the southern half of its range it exhibits complex patterns of morphological variation that have long presented taxonomic challenges. Phenetic analysis of morphological traits from over 1400 individuals from throughout the range were used to examine intra- and inter-population patterns of variation. Multivariate ordination and hierarchical cluster analysis were used to determine phenetic patterns linked with ecological and geographical distributions. These analyses suggest the hypothesis that this species comprises two lineages with a common origin but divergent in the presence or absence of glandularity: A. glandulosa Eastw. subsp. glandulosa, characterized by branchlets with long glandular hairs, scabrous or pubescent leaves, and nascent inflorescences with mostly foliaceous bracts; and A. glandulosa Eastw. subsp. cushingiana(Eastw.) Keeley, Vasey and Parker comb. nov., with non-glandular tomentose branchlets, glabrate or pubescent leaves and either foliaceous or short deltoid bracts. Populations dominated by one or the other of these morphotypes occur throughout the range and tend to be separated by elevation or distance from the coast, although mixed populations occur where these taxa come together.Two other glandular subspecies are named here. One is A. glandulosa Eastw. subsp. leucophyllaKeeley, Vasey and Parker, subsp. nov., with intensely glaucous leaves and commonly with foliaceous bracts. A second glandular subspecies is A. glandulosa Eastw. subsp. atumescens Keeley, Vasey & Parker, subsp. nov., a narrowly distributed Baja California endemic similar to the nominate subspecies except that it lacks a basal burl and does not resprout after fire.Of the non-glandular tomentose taxa, in addition to A. glandulosa subsp cushingiana, several others are also recognized. One is A. glandulosa Eastw. subsp. crassifolia (Jepson) Wells, a well established coastal San Diego endemic recognized by darker and thicker leaves and smaller and flatter fruits. Another is a newly described taxon A. glandulosa Eastw. subsp. erecta Keeley, Vasey & Parker, subsp. nov., an endemic to northern Baja California recognized by the erect nascent inflorescenses. Two others have glabrate leaves and highly reduced deltoid often marcescent bracts; A. glandulosasubsp. adamsii (Munz) Wells, which has intensely glaucous leaves and is distributed from interior Riverside Co. south, and A. glandulosa Eastw. subsp. gabrielensis (Wells) Keeley, Vasey and Parker comb. nov., which has bright lustrous green leaves and greater fusion of nutlets, and is distributed from the interior San Gabriel Mountains of Los Angeles Co. north to the Sierra Madre Mountains of Santa Barbara Co. All non-glandular plants with long setose or villous hairs are A. glandulosa Eastw. subsp. mollis (Adams) Wells. This taxon includes plants with foliaceous as well as reduced bracts and is distributed throughout the Transverse Ranges from Santa Barbara to San Bernardino counties, with some outlying populations further south. This taxon shows a marked tendency for reduced stomatal densities on the upper leaf surface in the westernmost populations. Although all of the A. glandulosataxa described here are known from allopatric populations, intergradations of these closely related taxa occur and thus some populations reflect a mixture of traits and can not be assigned a unique name of practical value.

Molecular mapping of powdery mildew resistance gene Eg-3 in cultivated oat (Avena sativa L. cv. Rollo).

PubMed

Mohler, Volker; Zeller, Friedrich J; Hsam, Sai L K

2012-05-01

Powdery mildew is a prevalent fungal disease affecting oat (Avena sativa L.) production in Europe. Common oat cultivar Rollo was previously shown to carry the powdery mildew resistance gene Eg-3 in common with cultivar Mostyn. The resistance gene was mapped with restriction fragment length polymorphism (RFLP) markers from Triticeae group-1 chromosomes using a population of F(3) lines from a cross between A. byzantina cv. Kanota and A. sativa cv. Rollo. This comparative mapping approach positioned Eg-3 between cDNA-RFLP marker loci cmwg706 and cmwg733. Since both marker loci were derived from the long arm of barley chromosome 1H, the subchromosomal location of Eg-3 was assumed to be on the long arm of oat chromosome 17. Amplified fragment length polymorphism (AFLP) marker technology featured as an efficient means for obtaining markers closely linked to Eg-3.

Tropisms of Avena coleoptiles: sine law for gravitropism, exponential law for photogravitropic equilibrium.

PubMed

Galland, Paul

2002-09-01

The quantitative relation between gravitropism and phototropism was analyzed for light-grown coleoptiles of Avena sativa (L.). With respect to gravitropism the coleoptiles obeyed the sine law. To study the interaction between light and gravity, coleoptiles were inclined at variable angles and irradiated for 7 h with unilateral blue light (466 nm) impinging at right angles relative to the axis of the coleoptile. The phototropic stimulus was applied from the side opposite to the direction of gravitropic bending. The fluence rate that was required to counteract the negative gravitropism increased exponentially with the sine of the inclination angle. To achieve balance, a linear increase in the gravitropic stimulus required compensation by an exponential increase in the counteracting phototropic stimulus. The establishment of photogravitropic equilibrium during continuous unilateral irradiation is thus determined by two different laws: the well-known sine law for gravitropism and a novel exponential law for phototropism described in this work.

Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch.

PubMed

den Bakker, Henk C; Manuel, Clyde S; Fortes, Esther D; Wiedmann, Martin; Nightingale, Kendra K

2013-09-01

Twenty Listeria-like isolates were obtained from environmental samples collected on a cattle ranch in northern Colorado; all of these isolates were found to share an identical partial sigB sequence, suggesting close relatedness. The isolates were similar to members of the genus Listeria in that they were Gram-stain-positive, short rods, oxidase-negative and catalase-positive; the isolates were similar to Listeria fleischmannii because they were non-motile at 25 °C. 16S rRNA gene sequencing for representative isolates and whole genome sequencing for one isolate was performed. The genome of the type strain of Listeria fleischmannii (strain LU2006-1(T)) was also sequenced. The draft genomes were very similar in size and the average MUMmer nucleotide identity across 91% of the genomes was 95.16%. Genome sequence data were used to design primers for a six-gene multi-locus sequence analysis (MLSA) scheme. Phylogenies based on (i) the near-complete 16S rRNA gene, (ii) 31 core genes and (iii) six housekeeping genes illustrated the close relationship of these Listeria-like isolates to Listeria fleischmannii LU2006-1(T). Sufficient genetic divergence of the Listeria-like isolates from the type strain of Listeria fleischmannii and differing phenotypic characteristics warrant these isolates to be classified as members of a distinct infraspecific taxon, for which the name Listeria fleischmannii subsp. coloradonensis subsp. nov. is proposed. The type strain is TTU M1-001(T) ( =BAA-2414(T) =DSM 25391(T)). The isolates of Listeria fleischmannii subsp. coloradonensis subsp. nov. differ from the nominate subspecies by the inability to utilize melezitose, turanose and sucrose, and the ability to utilize inositol. The results also demonstrate the utility of whole genome sequencing to facilitate identification of novel taxa within a well-described genus. The genomes of both subspecies of Listeria fleischmannii contained putative enhancin genes; the Listeria fleischmannii subsp. coloradonensis subsp. nov. genome also encoded a putative mosquitocidal toxin. The presence of these genes suggests possible adaptation to an insect host, and further studies are needed to probe niche adaptation of Listeria fleischmannii.

Rapid Assessment of the Viability of Mycobacterium avium subsp. paratuberculosis Cells after Heat Treatment, Using an Optimized Phage Amplification Assay▿

PubMed Central

Foddai, Antonio; Elliott, Christopher T.; Grant, Irene R.

2010-01-01

Thermal inactivation experiments were carried out to assess the utility of a recently optimized phage amplification assay to accurately enumerate viable Mycobacterium avium subsp. paratuberculosis cells in milk. Ultra-heat-treated (UHT) whole milk was spiked with large numbers of M. avium subsp. paratuberculosis organisms (106 to 107 CFU/ml) and dispensed in 100-μl aliquots in thin-walled 200-μl PCR tubes. A Primus 96 advanced thermal cycler (Peqlab, Erlangen, Germany) was used to achieve the following time and temperature treatments: (i) 63°C for 3, 6, and 9 min; (ii) 68°C for 20, 40, and 60 s; and (iii) 72°C for 5, 10, 15, and 25 s. After thermal stress, the number of surviving M. avium subsp. paratuberculosis cells was assessed by both phage amplification assay and culture on Herrold's egg yolk medium (HEYM). A high correlation between PFU/ml and CFU/ml counts was observed for both unheated (r2 = 0.943) and heated (r2 = 0.971) M. avium subsp. paratuberculosis cells. D and z values obtained using the two types of counts were not significantly different (P > 0.05). The D68°C, mean D63°C, and D72°C for four M. avium subsp. paratuberculosis strains were 81.8, 9.8, and 4.2 s, respectively, yielding a mean z value of 6.9°C. Complete inactivation of 106 to 107 CFU of M. avium subsp. paratuberculosis/ml milk was not observed for any of the time-temperature combinations studied; 5.2- to 6.6-log10 reductions in numbers were achieved depending on the temperature and time. Nonlinear thermal inactivation kinetics were consistently observed for this bacterium. This study confirms that the optimized phage assay can be employed in place of conventional culture on HEYM to speed up the acquisition of results (48 h instead of a minimum of 6 weeks) for inactivation experiments involving M. avium subsp. paratuberculosis-spiked samples. PMID:20097817

A Rapid Method for Quantifying Viable Mycobacterium avium subsp. paratuberculosis in Cellular Infection Assays

PubMed Central

Pooley, Hannah B.; de Silva, Kumudika; Purdie, Auriol C.; Begg, Douglas J.; Whittington, Richard J.

2016-01-01

ABSTRACT Determining the viability of bacteria is a key outcome of in vitro cellular infection assays. Currently, this is done by culture, which is problematic for fastidious slow-growing bacteria such as Mycobacterium avium subsp. paratuberculosis, where it can take up to 4 months to confirm growth. This study aimed to identify an assay that can rapidly quantify the number of viable M. avium subsp. paratuberculosis cells in a cellular sample. Three commercially available bacterial viability assays along with a modified liquid culture method coupled with high-throughput quantitative PCR growth detection were assessed. Criteria for assessment included the ability of each assay to differentiate live and dead M. avium subsp. paratuberculosis organisms and their accuracy at low bacterial concentrations. Using the culture-based method, M. avium subsp. paratuberculosis growth was reliably detected and quantified within 2 weeks. There was a strong linear association between the 2-week growth rate and the initial inoculum concentration. The number of viable M. avium subsp. paratuberculosis cells in an unknown sample was quantified based on the growth rate, by using growth standards. In contrast, none of the commercially available viability assays were suitable for use with samples from in vitro cellular infection assays. IMPORTANCE Rapid quantification of the viability of Mycobacterium avium subsp. paratuberculosis in samples from in vitro cellular infection assays is important, as it allows these assays to be carried out on a large scale. In vitro cellular infection assays can function as a preliminary screening tool, for vaccine development or antimicrobial screening, and also to extend findings derived from experimental animal trials. Currently, by using culture, it takes up to 4 months to obtain quantifiable results regarding M. avium subsp. paratuberculosis viability after an in vitro infection assay; however, with the quantitative PCR and liquid culture method developed, reliable results can be obtained at 2 weeks. This method will be important for vaccine and antimicrobial screening work, as it will allow a greater number of candidates to be screened in the same amount of time, which will increase the likelihood that a favorable candidate will be found to be subjected to further testing. PMID:27371585

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05.

PubMed

Perin, Luana Martins; Dal Bello, Barbara; Belviso, Simona; Zeppa, Giuseppe; Carvalho, Antônio Fernandes de; Cocolin, Luca; Nero, Luís Augusto

2015-12-02

Minas cheese is a popular dairy product in Brazil that is traditionally produced using raw or pasteurized cow milk. This study proposed an alternative production of Minas cheese using raw goat milk added of a nisin producer Lactococcus lactis subsp. lactis GLc05. An in situ investigation was carried on to evaluate the interactions between the L. lactis subsp. lactis GLc05 and the autochthonous microbiota of a Minas cheese during the ripening; production of biogenic amines (BAs) was assessed as a safety aspect. Minas cheese was produced in two treatments (A, by adding L. lactis subsp. lactis GLc05, and B, without adding this strain), in three independent repetitions (R1, R2, and R3). Culture dependent (direct plating) and independent (rep-PCR and PCR-DGGE) methods were employed to characterize the microbiota and to assess the possible interferences caused by L. lactis subsp. lactis GLc05. BA amounts were measured using HPLC. A significant decrease in coagulase-positive cocci was observed in the cheeses produced by adding L. lactis subsp. lactis GLc05 (cheese A). The rep-PCR and PCR-DGGE highlighted the differences in the microbiota of both cheeses, separating them into two different clusters. Lactococcus sp. was found as the main microorganism in both cheeses, and the microbiota of cheese A presented a higher number of species. High concentrations of tyramine were found in both cheeses and, at specific ripening times, the BA amounts in cheese B were significantly higher than in cheese A (p<0.05). The interaction of nisin producer L. lactis subsp. lactis GLc05 was demonstrated in situ, by demonstration of its influence in the complex microbiota naturally present in a raw goat milk cheese and by controlling the growth of coagulase-positive cocci. L. lactis subsp. lactis GLc05 influenced also the production of BA determining that their amounts in the cheeses were maintained at acceptable levels for human consumption. Copyright © 2015 Elsevier B.V. All rights reserved.

The genetics of obligate parthenogenesis in an aphid species and its consequences for the maintenance of alternative reproductive modes.

PubMed

Dedryver, C-A; Le Gallic, J-F; Mahéo, F; Simon, J-C; Dedryver, F

2013-01-01

Although loss of sex is widespread among metazoans, the genetic mechanisms underlying the transition to asexuality are poorly understood. Aphids are good models to address this issue because they frequently show reproductive-mode variation at the species level, involving cyclical parthenogens (CP) that reproduce sexually once a year and obligate parthenogens (OP) that reproduce asexually all year round. Here, we explore the genetic basis of OP in the cereal aphid Sitobion avenae by crossing several genotypes with contrasting reproductive modes and then characterising the reproductive phenotypes of F1 and F2 offspring. The analysis of phenotypic variation in F1 and F2 progenies suggests that at least two autosomal loci control OP in S. avenae. First, the transition to asexuality seems to depend on a single recessive locus, because the offspring from self-crossed cyclical parthenogenetic genotypes contain either 0 or 25% OP. Second, as we observed OP in the F1 progenies from crosses between CP and OP, and some CP in the offspring from outcrossed OP, a dominant 'suppressor' gene may also be involved, being inactive when in a recessive homozygous state in CP; this is the most parsimonious explanation for these results. This oligogenic inheritance of OP in S. avenae appears to be an efficient genetic system to generate new OP genotypes continually. It also allows asexuality-inducing alleles to be protected locally during harsh winters when extreme frost kills most OP, and then to spread very quickly after winter.

Identification and Pathogenicity of Bacteria Associated with Etiolation and Decline of Creeping Bentgrass Golf Course Putting Greens.

PubMed

Roberts, Joseph A; Ma, Bangya; Tredway, Lane P; Ritchie, David F; Kerns, James P

2018-01-01

Bacterial etiolation and decline has developed into a widespread issue with creeping bentgrass (CBG) (Agrostis stolonifera) putting green turf. The condition is characterized by an abnormal elongation of turfgrass stems and leaves that in rare cases progresses into a rapid and widespread necrosis and decline. Recent reports have cited bacteria, Acidovorax avenae and Xanthomonas translucens, as causal agents; however, few cases exist where either bacterium were isolated in conjunction with turf exhibiting bacterial disease symptoms. From 2010 to 2014, turfgrass from 62 locations submitted to the NC State Turf Diagnostic Clinic exhibiting bacterial etiolation and/or decline symptoms were sampled for the presence of bacterial pathogens. Isolated bacteria were identified using rRNA sequencing of the 16S subunit and internal transcribed spacer region (16S-23S or ITS). Results showed diverse bacteria isolated from symptomatic turf and A. avenae and X. translucens were only isolated in 26% of samples. Frequently isolated bacterial species were examined for pathogenicity to 4-week-old 'G2' CBG seedlings and 8-week-old 'A-1' CBG turfgrass stands in the greenhouse. While results confirmed pathogenicity of A. avenae and X. translucens, Pantoea ananatis was also shown to infect CBG turf; although pathogenicity varied among isolated strains. These results illustrate that multiple bacteria are associated with bacterial disease and shed new light on culturable bacteria living in CBG turfgrass putting greens. Future research to evaluate additional microorganisms (i.e., bacteria and fungi) could provide new information on host-microbe interactions and possibly develop ideas for management tactics to reduce turfgrass pests.

Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle.

PubMed

Kudo, Yuko; Oki, Kaihei; Watanabe, Koichi

2012-11-01

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii, the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii. Together, the results of phenotypic characterization, DNA-DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7%) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221(T) (=JCM 17838(T) =DSM 24966(T)).

First isolation of Mycoplasma capricolum subsp. capricolum, one of the causal agents of caprine contagious agalactia, on the island of Lanzarote (Spain).

PubMed

De la Fe, C; Gutiérrez, A; Poveda, J B; Assunção, P; Ramírez, A S; Fabelo, F

2007-03-01

During an unusually long period of bad weather, several outbreaks of caprine contagious agalactia (CCA) were reported in a number of flocks on the island of Lanzarote (Canary Islands, Spain). Clinical and subclinical mastitis in lactating goats and some cases of arthritis and pneumonia in kids were observed in the affected flocks. Mycoplasma capricolum subsp. capricolum was isolated as the main causal agent of the outbreaks, associated with M. mycoides subsp. mycoides "large colony type" (Mmm LC) in two flocks. This is the first report of an isolation of M. capricolum subsp. capricolum on the island of Lanzarote. The finding is of epidemiological importance and could complicate plans to control the disease. The significance of this mycoplasma species in association with CCA must now be studied in detail.

Identification of the ``a'' Genome of Finger Millet Using Chloroplast DNA

PubMed Central

Hilu, K. W.

1988-01-01

Finger millet (Eleusine corocana subsp. coracana), an important cereal in East Africa and India, is a tetraploid species with unknown genomic components. A recent cytogenetic study confirmed the direct origin of this millet from the tetraploid E. coracana subsp. africana but questioned Eleusine indica as a genomic donor. Chloroplast (ct) DNA sequence analysis using restriction fragment pattern was used to examine the phylogenetic relationships between E. coracana subsp. coracana (domesticated finger millet), E. coracana subspecies africana (wild finger millet), and E. indica. Eleusine tristachya was included since it is the only other annual diploid species in the genus with a basic chromosome number of x = 9 like finger millet. Eight of the ten restriction endonucleases used had 16 to over 30 restriction sites per genome and were informative. E. coracana subsp. coracana and subsp. africana and E. indica were identical in all the restriction sites surveyed, while the ct genome of E. tristachya differed consistently by at least one mutational event for each restriction enzyme surveyed. This random survey of the ct genomes of these species points out E. indica as one of the genome donors (maternal genome donor) of domesticated finger millet contrary to a previous cytogenetic study. The data also substantiate E. coracana subsp. africana as the progenitor of domesticated finger millet. The disparity between the cytogenetic and the molecular approaches is discussed in light of the problems associated with chromosome pairing and polyploidy. PMID:8608927

Profiles of Volatile Flavor Compounds in Milk Fermented with Different Proportional Combinations of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus.

PubMed

Dan, Tong; Wang, Dan; Wu, Shimei; Jin, Rulin; Ren, Weiyi; Sun, Tiansong

2017-09-29

Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus are key factors in the fermentation process and the final quality of dairy products worldwide. This study was performed to investigate the effects of the proportions of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus isolated from traditionally fermented dairy products in China and Mongolia on the profile of volatile compounds produced in samples. Six proportional combinations (1:1, 1:10, 1:50, 1:100, 1:1000, and 1:10,000) of L. delbrueckii subsp. bulgaricus IMAU20401 to S. thermophilus ND03 were considered, and the volatiles were identified and quantified by solid-phase microextraction and gas chromatography-mass spectrometry (SPME-GC-MS) against an internal standard. In total, 89 volatile flavor compounds, consisting of aldehydes, ketones, acids, alcohols, esters, and aromatic hydrocarbons, were identified. Among these, some key flavor volatile compounds were identified, including acetaldehyde, 3-methylbutanal, acetoin, 2-heptanone, acetic acid, butanoic acid, and 3-methyl-1-butanol. The of L. delbrueckii subsp. bulgaricus IMAU20401 to S. thermophilus ND03 influenced the type and concentration of volatiles produced. In particular, aldehydes and ketones were present at higher concentrations in the 1:1000 treatment combination than in the other combinations. Our findings emphasize the importance of selecting the appropriate proportions of L. delbrueckii subsp. bulgaricus and S. thermophilus for the starter culture in determining the final profile of volatiles and the overall flavor of dairy products.

Genetic analysis of a novel Xylella fastidiosa subspecies found in the southwestern United States.

PubMed

Randall, Jennifer J; Goldberg, Natalie P; Kemp, John D; Radionenko, Maxim; French, Jason M; Olsen, Mary W; Hanson, Stephen F

2009-09-01

Xylella fastidiosa, the causal agent of several scorch diseases, is associated with leaf scorch symptoms in Chitalpa tashkentensis, a common ornamental landscape plant used throughout the southwestern United States. For a number of years, many chitalpa trees in southern New Mexico and Arizona exhibited leaf scorch symptoms, and the results from a regional survey show that chitalpa trees from New Mexico, Arizona, and California are frequently infected with X. fastidiosa. Phylogenetic analysis of multiple loci was used to compare the X. fastidiosa infecting chitalpa strains from New Mexico, Arizona, and trees imported into New Mexico nurseries with previously reported X. fastidiosa strains. Loci analyzed included the 16S ribosome, 16S-23S ribosomal intergenic spacer region, gyrase-B, simple sequence repeat sequences, X. fastidiosa-specific sequences, and the virulence-associated protein (VapD). This analysis indicates that the X. fastidiosa isolates associated with infected chitalpa trees in the Southwest are a highly related group that is distinct from the four previously defined taxons X. fastidiosa subsp. fastidiosa (piercei), X. fastidiosa subsp. multiplex, X. fastidiosa subsp. sandyi, and X. fastidiosa subsp. pauca. Therefore, the classification proposed for this new subspecies is X. fastidiosa subsp. tashke.

The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains.

PubMed

Pfeiffer, Friedhelm; Zamora-Lagos, Maria-Antonia; Blettinger, Martin; Yeroslaviz, Assa; Dahl, Andreas; Gruber, Stephan; Habermann, Bianca H

2018-01-05

Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. Here we report the finalized genome sequence of the environmental strain Aeromonas salmonicida subsp. pectinolytica 34mel, for which only a draft genome with 253 contigs is currently available. Successful completion of the transposon-rich genome critically depended on the PacBio long read sequencing technology. Using finalized genome sequences of A. salmonicida subsp. pectinolytica and other Aeromonads, we report the detailed analysis of the transposon composition of these bacterial species. Mobilome evolution is exemplified by a complex transposon, which has shifted from pathogenicity-related to environmental-related gene content in A. salmonicida subsp. pectinolytica 34mel. Obtaining the complete, circular genome of A. salmonicida subsp. pectinolytica allowed us to perform an in-depth analysis of its mobilome. We demonstrate the mobilome-dependent evolution of this strain's genetic profile from pathogenic to environmental.

Isolation of Campylobacter fetus subsp. jejuni from migratory waterfowl.

PubMed Central

Luechtefeld, N A; Blaser, M J; Reller, L B; Wang, W L

1980-01-01

Since the sources from which humans acquire Campylobacter enteritis are only partially known, we studied the frequency of carriage of Campylobacter fetus subsp. jejuni in migratory waterfowl. Cecal contents of various species of wild ducks were cultured on selective media that contained antibiotics to inhibit normal flora. Thirty-five percent of the 445 ducks cultured harbored C. fetus subsp. jejuni. Migratory waterfowl are yet another reservoir for this enteric pathogen and may be of public health importance for humans in the contamination of water or when used as food. PMID:7217334

Electrotransformation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis with Various Plasmids

PubMed Central

Serror, Pascale; Sasaki, Takashi; Ehrlich, S. Dusko; Maguin, Emmanuelle

2002-01-01

We describe, for the first time, a detailed electroporation procedure for Lactobacillus delbrueckii. Three L. delbrueckii strains were successfully transformed. Under optimal conditions, the transformation efficiency was 104 transformants per μg of DNA. Using this procedure, we identified several plasmids able to replicate in L. delbrueckii and integrated an integrative vector based on phage integrative elements into the L. delbrueckii subsp. bulgaricus chromosome. These vectors provide a good basis for developing molecular tools for L. delbrueckii and open the field of genetic studies in L. delbrueckii. PMID:11772607

Campylobacter fetus subsp. jejuni in poultry reared under different management systems in Nigeria.

PubMed

Adekeye, J O; Abdu, P A; Bawa, E K

1989-01-01

Cloacal swabs from 487 live birds in 36 flocks and 70 poultry carcasses were cultured for Campylobacter fetus subsp. jejuni. It was isolated from 12.3% of the birds in 19 flocks. Chickens, turkeys, and guinea fowl differed from one another in isolation rates of the organism. Management system affected its occurrence, and only 7.1% of eviscerated carcasses yielded it. It was concluded that bird species, management system, and immersing slaughtered poultry in boiling water before dressing affect recovery of C. fetus subsp. jejuni from live birds and carcasses.

Lactobacillus plantarum subsp. argentoratensis subsp. nov., isolated from vegetable matrices.

PubMed

Bringel, Françoise; Castioni, Anna; Olukoya, Daniel K; Felis, Giovanna E; Torriani, Sandra; Dellaglio, Franco

2005-07-01

Fourteen strains isolated from vegetable sources and identified as belonging to Lactobacillus plantarum presented an atypical pattern of amplification with a species-specific multiplex-PCR assay. Phylogenetic analysis of two protein-encoding genes, recA (encoding the recombinase A protein) and cpn60 (encoding the GroEL chaperonin), as well as phenotypic and genomic traits revealed a homogeneous group of very closely related strains for which subspecies status is proposed, with the name Lactobacillus plantarum subsp. argentoratensis. The type strain is DKO 22(T) (=CIP 108320(T)=DSM 16365(T)).

Comparison of culture and a novel 5' Taq nuclease assay for direct detection of Campylobacter fetus subsp. venerealis in clinical specimens from cattle.

PubMed

McMillen, Lyle; Fordyce, Geoffry; Doogan, Vivienne J; Lew, Ala E

2006-03-01

A Campylobacter fetus subsp. venerealis-specific 5' Taq nuclease PCR assay using a 3' minor groove binder-DNA probe (TaqMan MGB) was developed based on a subspecies-specific fragment of unknown identity (S. Hum, K. Quinn, J. Brunner, and S. L. On, Aust. Vet. J. 75:827-831, 1997). The assay specifically detected four C. fetus subsp. venerealis strains with no observed cross-reaction with C. fetus subsp. fetus-related Campylobacter species or other bovine venereal microflora. The 5' Taq nuclease assay detected approximately one single cell compared to 100 and 10 cells in the conventional PCR assay and 2,500 and 25,000 cells from selective culture from inoculated smegma and mucus, respectively. The respective detection limits following the enrichments from smegma and mucus were 5,000 and 50 cells/inoculum for the conventional PCR compared to 500 and 50 cells/inoculum for the 5' Taq nuclease assay. Field sampling confirmed the sensitivity and the specificity of the 5' Taq nuclease assay by detecting an additional 40 bulls that were not detected by culture. Urine-inoculated samples demonstrated comparable detection of C. fetus subsp. venerealis by both culture and the 5' Taq nuclease assay; however, urine was found to be less effective than smegma for bull sampling. Three infected bulls were tested repetitively to compare sampling tools, and the bull rasper proved to be the most suitable, as evidenced by the improved ease of specimen collection and the consistent detection of higher levels of C. fetus subsp. venerealis. The 5' Taq nuclease assay demonstrates a statistically significant association with culture (chi2 = 29.8; P < 0.001) and significant improvements for the detection of C. fetus subsp. venerealis-infected animals from crude clinical extracts following prolonged transport.

Salmonella enterica Suppresses Pectobacterium carotovorum subsp. carotovorum Population and Soft Rot Progression by Acidifying the Microaerophilic Environment

PubMed Central

Kwan, Grace; Charkowski, Amy O.; Barak, Jeri D.

2013-01-01

ABSTRACT Although enteric human pathogens are usually studied in the context of their animal hosts, a significant portion of their life cycle occurs on plants. Plant disease alters the phyllosphere, leading to enhanced growth of human pathogens; however, the impact of human pathogens on phytopathogen biology and plant health is largely unknown. To characterize the interaction between human pathogens and phytobacterial pathogens in the phyllosphere, we examined the interactions between Pectobacterium carotovorum subsp. carotovorum and Salmonella enterica or Escherichia coli O157:H7 with regard to bacterial populations, soft rot progression, and changes in local pH. The presence of P. carotovorum subsp. carotovorum enhanced the growth of both S. enterica and E. coli O157:H7 on leaves. However, in a microaerophilic environment, S. enterica reduced P. carotovorum subsp. carotovorum populations and soft rot progression by moderating local environmental pH. Reduced soft rot was not due to S. enterica proteolytic activity. Limitations on P. carotovorum subsp. carotovorum growth, disease progression, and pH elevation were not observed on leaves coinoculated with E. coli O157:H7 or when leaves were coinoculated with S. enterica in an aerobic environment. S. enterica also severely undermined the relationship between the phytobacterial population and disease progression of a P. carotovorum subsp. carotovorum budB mutant defective in the 2,3-butanediol pathway for acid neutralization. Our results show that S. enterica and E. coli O157:H7 interact differently with the enteric phytobacterial pathogen P. carotovorum subsp. carotovorum. S. enterica inhibition of soft rot progression may conceal a rapidly growing human pathogen population. Whereas soft rotted produce can alert consumers to the possibility of food-borne pathogens, healthy-looking produce may entice consumption of contaminated vegetables. PMID:23404399

Infection of sea lamprey with an unusual strain of Aeromonas salmonicida

USGS Publications Warehouse

Diamanka, Arfang; Loch, Thomas P.; Cipriano, Rocco C.; Winters, Andrew D.; Faisal, Mohamed

2014-01-01

The invasion of the Laurentian Great Lakes by the fish-parasitic sea lamprey has led to catastrophic consequences, including the potential introduction of fish pathogens. Aeromonas salmonicida is a bacterial fish pathogen that causes devastating losses worldwide. Currently, there are five accepted subspecies of Aeromonas salmonicida: A. salmonicida subsp. salmonicida, masoucida, smithia, achromogenes, and pectinolytica. We discuss the discovery of an isolate of A. salmonicida that is pathogenic to rainbow trout (Oncorhynchus mykiss) and exhibits unique phenotypic and molecular characteristics. We examined 181 adult sea lamprey (Petromyzon marinus) from the Humber River (Lake Ontario watershed) and 162 adult sea lamprey from Duffins Creek (Lake Ontario watershed) during the spring seasons of 2005–11. Among those, 4/343 (1.2%) sea lamprey were culture positive for A. salmonicida, whereby biochemical and molecular studies identified three of the isolates as A. salmonicida subsp. salmonicida. The remaining isolate (As-SL1) recovered from Humber River sea lamprey was phenotypically more similar to A. salmonicida subsp. salmonicida than to the four other A. salmonicida subspecies. However, unlike A. salmonicida subsp. salmonicida, As-SL1 was sucrose positive, produced an acid-over-acid reaction on triple-sugar iron medium and did not amplify with A. salmonicida subsp. salmonicida specific primers. Phylogenetic analysis based on partial stretches of the 16S rRNA and DNA gyrase subunit B genes further confirmed that the As-SL1 isolate was not A. salmonicida subsp. masoucida, smithia, achromogenes, or pectinolytica. Based on our analyses, the As-SL1 isolate is either an unusual strain of A. salmonicida subsp. salmonicida or a novel A. salmonicida subspecies. The four A. salmonicida isolates that were recovered from sea lamprey were pathogenic to rainbow trout in experimental challenge studies. Our study also underscores the potential role of sea lamprey in the ecology of infectious fish diseases.

Culture Phenotypes of Genomically and Geographically Diverse Mycobacterium avium subsp. paratuberculosis Isolates from Different Hosts▿

PubMed Central

Whittington, Richard J.; Marsh, Ian B.; Saunders, Vanessa; Grant, Irene R.; Juste, Ramon; Sevilla, Iker A.; Manning, Elizabeth J. B.; Whitlock, Robert H.

2011-01-01

Mycobacterium avium subsp. paratuberculosis causes paratuberculosis (Johne's disease) in ruminants in most countries. Historical data suggest substantial differences in culturability of M. avium subsp. paratuberculosis isolates from small ruminants and cattle; however, a systematic comparison of culture media and isolates from different countries and hosts has not been undertaken. Here, 35 field isolates from the United States, Spain, Northern Ireland, and Australia were propagated in Bactec 12B medium and Middlebrook 7H10 agar, genomically characterized, and subcultured to Lowenstein-Jensen (LJ), Herrold's egg yolk (HEY), modified Middlebrook 7H10, Middlebrook 7H11, and Watson-Reid (WR) agars, all with and without mycobactin J and some with sodium pyruvate. Fourteen genotypes of M. avium subsp. paratuberculosis were represented as determined by BstEII IS900 and IS1311 restriction fragment length polymorphism analysis. There was no correlation between genotype and overall culturability, although most S strains tended to grow poorly on HEY agar. Pyruvate was inhibitory to some isolates. All strains grew on modified Middlebrook 7H10 agar but more slowly and less prolifically on LJ agar. Mycobactin J was required for growth on all media except 7H11 agar, but growth was improved by the addition of mycobactin J to 7H11 agar. WR agar supported the growth of few isolates. The differences in growth of M. avium subsp. paratuberculosis that have historically been reported in diverse settings have been strongly influenced by the type of culture medium used. When an optimal culture medium, such as modified Middlebrook 7H10 agar, is used, very little difference between the growth phenotypes of diverse strains of M. avium subsp. paratuberculosis was observed. This optimal medium is recommended to remove bias in the isolation and cultivation of M. avium subsp. paratuberculosis. PMID:21430104

Infection of sea lamprey with an unusual strain of Aeromonas salmonicida.

PubMed

Diamanka, Arfang; Loch, Thomas P; Cipriano, Rocco C; Winters, Andrew D; Faisal, Mohamed

2014-04-01

The invasion of the Laurentian Great Lakes by the fish-parasitic sea lamprey has led to catastrophic consequences, including the potential introduction of fish pathogens. Aeromonas salmonicida is a bacterial fish pathogen that causes devastating losses worldwide. Currently, there are five accepted subspecies of Aeromonas salmonicida: A. salmonicida subsp. salmonicida, masoucida, smithia, achromogenes, and pectinolytica. We discuss the discovery of an isolate of A. salmonicida that is pathogenic to rainbow trout (Oncorhynchus mykiss) and exhibits unique phenotypic and molecular characteristics. We examined 181 adult sea lamprey (Petromyzon marinus) from the Humber River (Lake Ontario watershed) and 162 adult sea lamprey from Duffins Creek (Lake Ontario watershed) during the spring seasons of 2005-11. Among those, 4/343 (1.2%) sea lamprey were culture positive for A. salmonicida, whereby biochemical and molecular studies identified three of the isolates as A. salmonicida subsp. salmonicida. The remaining isolate (As-SL1) recovered from Humber River sea lamprey was phenotypically more similar to A. salmonicida subsp. salmonicida than to the four other A. salmonicida subspecies. However, unlike A. salmonicida subsp. salmonicida, As-SL1 was sucrose positive, produced an acid-over-acid reaction on triple-sugar iron medium and did not amplify with A. salmonicida subsp. salmonicida specific primers. Phylogenetic analysis based on partial stretches of the 16S rRNA and DNA gyrase subunit B genes further confirmed that the As-SL1 isolate was not A. salmonicida subsp. masoucida, smithia, achromogenes, or pectinolytica. Based on our analyses, the As-SL1 isolate is either an unusual strain of A. salmonicida subsp. salmonicida or a novel A. salmonicida subspecies. The four A. salmonicida isolates that were recovered from sea lamprey were pathogenic to rainbow trout in experimental challenge studies. Our study also underscores the potential role of sea lamprey in the ecology of infectious fish diseases.

H(+) -ATPase-defective variants of Lactobacillus delbrueckii subsp. bulgaricus contribute to inhibition of postacidification of yogurt during chilled storage.

PubMed

Wang, Xinhui; Ren, Hongyang; Liu, Dayu; Wang, Bing; Zhu, Wenyou; Wang, Wei

2013-02-01

Continued acid production by Lactobacillus delbrueckii subsp. bulgaricus during the chilled storage of yogurt is the major cause of postacidification, resulting in a short shelf life. Two H(+) -ATPase defective variants of L. delbrueckii subsp. bulgaricus were successfully isolated and their H(+) -ATPase activities were reduced by 51.3% and 34.3%, respectively. It was shown that growth and acid production of variants were remarkably inhibited. The variants were more sensitive to acidic condition and had a significant rate for inactivation of H(+) -ATPase by N, N-dicyclohexylcarbodiimide (DCCD), along with a low H(+) -extrusion, suggesting that H(+) -ATPase is direct response for H(+) -extrusion. In addition, the variants were also more sensitive to NaCl, while H(+) -ATPase activities of variants and parent strain were significantly enhanced by NaCl stress. Obviously, H(+) -ATPase might be involved in Na(+) transportation. Furthermore, variants were inoculated in fermented milk to ferment yogurt. There was no significant difference in flavor, whereas the postacidification of yogurt during chilled storage was remarkably inhibited. It is suggested that application of L. delbrueckii subsp. bulgaricus with reduced H(+) -ATPase activity in yogurt fermentation is one of effect, economic and simple avenues of inhibiting postacidification of yogurt during refrigerated storage, giving a longer shelf life. During yogurt fermentation, continued acid production by Lactobacillus delbrueckii subsp. bulgaricus during the chilled storage of yogurt leads to milk fermentation with high postacidification, resulting in a short shelf life. In this work, 2 acid-sensitive variant strains of L. delbrueckii subsp. bulgaricus were isolated. The characteristics related to H(+) -ATPase were compared and it was observed that milk fermented by the variants had lower postacidification, giving a longer shelf life. Application of L. delbrueckii subsp. bulgaricus with reduced H(+) -ATPase activity in yogurt fermentation might be one of effect, economic and simple avenues of inhibiting yogurt postacidification during chilled storage, giving a longer shelf life. © 2013 Institute of Food Technologists®

Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae).

PubMed

Wagner, Warren L; Krakos, Kyra N; Hoch, Peter C

2013-01-01

The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri.

Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae)

PubMed Central

Wagner, Warren L.; Krakos, Kyra N.; Hoch, Peter C.

2013-01-01

Abstract The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri. PMID:24399892

The prevalence of bovine venereal campylobacteriosis in cattle herds in the Lake Chad basin of Nigeria.

PubMed

Mshelia, Gideon Dauda; Amin, Jibrilla Dahiru; Egwu, Godwin Onyeamaechi; Woldehiwet, Zerai; Murray, Richard Donald

2012-10-01

The prevalence of bovine venereal campylobacteriosis (BVC) was investigated in the Lake Chad basin of Nigeria. Preputial washings and cervico-vaginal mucus samples were obtained from 270 cattle presenting a history of abortion and lowered fertility, kept in traditional and institutional farms. All the samples investigated were cultured using standard bacteriological technique. Campylobacter fetus was isolated from six bulls and four cows. In all cattle sampled, the isolation rates were 2.2% for C. fetus subsp. venerealis and 1.5% for C. fetus subsp. fetus; the herd and within-herd prevalence rates for C. fetus were 22.2% and 3.4%, respectively, while the overall active infectivity rate was 3.7%. BVC probably contributes to lowered fertility and abortions found in cattle in the Lake Chad basin of Nigeria, associated more with C. fetus subsp. venerealis than C. fetus subsp. fetus.

Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean.

PubMed

González, Ana J; Trapiello, Estefanía

2014-05-01

A yellow Gram-reaction-positive bacterium isolated from bean seeds (Phaseolus vulgaris L.) was identified as Clavibacter michiganensis by 16S rRNA gene sequencing. Molecular methods were employed in order to identify the subspecies. Such methods included the amplification of specific sequences by PCR, 16S amplified rDNA restriction analysis (ARDRA), RFLP and multilocus sequence analysis as well as the analysis of biochemical and phenotypic traits including API 50CH and API ZYM results. The results showed that strain LPPA 982T did not represent any known subspecies of C. michiganensis. Pathogenicity tests revealed that the strain is a bean pathogen causing a newly identified bacterial disease that we name bacterial bean leaf yellowing. On the basis of these results, strain LPPA 982T is regarded as representing a novel subspecies for which the name Clavibacter michiganensis subsp. phaseoli subsp. nov. is proposed. The type strain is LPPA 982T (=CECT 8144T=LMG 27667T).

Co-isolation of Bartonella henselae and Bartonella vinsonii subsp. berkhoffii from blood, joint and subcutaneous seroma fluids from two naturally infected dogs.

PubMed

Diniz, Pedro Paulo Vissotto de Paiva; Wood, Michael; Maggi, Ricardo G; Sontakke, Sushama; Stepnik, Matt; Breitschwerdt, Edward B

2009-09-18

This report describes the clinical presentation, isolation and treatment of two dogs naturally infected with Bartonella henselae and Bartonella vinsonii subsp. berkhoffii. Chronic and progressive polyarthritis was the primary complaint for dog #1, from which B. henselae and B. vinsonii subsp. berkhoffii were cultured on three independent occasions from blood and joint fluid samples, despite administration of nearly 4 months of non-consecutive antibiotic therapy. A clinically atypical and progressively severe trauma-associated seroma was the primary complaint for dog #2, from which B. henselae and B. vinsonii subsp. berkhoffii were isolated from serum, blood and seroma fluid. Dogs can be co-infected with two Bartonella spp. and infection with these organisms should not be ruled out if specific antibodies are not detected. Specialized culture techniques should be used for isolation and to assess antibiotic efficacy.

Septic pneumonic tularaemia caused by Francisella tularensis subsp. holarctica biovar II.

PubMed

Fritzsch, Joerg; Splettstoesser, Wolf D

2010-09-01

This case of pneumonic tularaemia elucidates two aspects: it is believed to be the first documented case of bacteraemia caused by Francisella tularensis subsp. holarctica biovar II; furthermore, it illustrates the remission of septic pneumonic tularaemia without appropriate anti-infective therapy. A blood culture from a patient with community-acquired pneumonia was found to be positive for F. tularensis subsp. holarctica biovar II after 10 days of cultivation. Meanwhile, the patient had been treated with ceftriaxone, followed by sultamicillin and clindamycin. The patient continued suffering from fever of up to 40.7 degrees C and rising C-reactive protein (CRP) for 4 days before the fever and CRP declined. The isolated strain was later tested and found to be resistant to the antibiotics used. The present case underlines that F. tularensis subsp. holarctica infections may cause severe symptoms but mostly have a favourable outcome.

Bifidobacterium animalis subsp. lactis decreases urinary oxalate excretion in a mouse model of primary hyperoxaluria

PubMed Central

Whittamore, Jonathan M.; Hatch, Marguerite

2015-01-01

Hyperoxaluria significantly increases the risk of calcium oxalate kidney stone formation. Since several bacteria have been shown to metabolize oxalate in vitro, including probiotic bifidobacteria, we focused on the efficiency and possible mechanisms by which bifidobacteria can infuence oxalate handling in vivo, especially in the intestines, and compared these results with the reported effects of Oxalobacter formigenes. Bifidobacterium animalis subsp. lactis DSM 10140 and B. adolescentis ATCC 15703 were administered to wild-type (WT) mice and to mice defcient in the hepatic enzyme alanine-glyoxylate aminotransferase (Agxt−/−, a mouse model of Primary Hyperoxaluria) that were fed an oxalate-supplemented diet. The administration of B. animalis subsp. lactis led to a significant decrease in urinary oxalate excretion in WT and Agxt−/− mice when compared to treatment with B. adolescent-is. Detection of B. animalis subsp. lactis in feces revealed that 3 weeks after oral gavage with the bacteria 64 % of WT mice, but only 37 % of Agxt−/− mice were colonized. Examining intestinal oxalate fuxes showed there were no significant changes to net oxalate secretion in colonized animals and were therefore not associated with the changes in urinary oxalate excretion. These results indicate that colonization with B. animalis subsp. lactis decreased urinary oxalate excretion by degrading dietary oxalate thus limiting its absorption across the intestine but it did not promote enteric oxalate excretion as reported for O. formigenes. Preventive or therapeutic administration of B. animalis subsp. lactis appears to have some potential to beneficially infuence dietary hyperoxaluria in mice. PMID:25269440

Cell surface characteristics of Lactobacillus casei subsp. casei, Lactobacillus paracasei subsp. paracasei, and Lactobacillus rhamnosus strains.

PubMed Central

Pelletier, C; Bouley, C; Cayuela, C; Bouttier, S; Bourlioux, P; Bellon-Fontaine, M N

1997-01-01

Hydrophilic and electrostatic cell surface properties of eight Lactobacillus strains were characterized by using the microbial adhesion to solvents method and microelectrophoresis, respectively. All strains appeared relatively hydrophilic. The strong microbial adhesion to chloroform, an acidic solvent, in comparison with microbial adhesion to hexadecane, an apolar n-alkane, demonstrated the particularity of lactobacilli to have an important electron donor and basic character and consequently their potential ability to generate Lewis acid-base interactions with a support. Regardless of their electrophoretic mobility (EM), strains were in general slightly negatively charged at alkaline pH. A pH-dependent behavior concerning cell surface charges was observed. The EM decreased progressively with more acidic pHs for the L. casei subsp. casei and L. paracasei subsp. paracasei strains until the isoelectric point (IEP), i.e., the pH value for which the EM is zero. On the other hand, the EM for the L. rhamnosus strains was stable from pH 8 to pH 3 to 4, at which point there was a shift near the IEP. Both L. casei subsp. casei and L. paracasei subsp. paracasei strains were characterized by an IEP of around 4, whereas L. rhamnosus strains possessed a markedly lower IEP of 2. The present study showed that the cell surface physicochemical properties of lactobacilli seem to be, at least in part and under certain experimental conditions, particular to the bacterial species. Such differences detected between species are likely to be accompanied by some particular changes in cell wall chemical composition. PMID:9143109

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti.

PubMed

Franco, Fernando Faria; Jojima, Cecília Leiko; Perez, Manolo Fernandez; Zappi, Daniela Cristina; Taylor, Nigel; Moraes, Evandro Marsola

2017-11-01

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis , C. fernambucensis subsp. sericifer , and C. insularis . These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis , northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis , southern distribution of C. fernambucensis subsp. sericifer , and northern distribution of C. fernambucensis subsp. sericifer . Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.

Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso.

PubMed

Adimpong, David B; Nielsen, Dennis S; Sørensen, Kim I; Vogensen, Finn K; Sawadogo-Lingani, Hagrétou; Derkx, Patrick M F; Jespersen, Lene

2013-10-01

Lactobacillus delbrueckii is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9(T), was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA-DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species L. delbrueckii. The genome sequence of isolate ZN7a-9(T) was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9(T) together with 41 additional L. delbrueckii strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of L. delbrueckii represented by strain ZN7a-9(T) as it clustered with L. delbrueckii strains unassigned to any of the recognized subspecies of L. delbrueckii. Strain ZN7a-9(T) additionally differed from the recognized type strains of the subspecies of L. delbrueckii with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9(T) represents a novel subspecies of L. delbrueckii closely related to Lactobacillus delbrueckii subsp. lactis and Lactobacillus delbrueckii subsp. delbrueckii for which the name Lactobacillus delbrueckii subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9(T) = DSM 26046(T) = LMG 27067(T).

Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment.

PubMed

Waleron, Małgorzata; Waleron, Krzysztof; Podhajska, Anna J; Lojkowska, Ewa

2002-02-01

Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (AluI, HinfI, TasI and Tru1I), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (Erwinia amylovora, Erwinia ananas, Erwinia cacticida, Erwinia cypripedii, Erwinia herbicola, Erwinia mallotivora, Erwinia milletiae, Erwinia nigrifluens, Erwinia persicina, Erwinia psidii, Erwinia quercina, Erwinia rhapontici, Erwinia rubrifaciens, Erwinia salicis, Erwinia stewartii, Erwinia tracheiphila, Erwinia uredovora, Erwinia carotovora subsp. atroseptica, Erwinia carotovora subsp. betavasculorum, Erwinia carotovora subsp. odorifera and Erwinia carotovora subsp. wasabiae). However, in two cases, Erwinia chrysanthemi and Erwinia carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.

Isolation of Vibrio tapetis from two native fish species (Genypterus chilensis and Paralichthys adspersus) reared in Chile and description of Vibrio tapetis subsp. quintayensis subsp. nov.

PubMed

Levican, Arturo; Lasa, Aide; Irgang, Rute; Romalde, Jesús L; Poblete-Morales, Matías; Avendaño-Herrera, Ruben

2017-04-01

A group of seven Chilean isolates presumptively belonging to Vibrio tapetis was isolated from diseased fine flounders (Paralichthys adspersus) and red conger eel (Genypterus chilensis) experimentally reared in Quintay (Chile). All isolates were confirmed as members of V. tapetis on the basis of matrix-assisted laser desorption ionization time-of-flight MS, 16S rRNA gene sequencing, DNA-DNA hybridization values and G+C content. The ERIC-PCR and REP-PCR patterns were homogeneous among those isolates recovered from the same host (red conger or fine flounders), but distinct from the type strains V. tapetis subsp. tapetis CECT 4600T and V. tapetis subsp. britannicus CECT 8161T. On the basis of atpA, rpoA, rpoD, recA and pyrH gene sequence similarities (99.7-100 %) and clustering in the phylogenetic trees, the red conger isolates (Q20, Q047, Q48 and Q50) were confirmed as representing V. tapetis subsp. tapetis. However, they differed from V. tapetis subsp. tapetis CECT 4600T in their lipase, alpha quimiotripsin and non-acid phosphatase production. On the other hand, the fine flounder isolates (QL-9T, QL-35 and QL-41) showed rpoD, recA and pyrH gene sequence similarities ranging from 91.6 to 97.7 % with the type strains of the two V. tapetis subspecies (CECT 4600T and CECT 8161T) and consistently clustered together as an independent phylogenetic line within V. tapetis. Moreover, they could be differentiated phenotypically from strains CECT 4600T and CECT 8161T by nine and three different biochemical tests, respectively. In conclusion, the presence of V. tapetis in diseased red conger eel and fine flounder was demonstrated, extending the known host range and geographical location for this pathogen. Furthermore, this study demonstrates that the three isolates from fine flounder represent a novel subdivision within V. tapetis, for which the name V. tapetis subsp. quintayensis subsp. nov. is proposed and with QL-9T (=CECT 8851T=LMG 28759T) as the type strain. Although QL-9T was isolated from kidney of diseased fine flounder specimens, the challenge assays showed that it was non-pathogenic for this species.

Differential Substrate Usage and Metabolic Fluxes in Francisella tularensis Subspecies holarctica and Francisella novicida

PubMed Central

Chen, Fan; Rydzewski, Kerstin; Kutzner, Erika; Häuslein, Ina; Schunder, Eva; Wang, Xinzhe; Meighen-Berger, Kevin; Grunow, Roland; Eisenreich, Wolfgang; Heuner, Klaus

2017-01-01

Francisella tularensis is an intracellular pathogen for many animals causing the infectious disease, tularemia. Whereas F. tularensis subsp. holarctica is highly pathogenic for humans, F. novicida is almost avirulent for humans, but virulent for mice. In order to compare metabolic fluxes between these strains, we performed 13C-labeling experiments with F. tularensis subsp. holarctica wild type (beaver isolate), F. tularensis subsp. holarctica strain LVS, or F. novicida strain U112 in complex media containing either [U-13C6]glucose, [1,2-13C2]glucose, [U-13C3]serine, or [U-13C3]glycerol. GC/MS-based isotopolog profiling of amino acids, polysaccharide-derived glucose, free fructose, amino sugars derived from the cell wall, fatty acids, 3-hydroxybutyrate, lactate, succinate and malate revealed uptake and metabolic usage of all tracers under the experimental conditions with glucose being the major carbon source for all strains under study. The labeling patterns of the F. tularensis subsp. holarctica wild type were highly similar to those of the LVS strain, but showed remarkable differences to the labeling profiles of the metabolites from the F. novicida strain. Glucose was directly used for polysaccharide and cell wall biosynthesis with higher rates in F. tularensis subsp. holarctica or metabolized, with higher rates in F. novicida, via glycolysis and the non-oxidative pentose phosphate pathway (PPP). Catabolic turnover of glucose via gluconeogenesis was also observed. In all strains, Ala was mainly synthesized from pyruvate, although no pathway from pyruvate to Ala is annotated in the genomes of F. tularensis and F. novicida. Glycerol efficiently served as a gluconeogenetic substrate in F. novicida, but only less in the F. tularensis subsp. holarctica strains. In any of the studied strains, serine did not serve as a major substrate and was not significantly used for gluconeogenesis under the experimental conditions. Rather, it was only utilized, at low rates, in downstream metabolic processes, e.g., via acetyl-CoA in the citrate cycle and for fatty acid biosynthesis, especially in the F. tularensis subsp. holarctica strains. In summary, the data reflect differential metabolite fluxes in F. tularensis subsp. holarctica and F. novicida suggesting that the different utilization of substrates could be related to host specificity and virulence of Francisella. PMID:28680859

Proposal to rename Carnobacterium inhibens as Carnobacterium inhibens subsp. inhibens subsp. nov. and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a psychrotolerant bacterium isolated from Siberian permafrost.

PubMed

Nicholson, Wayne L; Zhalnina, Kateryna; de Oliveira, Rafael R; Triplett, Eric W

2015-02-01

A novel, psychrotolerant facultative anaerobe, strain WN1359(T), was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive-staining, non-motile, rod-shaped cells were observed with sizes of 1-2 µm long and 0.4-0.5 µm wide. Growth occurred in the range of pH 5.8-9.0 with optimal growth at pH 7.8-8.6 (pH optimum 8.2). The novel isolate grew at temperatures from 0-37 °C and optimal growth occurred at 25 °C. The novel isolate does not require NaCl; growth was observed between 0 and 8.8 % (1.5 M) NaCl with optimal growth at 0.5 % (w/v) NaCl. The isolate was a catalase-negative, facultatively anaerobic chemo-organoheterotroph that used sugars but not several single amino acids or dipeptides as substrates. The major metabolic end-product was lactic acid in the ratio of 86 % l-lactate : 14 % d-lactate. Strain WN1359(T) was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin and vancomycin, and resistant to nalidixic acid and aztreonam. The fatty acid content was predominantly unsaturated (70.2 %), branched-chain unsaturated (11.7 %) and saturated (12.5 %). The DNA G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7 % sequence identity between strain WN1359(T) and Carnobacterium inhibens. Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359(T) belonging to the species C. inhibens. On the basis of these results, the permafrost isolate WN1359(T) represents a novel subspecies of C. inhibens, for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed. The type strain is WN1359(T) ( = ATCC BAA-2557(T) = DSM 27470(T)). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is created automatically. An emended description of C. inhibens is also provided. © 2015 IUMS.

Analysis, annotation, and profiling of the oat seed transcriptome

USDA-ARS?s Scientific Manuscript database

Novel high-throughput next generation sequencing (NGS) technologies are providing opportunities to explore genomes and transcriptomes in a cost-effective manner. To construct a gene expression atlas of developing oat (Avena sativa) seeds, two software packages specifically designed for RNA-seq (Trin...

Proteomic analysis shows that stress response proteins are significantly up-regulated in resistant diploid wheat (Triticum monococcum) in response to attack by the grain aphid (Sitobion avenae).

PubMed

Guan, Wenzhu; Ferry, Natalie; Edwards, Martin G; Bell, Howard A; Othman, Hamizah; Gatehouse, John A; Gatehouse, Angharad M R

2015-01-01

The grain aphid Sitobion avenae (F.) is a major pest of wheat, acting as a virus vector as well as causing direct plant damage. Commonly grown wheat varieties in the UK have only limited resistance to this pest. The present study was carried out to investigate the potential of a diploid wheat line (ACC20 PGR1755), reported as exhibiting resistance to S. avenae, to serve as a source of resistance genes. The diploid wheat line was confirmed as partially resistant, substantially reducing the fecundity, longevity and growth rate of the aphid. Proteomic analysis showed that approximately 200 protein spots were reproducibly detected in leaf extracts from both the resistant line and a comparable susceptible line (ACC5 PGR1735) using two-dimensional gel electrophoresis and image comparison software. Twenty-four spots were significantly up-regulated (>2-fold) in the resistant line after 24 h of aphid feeding (13 and 11 involved in local and systemic responses, respectively). Approximately 50 % of all differentially expressed protein spots were identified by a combination of database searching with MS and MS/MS data, revealing that the majority of proteins up-regulated by aphid infestation were involved in metabolic processes (including photosynthesis) and transcriptional regulation. However, in the resistant line only, several stress response proteins (including NBS-LRR-like proteins) and oxidative stress response proteins were identified as up-regulated in response to aphid feeding, as well as proteins involved in DNA synthesis/replication/repair. This study indicates that the resistant diploid line ACC20 PGR1755 may provide a valuable resource in breeding wheat for resistance to aphids.

Cardiovascular fitness in adolescents: the influence of sexual maturation status-the AVENA and EYHS studies.

PubMed

Ortega, Francisco B; Ruiz, Jonatan R; Mesa, Jose L; Gutiérrez, Angel; Sjöström, Michael

2007-01-01

The purposes were: (1) to determine the influence of sexual maturation status and body composition by comparing cardiovascular fitness (CVF) level in two adolescent populations from the south and the north of Europe; (2) to describe the associations between CVF and sexual maturation status in adolescence. A total of 1,867 Spanish adolescents from the AVENA study and 472 from the Swedish part of the EYHS were selected for this report (aged 14-16 years). CVF (expressed by the maximal oxygen consumption) was estimated from 20 m shuttle run test in the AVENA study and from a maximal ergometer cycle test in the EYHS. Sexual maturation status was classified according to Tanner stages. Body fat percentage (BF%) was estimated from skinfold thicknesses. Expressing CVF in different ways (in absolute value and in relation to weight or fat free mass; FFM) resulted in two different results with regard to CVF interpretation and comparison between the study populations. A higher CVF, as expressed in relation to FFM, was observed in the Spanish when compared to Swedish adolescents (P = 0.001). However, after adjusting for both sexual maturation status and BF%, the difference disappeared in males, while it remained significant in females (P = 0.001). CVF was negatively associated with sexual maturation status in males (P = 0.001). However, after adjusting for BF%, the association disappeared in males, while it was significant in females (P = 0.05). These results suggest that for CVF comparisons and interpretation in adolescent populations, sexual maturation status and BF%, as well as the way to express the CVF, should be taken into account. Copyright 2007 Wiley-Liss, Inc.

Draft genome sequence of Xylella fastidiosa subsp. fastidiosa strain Stag’s Leap

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa subsp. fastidiosa causes Pierce’s disease of grapevine. Presented here is the draft genome sequence of the Stag’s Leap strain, previously used in pathogenicity/virulence assays to evaluate grapevine germplasm bearing Pierce’s disease....

Complete genome sequence of Campylobacter fetus subsp. testudinum type strain 03-427T

USDA-ARS?s Scientific Manuscript database

Campylobacter fetus subsp. testudinum has been isolated from reptiles and humans. This Campylobacter subspecies is genetically distinct from other C. fetus subspecies. Here we present the first whole genome sequence for this C. fetus subspecies....

[Chalcones from Bauhinia glauca subsp. pernervosa].

PubMed

Wu, Zengbao; Wang, Bin; Zhao, Yuying; Yang, Xiuwei; Liang, Hong

2009-07-01

To study the chemical constituents of Bauhinia glauca subsp. pernervosa. The coulis of B. glauca subsp. pernervosa were extracted with 95% EtOH at room temperature. The compounds were isolated and separated by chromatographic techniques, and structures were identified by spectroscopic methods. Seven chalcones were isolated and identified: butein-4-methyl ether (1), isoliquiritigenin (2), butein (3), isoliquiritigenin-2'-methyl ether (4), 2',4'-dihydroxychalcone (5), isoliquiritigenin-4-methyl ether (6), 4-hydroxy-2',4'-dimethoxychalcone (7). Compounds 1, 3, and 7 were isolated from the genus Bauhinia for the first time, the other compounds were obtained from this plant for the first time.

Essential oil composition and enantiomeric distribution of fenchone and camphor of Lavandula cariensis and L. stoechas subsp. stoechas grown in Greece.

PubMed

Tzakou, Olga; Bazos, Ioannis; Yannitsaros, Artemios

2009-08-01

The essential oils from leaves and inflorescences of L. cariensis Boiss. and L. stoechas L. subsp. stoechas collected in Greece were analyzed by GC and GC/MS. In the inflorescences and leaves essential oils of L. cariensis the most abundant metabolite was camphor (51.8, 48.8% respectively), whereas in the essential oils of L. stoechas subsp. stoechas, the main constituents were fenchone (39.9, 21.0% respectively) and camphor (24.2, 26.3% respectively). Both enantiomers of camphor were present, whereas only (+) fenchone was detected.

Draft Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a Citrate-Fermenting Strain

PubMed Central

Zuljan, Federico; Espariz, Martín; Blancato, Victor S.; Esteban, Luis; Alarcón, Sergio

2016-01-01

We report the draft genome sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a natural strain isolated from artisanal cheese from northwest Argentina. L. lactis subsp. lactis bv. diacetylactis is one of the most important microorganisms used as starter culture around the world. The CRL264 strain constitutes a model microorganism in the studies on the generation of aroma compounds (diacetyl, acetoin, and 2,3-butanediol) by lactic acid bacteria. Our genome analysis shows similar genetic organization to other available genomes of L. lactis bv. diacetylactis strains. PMID:26847906

Factors Affecting Exocellular Polysaccharide Production by Lactobacillus delbrueckii subsp. bulgaricus Grown in a Chemically Defined Medium†

PubMed Central

Petry, Sandrine; Furlan, Sylviane; Crepeau, Marie-Jeanne; Cerning, Jutta; Desmazeaud, Michel

2000-01-01

We developed a chemically defined medium (CDM) containing lactose or glucose as the carbon source that supports growth and exopolysaccharide (EPS) production of two strains of Lactobacillus delbrueckii subsp. bulgaricus. The factors found to affect EPS production in this medium were oxygen, pH, temperature, and medium constituents, such as orotic acid and the carbon source. EPS production was greatest during the stationary phase. Composition analysis of EPS isolated at different growth phases and produced under different fermentation conditions (varying carbon source or pH) revealed that the component sugars were the same. The EPS from strain L. delbrueckii subsp. bulgaricus CNRZ 1187 contained galactose and glucose, and that of strain L. delbrueckii subsp. bulgaricus CNRZ 416 contained galactose, glucose, and rhamnose. However, the relative proportions of the individual monosaccharides differed, suggesting that repeating unit structures can vary according to specific medium alterations. Under pH-controlled fermentation conditions, L. delbrueckii subsp. bulgaricus strains produced as much EPS in the CDM as in milk. Furthermore, the relative proportions of individual monosaccharides of EPS produced in pH-controlled CDM or in milk were very similar. The CDM we developed may be a useful model and an alternative to milk in studies of EPS production. PMID:10919802

Bacteriocin-like inhibitor substances produced by Mexican strains of Bacillus thuringiensis.

PubMed

Barboza-Corona, J Eleazar; Vázquez-Acosta, Herminia; Bideshi, Dennis K; Salcedo-Hernández, Rubén

2007-02-01

Bacteriocins are antimicrobial peptides synthesized and secreted by bacteria and could potentially be used as natural food preservatives. Here, we report the production of bacteriocin-like inhibitor substances (Bt-BLIS) by five Mexican strains of Bacillus thuringiensis. Bacillus thuringiensis subsp. morrisoni (LBIT 269), B. thuringiensis subsp. kurstaki (LBIT 287), B. thuringiensis subsp kenyae (LBIT 404), B. thuringiensis subsp. entomocidus (LBIT 420) and B. thuringiensis subsp. tolworthi (LBIT 524) produced proteinaceous Bt-BLIS with high levels of activity against Bacillus cereus and other gram-positive bacteria. Although none was active against the gram-negative bacteria, Escherichia coli, Shigella species and Pseudomonas aeruginosa, the five Bt-BLIS demonstrated antimicrobial activity against Vibrio cholerae, the etiologic agent of cholera. Biochemical and biophysical studies demonstrated that the five Bt-BLIS could be categorized into two groups, those produced by LBIT 269 and 287 (Group A) and LBIT 404, 420, 524 (Group B), based on relative time of peptide synthesis, distinctive bacterial target specificity and stability in a wide range of temperatures and pH. Because of their stability and bactericidal activities against B. cereus and V. cholerae agents of emetic, diarrheal and lethal syndromes in humans, these Bt-BLIS could potentially be used as biodegradable preservatives in the food industry.

Survival of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus in the Terminal Ileum of Fistulated Göttingen Minipigs

PubMed Central

Lick, Sonja; Drescher, Karsten; Heller, Knut J.

2001-01-01

The ability of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus administered in yogurt to survive the passage through the upper gastrointestinal tract was investigated with Göttingen minipigs that were fitted with ileum T-cannulas. After ingestion of yogurt containing viable microorganisms, ileostomy samples were collected nearly every hour beginning 3 h after food uptake. Living L. delbrueckii subsp. bulgaricus and S. thermophilus were detected in the magnitude of 106 to 107 per gram of intestinal contents (wet weight) in all animals under investigation. A calculation of the minimum amount of surviving bacteria that had been administered is presented. Total DNA extracted from ileostomy samples was subjected to PCR, which was species specific for L. delbrueckii and S. thermophilus and subspecies specific for L. delbrueckii subsp. bulgaricus. All three bacterial groups could be detected by PCR after yogurt uptake but not after uptake of a semisynthetic diet. One pig apparently had developed an endogenous L. delbrueckii flora. When heat-treated yogurt was administered, L. delbrueckii was detected in all animals. S. thermophilus or L. delbrueckii subsp. bulgaricus was not detected, indicating that heat-inactivated cells and their DNAs had already been digested and their own L. delbrueckii flora had been stimulated for growth. PMID:11526016

Inhibition of protein glycation by essential oils of branchlets and fruits of Juniperus communis subsp. hemisphaerica

PubMed Central

Asgary, S.; Naderi, G.A.; Shams Ardekani, M.R.; Sahebkar, A.; Airin, A.; Aslani, S.; Kasher, T.; Emami, S.A.

2014-01-01

Oxidative stress and protein glycation play pivotal roles in the pathophysiology of diabetes mellitus and its vascular complications. The present study aimed to investigate the anti-glycation properties of essential oils obtained from different parts of Juniperus communis subsp. hemisphaerica. The branchlets of male tree (BMT) and branchlets of female (BFT) tree, and fruits of J. communis subsp. hemisphaerica were extracted using steam distillation method. The oils were phytochemically analyzed using gas chromatography-mass spectrometry. Anti-glycation properties were evaluated using hemoglobin and insulin glycation assays. Overall, 18 volatile components were identified in the J. communis subsp. hemisphaerica oils, amounting to 82.1%, 100.0% and 96.4% of the BMT, BFT and fruit oils, respectively. Promising inhibitory activity was observed from all concentrations of the tested oils in the hemoglobin and insulin glycation assays. The inhibitory activities peaked to 89.9% (BFT oil; 200 μg mL-1) and 81.0% (BFT oil; 600 μg mL-1) in the hemoglobin and insulin glycation assays, respectively. The evidence from this study suggests that essential oils obtained from the fruits and branchlets of J. communis subsp. hemisphaerica possess anti-glycation properties. These activities may find implication for the prevention and treatment of diabetic complications. PMID:25657787

Inhibition of protein glycation by essential oils of branchlets and fruits of Juniperus communis subsp. hemisphaerica.

PubMed

Asgary, S; Naderi, G A; Shams Ardekani, M R; Sahebkar, A; Airin, A; Aslani, S; Kasher, T; Emami, S A

2014-01-01

Oxidative stress and protein glycation play pivotal roles in the pathophysiology of diabetes mellitus and its vascular complications. The present study aimed to investigate the anti-glycation properties of essential oils obtained from different parts of Juniperus communis subsp. hemisphaerica. The branchlets of male tree (BMT) and branchlets of female (BFT) tree, and fruits of J. communis subsp. hemisphaerica were extracted using steam distillation method. The oils were phytochemically analyzed using gas chromatography-mass spectrometry. Anti-glycation properties were evaluated using hemoglobin and insulin glycation assays. Overall, 18 volatile components were identified in the J. communis subsp. hemisphaerica oils, amounting to 82.1%, 100.0% and 96.4% of the BMT, BFT and fruit oils, respectively. Promising inhibitory activity was observed from all concentrations of the tested oils in the hemoglobin and insulin glycation assays. The inhibitory activities peaked to 89.9% (BFT oil; 200 μg mL(-1)) and 81.0% (BFT oil; 600 μg mL(-1)) in the hemoglobin and insulin glycation assays, respectively. The evidence from this study suggests that essential oils obtained from the fruits and branchlets of J. communis subsp. hemisphaerica possess anti-glycation properties. These activities may find implication for the prevention and treatment of diabetic complications.

So close and yet so far – Molecular Microbiology of Campylobacter fetus subspecies

PubMed Central

Sprenger, H.; Zechner, E. L.; Gorkiewicz, G.

2012-01-01

Campylobacter fetus comprises two subspecies, C. fetus subsp. fetus and C. fetus subsp. venerealis, which are considered emerging pathogens in humans and animals. Comparisons at the genome level have revealed modest subspecies-specific variation; nevertheless, these two subspecies show distinct host and niche preferences. C. fetus subsp. fetus is a commensal and pathogen of domesticated animals that can be transmitted to humans via contaminated food. The clinical features of human infection can be severe, especially in impaired hosts. In contrast, C. fetus subsp. venerealis is a sexually transmitted pathogen essentially restricted to cattle. Infections leading to bovine venereal campylobacteriosis cause substantial economic losses due to abortion and infertility. Recent genome sequencing of the two subspecies has advanced our understanding of C. fetus adaptations through comparative genomics and the identification of subspecies-specific gene regions predicted to be involved in pathogenesis. The most striking difference between the subspecies is the highly subspecies-specific association of a pathogenicity island in the C. fetus subsp. venerealis chromosome. The inserted region encodes a Type 4 secretion system, which contributes to virulence properties of this organism in vitro. This review describes the main differences in epidemiological, phenotypic, and molecular characteristics of the two subspecies and summarizes recent advances towards understanding the molecular mechanisms of C. fetus pathogenesis. PMID:24611123

A 38-Kilobase Pathogenicity Island Specific for Mycobacterium avium subsp. paratuberculosis Encodes Cell Surface Proteins Expressed in the Host

PubMed Central

Stratmann, Janin; Strommenger, Birgit; Goethe, Ralph; Dohmann, Karen; Gerlach, Gerald-F.; Stevenson, Karen; Li, Ling-ling; Zhang, Qing; Kapur, Vivek; Bull, Tim J.

2004-01-01

We have used representational difference analysis to identify a novel Mycobacterium avium subsp. paratuberculosis-specific ABC transporter operon (mpt), which comprises six open reading frames designated mptA to -F and is immediately preceded by two putative Fur boxes. Functional genomics revealed that the mpt operon is flanked on one end by a fep cluster encoding proteins involved in the uptake of Fe3+ and on the other end by a sid cluster encoding non-ribosome-dependent heterocyclic siderophore synthases. Together these genes form a 38-kb M. avium subsp. paratuberculosis-specific locus flanked by an insertion sequence similar to IS1110. Expression studies using Western blot analyses showed that MptC is present in the envelope fraction of M. avium subsp. paratuberculosis. The MptD protein was shown to be surface exposed, using a specific phage (fMptD) isolated from a phage-peptide library, by differential screening of Mycobacterium smegmatis transformants. The phage fMptD-derived peptide could be used in a peptide-mediated capture PCR with milk from infected dairy herds, thereby showing surface-exposed expression of the MptD protein in the host. Together, these data suggest that the 38-kb locus constitutes an M. avium subsp. paratuberculosis pathogenicity island. PMID:14977927

Bioaccessible Antioxidants in Milk Fermented by Bifidobacterium longum subsp. longum Strains

PubMed Central

Gagnon, Mérilie; Savard, Patricia; Rivière, Audrey; LaPointe, Gisèle

2015-01-01

Bifidobacterium longum subsp. longum is among the dominant species of the human gastrointestinal microbiota and could thus have potential as probiotics. New targets such as antioxidant properties have interest for beneficial effects on health. The objective of this study was to evaluate the bioaccessibility of antioxidants in milk fermented by selected B. longum subsp. longum strains during in vitro dynamic digestion. The antioxidant capacity of cell extracts from 38 strains, of which 32 belong to B. longum subsp. longum, was evaluated with the ORAC (oxygen radical absorbance capacity) method. On the basis of screening and gene sequence typing by multilocus locus sequence analysis (MLSA), five strains were chosen for fermenting reconstituted skim milk. Antioxidant capacity varied among the strains tested (P = 0.0009). Two strains of B. longum subsp. longum (CUETM 172 and 171) showed significantly higher ORAC values than the other bifidobacteria strains. However, there does not appear to be a relationship between gene sequence types and antioxidant capacity. The milk fermented by each of the five strains selected (CUETM 268, 172, 245, 247, or PRO 16-10) did not have higher initial ORAC values compared to the nonfermented milk samples. However, higher bioaccessibility of antioxidants in fermented milk (175–358%) was observed during digestion. PMID:25802836

Effect of chemical systemic acquired resistance elicitors on avenanthramide biosynthesis in oat (Avena sativa)

USDA-ARS?s Scientific Manuscript database

Oats produce a group of phenolic antioxidants termed avenanthramides. These metabolites are, among food crops, unique to oats and have shown some desirable nutritional characteristics, in experimental systems, such as inhibiting atherosclerotic plaque formation and reducing inflammatory responses. ...

Composition and potency characterization of Mycobacterium avium subsp. paratuberculosis purified protein derivatives

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) purified protein derivatives (PPDs) are immunologic reagents prepared from cultured filtrates of the type strain ATCC 19698. Traditional production consists of floating culture incubation at 37oC, organism inactivation by autoclaving, coarse filtrat...

Electrophoretic study of enzymes from cereal aphid populations : 4. Detection of hidden genetic variation within populations of the grain aphid Sitobion avenae (F.) (Hemiptera: Aphididae).

PubMed

Loxdale, H D; Rhodes, J A; Fox, J S

1985-07-01

A study of variation in three peptidases (PEP-3 to -5) in a parthenogenetic S. avenae field population at Rothamsted using serial one-dimensional polyacrylamide gel electrophoresis (involving changes of gel concentration and electrophoretic run-time) increased the overall number of "allozymes" (mobility variants) detected from 10 under standard conditions (6% gels, 2 h run-time) to 22, as well as revealing putative heterozygous banding patterns under some test conditions. However, an examination of another enzyme, 6-phosphogluconate dehydrogenase (6-PGD) in a sample collected at Rothamsted the following year failed, using a combination of serial methods (changes of gel concentration) and isoelectric focusing, to increase the total number of 6-PGD bands separated (seven, none of which appeared to be allelic in origin). Nevertheless, some major bands were split into several bands, whilst other infrequent bands were either gained or lost. The findings are briefly discussed.

The occurrence of two species of Entomophthorales (Entomophthoromycota), pathogens of Sitobion avenae and Myzus persicae (Hemiptera: Aphididae), in Tunisia.

PubMed

Ben Fekih, Ibtissem; Boukhris-Bouhachem, Sonia; Eilenberg, Jørgen; Allagui, Mohamed Bechir; Jensen, Annette Bruun

2013-01-01

The natural occurrence of entomophthoralean fungi pathogenic towards aphids on cereal and potato crops was investigated in the years 2009, 2010, and 2011. Infected aphids were sampled in three bioclimatic zones in Tunisia (Beja, Cap bon, and Kairouan) and fungal species were determined based on morphological characters such as shape, size, and number of nuclei in the primary conidia. Polymerase Chain Reaction (PCR) on the internal transcribed spacer 1 region (ITS1) was used to verify morphological determination. Both methods gave consistent results and we documented for the first time the natural occurrence of two fungal species from the order Entomophthorales (phylum Entomophthoromycota), Pandora neoaphidis and Entomophthora planchoniana. Both fungi were recorded on the aphid species Sitobion avenae and Myzus persicae on barley ears and potato leaves, respectively. Moreover, natural mixed infections by both species (P. neoaphidis and E. planchoniana) were documented on the target aphids. This investigation provides basic information of entomopathogenic fungi infecting economically important aphids in Tunisia.

Isolation of Mycobacterium avium subsp. paratuberculosis from Free-Ranging Birds and Mammals on Livestock Premises

PubMed Central

Corn, Joseph L.; Manning, Elizabeth J. B.; Sreevatsan, Srinand; Fischer, John R.

2005-01-01

Surveys for Mycobacterium avium subsp. paratuberculosis infection in free-ranging mammals and birds were conducted on nine dairy and beef cattle farms in Wisconsin and Georgia. Specimens were collected from 774 animals representing 25 mammalian and 22 avian species. Specimens of ileum, liver, intestinal lymph nodes, and feces were harvested from the larger mammals; a liver specimen and the gastrointestinal tract were harvested from birds and small mammals. Cultures were performed by using radiometric culture and acid-fast isolates were identified by 16S/IS900/IS1311 PCR and mycobactin dependency characteristics. M. avium subsp. paratuberculosis was cultured from tissues and feces from 39 samples from 30 animals representing nine mammalian and three avian species. The prevalence of infected wild animals by premises ranged from 2.7 to 8.3% in Wisconsin and from 0 to 6.0% in Georgia. Shedding was documented in seven (0.9%) animals: three raccoons, two armadillos, one opossum, and one feral cat. The use of two highly polymorphic short sequence repeat loci for analysis of 29 of the 39 strains identified 10 alleles. One allelic pattern broadly shared in domestic ruminants (“7,5”) appeared in approximately one-third of the wildlife M. avium subsp. paratuberculosis isolates studied. Given the few cases of shedding by free-ranging animals compared to the volume of contaminated manure produced by infected domestic ruminant livestock, contamination of the farm environment by infected wildlife was negligible. Wildlife may, however, have epidemiological significance for farms where M. avium subsp. paratuberculosis recently has been eliminated or on farms free of M. avium subsp. paratuberculosis but located in the geographic vicinity of farms with infected livestock. PMID:16269731

Intersubspecific Recombination in Xylella fastidiosa Strains Native to the United States: Infection of Novel Hosts Associated with an Unsuccessful Invasion

PubMed Central

Hopkins, Donald L.; Morano, Lisa D.; Russell, Stephanie E.; Stouthamer, Richard

2014-01-01

The bacterial pathogen Xylella fastidiosa infects xylem and causes disease in many plant species in the Americas. Different subspecies of this bacterium and different genotypes within subspecies infect different plant hosts, but the genetics of host adaptation are unknown. Here we examined the hypothesis that the introduction of novel genetic variation via intersubspecific homologous recombination (IHR) facilitates host shifts. We investigated IHR in 33 X. fastidiosa subsp. multiplex isolates previously identified as recombinant based on 8 loci (7 multilocus sequence typing [MLST] loci plus 1 locus). We found significant evidence of introgression from X. fastidiosa subsp. fastidiosa in 4 of the loci and, using published data, evidence of IHR in 6 of 9 additional loci. Our data showed that IHR regions in 2 of the 4 loci were inconsistent (12 mismatches) with X. fastidiosa subsp. fastidiosa alleles found in the United States but consistent with alleles from Central America. The other two loci were consistent with alleles from both regions. We propose that the recombinant forms all originated via genomewide recombination of one X. fastidiosa subsp. multiplex ancestor with one X. fastidiosa subsp. fastidiosa donor from Central America that was introduced into the United States but subsequently disappeared. Using all of the available data, 5 plant hosts of the recombinant types were identified, 3 of which also supported non-IHR X. fastidiosa subsp. multiplex, but 2 were unique to recombinant types from blueberry (7 isolates from Georgia, 3 from Florida); and blackberry (1 each from Florida and North Carolina), strongly supporting the hypothesis that IHR facilitated a host shift to blueberry and possibly blackberry. PMID:24296499

ANTIFUNGAL POTENTIAL OF LEAF EXTRACTS OF LEGUMINOUS TREES AGAINST SCLEROTIUM ROLFSII.

PubMed

Sana, Nighat; Shoaib, Amna; Javaid, Arshad

2016-01-01

Sclerotium rolfsii Sacc. is a destructive soil-borne plant pathogen that infects over 500 plant species and causes significant yield losses in many economically important plant species. Synthetic fungicides used to combat the menace also pollute the environment and cause health hazards. In order to search environmental friendly alternatives from natural resources, methanolic extracts of three leguminous tree species namely Acacia nilotica (L.) Willd. ex Delile subsp. indica (Benth.) Brenan, Prosopis juliflora (Sw.) DC. and Albizia lebbeck (L.) Benth. were evaluated for their antifungal activity against S. rolfsii and A. nilotica subsp. indica exhibited the maximum fungicidal potential. Two hundred grams dried leaf material of each of the three test plant species were extracted with methanol for two weeks. After filtration, methanol was evaporated on a rotary evaporator. Malt extract broth was used to make various concentrations of the crude methanolic extracts and their antifungal potential was determined by comparing the fungal biomass in various treatments with control. Chemical composition of methanolic leaf extract of A. nilotica subsp. indica was determined through GC-MS analysis. Methanolic leaf extract of A. nilotica subsp. indica showed the highest fungicidal activity. Fungal biomass was decreased by 17-55% due to various concentrations of this extract over control. Different concentrations of P. juliflora reduced fungal biomass by 3-52%. Fourteen compounds were identified in methanolic extract of A. nilotica subsp. indica . 9,12,15-octadecatrienoic acid, methyl ester, (Z,Z,Z,)- (16.59%) was the most abundant compound followed by 1-pentanol, 2 methyl-, acetate (14.80%); hexanedioic acid, dimethyl ester (13.10%) and cyclotriaconta- 1, 7, 16, 22-tetraone (10.28%). This study concludes that methanolic leaf extract of A. nilotica subsp. indica can be used for management of S. rolfsii .

ANTIFUNGAL POTENTIAL OF LEAF EXTRACTS OF LEGUMINOUS TREES AGAINST SCLEROTIUM ROLFSII

PubMed Central

Sana, Nighat; Shoaib, Amna; Javaid, Arshad

2016-01-01

Background: Sclerotium rolfsii Sacc. is a destructive soil-borne plant pathogen that infects over 500 plant species and causes significant yield losses in many economically important plant species. Synthetic fungicides used to combat the menace also pollute the environment and cause health hazards. In order to search environmental friendly alternatives from natural resources, methanolic extracts of three leguminous tree species namely Acacia nilotica (L.) Willd. ex Delile subsp. indica (Benth.) Brenan, Prosopis juliflora (Sw.) DC. and Albizia lebbeck (L.) Benth. were evaluated for their antifungal activity against S. rolfsii and A. nilotica subsp. indica exhibited the maximum fungicidal potential. Materials and Methods: Two hundred grams dried leaf material of each of the three test plant species were extracted with methanol for two weeks. After filtration, methanol was evaporated on a rotary evaporator. Malt extract broth was used to make various concentrations of the crude methanolic extracts and their antifungal potential was determined by comparing the fungal biomass in various treatments with control. Chemical composition of methanolic leaf extract of A. nilotica subsp. indica was determined through GC-MS analysis. Results: Methanolic leaf extract of A. nilotica subsp. indica showed the highest fungicidal activity. Fungal biomass was decreased by 17-55% due to various concentrations of this extract over control. Different concentrations of P. juliflora reduced fungal biomass by 3-52%. Fourteen compounds were identified in methanolic extract of A. nilotica subsp. indica. 9,12,15-octadecatrienoic acid, methyl ester, (Z,Z,Z,)- (16.59%) was the most abundant compound followed by 1-pentanol, 2 methyl-, acetate (14.80%); hexanedioic acid, dimethyl ester (13.10%) and cyclotriaconta- 1, 7, 16, 22-tetraone (10.28%). Conclusion: This study concludes that methanolic leaf extract of A. nilotica subsp. indica can be used for management of S. rolfsii. PMID:28487894

Development and Evaluation of a Novel Multicopy-Element-Targeting Triplex PCR for Detection of Mycobacterium avium subsp. paratuberculosis in Feces

PubMed Central

Garrido, Joseba M.; Molina, Elena; Geijo, María V.; Elguezabal, Natalia; Vázquez, Patricia; Juste, Ramón A.

2014-01-01

The enteropathy called paratuberculosis (PTB), which mainly affects ruminants and has a worldwide distribution, is caused by Mycobacterium avium subsp. paratuberculosis. This disease significantly reduces the cost-effectiveness of ruminant farms, and therefore, reliable and rapid detection methods are needed to control the spread of the bacterium in livestock and in the environment. The aim of this study was to identify a specific and sensitive combination of DNA extraction and amplification to detect M. avium subsp. paratuberculosis in feces. Negative bovine fecal samples were inoculated with increasing concentrations of two different bacterial strains (field and reference) to compare the performance of four extraction and five amplification protocols. The best results were obtained using the JohnePrep and MagMax extraction kits combined with an in-house triplex real-time PCR designed to detect IS900, ISMap02 (an insertion sequence of M. avium subsp. paratuberculosis present in 6 copies per genome), and an internal amplification control DNA simultaneously. These combinations detected 10 M. avium subsp. paratuberculosis cells/g of spiked feces. The triplex PCR detected 1 fg of genomic DNA extracted from the reference strain K10. The performance of the robotized version of the MagMax extraction kit combined with the IS900 and ISMap02 PCR was further evaluated using 615 archival fecal samples from the first sampling of nine Friesian cattle herds included in a PTB control program and followed up for at least 4 years. The analysis of the results obtained in this survey demonstrated that the diagnostic method was highly specific and sensitive for the detection of M. avium subsp. paratuberculosis in fecal samples from cattle and a very valuable tool to be used in PTB control programs. PMID:24727272

Large-Scale Intersubspecific Recombination in the Plant-Pathogenic Bacterium Xylella fastidiosa Is Associated with the Host Shift to Mulberry

PubMed Central

Schuenzel, Erin L.; Scally, Mark; Bromley, Robin E.; Stouthamer, Richard

2014-01-01

Homologous recombination plays an important role in the structuring of genetic variation of many bacteria; however, its importance in adaptive evolution is not well established. We investigated the association of intersubspecific homologous recombination (IHR) with the shift to a novel host (mulberry) by the plant-pathogenic bacterium Xylella fastidiosa. Mulberry leaf scorch was identified about 25 years ago in native red mulberry in the eastern United States and has spread to introduced white mulberry in California. Comparing a sequence of 8 genes (4,706 bp) from 21 mulberry-type isolates to published data (352 isolates representing all subspecies), we confirmed previous indications that the mulberry isolates define a group distinct from the 4 subspecies, and we propose naming the taxon X. fastidiosa subsp. morus. The ancestry of its gene sequences was mixed, with 4 derived from X. fastidiosa subsp. fastidiosa (introduced from Central America), 3 from X. fastidiosa subsp. multiplex (considered native to the United States), and 1 chimeric, demonstrating that this group originated by large-scale IHR. The very low within-type genetic variation (0.08% site polymorphism), plus the apparent inability of native X. fastidiosa subsp. multiplex to infect mulberry, suggests that this host shift was achieved after strong selection acted on genetic variants created by IHR. Sequence data indicate that a single ancestral IHR event gave rise not only to X. fastidiosa subsp. morus but also to the X. fastidiosa subsp. multiplex recombinant group which infects several hosts but is the only type naturally infecting blueberry, thus implicating this IHR in the invasion of at least two novel native hosts, mulberry and blueberry. PMID:24610840

Large-scale intersubspecific recombination in the plant-pathogenic bacterium Xylella fastidiosa is associated with the host shift to mulberry.

PubMed

Nunney, Leonard; Schuenzel, Erin L; Scally, Mark; Bromley, Robin E; Stouthamer, Richard

2014-05-01

Homologous recombination plays an important role in the structuring of genetic variation of many bacteria; however, its importance in adaptive evolution is not well established. We investigated the association of intersubspecific homologous recombination (IHR) with the shift to a novel host (mulberry) by the plant-pathogenic bacterium Xylella fastidiosa. Mulberry leaf scorch was identified about 25 years ago in native red mulberry in the eastern United States and has spread to introduced white mulberry in California. Comparing a sequence of 8 genes (4,706 bp) from 21 mulberry-type isolates to published data (352 isolates representing all subspecies), we confirmed previous indications that the mulberry isolates define a group distinct from the 4 subspecies, and we propose naming the taxon X. fastidiosa subsp. morus. The ancestry of its gene sequences was mixed, with 4 derived from X. fastidiosa subsp. fastidiosa (introduced from Central America), 3 from X. fastidiosa subsp. multiplex (considered native to the United States), and 1 chimeric, demonstrating that this group originated by large-scale IHR. The very low within-type genetic variation (0.08% site polymorphism), plus the apparent inability of native X. fastidiosa subsp. multiplex to infect mulberry, suggests that this host shift was achieved after strong selection acted on genetic variants created by IHR. Sequence data indicate that a single ancestral IHR event gave rise not only to X. fastidiosa subsp. morus but also to the X. fastidiosa subsp. multiplex recombinant group which infects several hosts but is the only type naturally infecting blueberry, thus implicating this IHR in the invasion of at least two novel native hosts, mulberry and blueberry.

Intersubspecific recombination in Xylella fastidiosa Strains native to the United States: infection of novel hosts associated with an unsuccessful invasion.

PubMed

Nunney, Leonard; Hopkins, Donald L; Morano, Lisa D; Russell, Stephanie E; Stouthamer, Richard

2014-02-01

The bacterial pathogen Xylella fastidiosa infects xylem and causes disease in many plant species in the Americas. Different subspecies of this bacterium and different genotypes within subspecies infect different plant hosts, but the genetics of host adaptation are unknown. Here we examined the hypothesis that the introduction of novel genetic variation via intersubspecific homologous recombination (IHR) facilitates host shifts. We investigated IHR in 33 X. fastidiosa subsp. multiplex isolates previously identified as recombinant based on 8 loci (7 multilocus sequence typing [MLST] loci plus 1 locus). We found significant evidence of introgression from X. fastidiosa subsp. fastidiosa in 4 of the loci and, using published data, evidence of IHR in 6 of 9 additional loci. Our data showed that IHR regions in 2 of the 4 loci were inconsistent (12 mismatches) with X. fastidiosa subsp. fastidiosa alleles found in the United States but consistent with alleles from Central America. The other two loci were consistent with alleles from both regions. We propose that the recombinant forms all originated via genomewide recombination of one X. fastidiosa subsp. multiplex ancestor with one X. fastidiosa subsp. fastidiosa donor from Central America that was introduced into the United States but subsequently disappeared. Using all of the available data, 5 plant hosts of the recombinant types were identified, 3 of which also supported non-IHR X. fastidiosa subsp. multiplex, but 2 were unique to recombinant types from blueberry (7 isolates from Georgia, 3 from Florida); and blackberry (1 each from Florida and North Carolina), strongly supporting the hypothesis that IHR facilitated a host shift to blueberry and possibly blackberry.

Production of Angiotensin-I-Converting-Enzyme-Inhibitory Peptides in Fermented Milks Started by Lactobacillus delbrueckii subsp. bulgaricus SS1 and Lactococcus lactis subsp. cremoris FT4

PubMed Central

Gobbetti, M.; Ferranti, P.; Smacchi, E.; Goffredi, F.; Addeo, F.

2000-01-01

Two fermented milks containing angiotensin-I-converting-enzyme (ACE)-inhibitory peptides were produced by using selected Lactobacillus delbrueckii subsp. bulgaricus SS1 and L. lactis subsp. cremoris FT4. The pH 4.6-soluble nitrogen fraction of the two fermented milks was fractionated by reversed-phase fast-protein liquid chromatography. The fractions which showed the highest ACE-inhibitory indexes were further purified, and the related peptides were sequenced by tandem fast atom bombardment-mass spectrometry. The most inhibitory fractions of the milk fermented by L. delbrueckii subsp. bulgaricus SS1 contained the sequences of β-casein (β-CN) fragment 6-14 (f6-14), f7-14, f73-82, f74-82, and f75-82. Those from the milk fermented by L. lactis subsp. cremoris FT4 contained the sequences of β-CN f7-14, f47-52, and f169-175 and κ-CN f155-160 and f152-160. Most of these sequences had features in common with other ACE-inhibitory peptides reported in the literature. In particular, the β-CN f47-52 sequence had high homology with that of angiotensin-II. Some of these peptides were chemically synthesized. The 50% inhibitory concentrations (IC50s) of the crude purified fractions containing the peptide mixture were very low (8.0 to 11.2 mg/liter). When the synthesized peptides were used individually, the ACE-inhibitory activity was confirmed but the IC50s increased considerably. A strengthened inhibitory effect of the peptide mixtures with respect to the activity of individual peptides was presumed. Once generated, the inhibitory peptides were resistant to further proteolysis either during dairy processing or by trypsin and chymotrypsin. PMID:10966406

In Silico Identification of Epitopes in Mycobacterium avium subsp. paratuberculosis Proteins That Were Upregulated under Stress Conditions

PubMed Central

Gurung, Ratna B.; Purdie, Auriol C.; Begg, Douglas J.

2012-01-01

Johne's disease in ruminants is caused by Mycobacterium avium subsp. paratuberculosis. Diagnosis of M. avium subsp. paratuberculosis infection is difficult, especially in the early stages. To date, ideal antigen candidates are not available for efficient immunization or immunodiagnosis. This study reports the in silico selection and subsequent analysis of epitopes of M. avium subsp. paratuberculosis proteins that were found to be upregulated under stress conditions as a means to identify immunogenic candidate proteins. Previous studies have reported differential regulation of proteins when M. avium subsp. paratuberculosis is exposed to stressors which induce a response similar to dormancy. Dormancy may be involved in evading host defense mechanisms, and the host may also mount an immune response against these proteins. Twenty-five M. avium subsp. paratuberculosis proteins that were previously identified as being upregulated under in vitro stress conditions were analyzed for B and T cell epitopes by use of the prediction tools at the Immune Epitope Database and Analysis Resource. Major histocompatibility complex class I T cell epitopes were predicted using an artificial neural network method, and class II T cell epitopes were predicted using the consensus method. Conformational B cell epitopes were predicted from the relevant three-dimensional structure template for each protein. Based on the greatest number of predicted epitopes, eight proteins (MAP2698c [encoded by desA2], MAP2312c [encoded by fadE19], MAP3651c [encoded by fadE3_2], MAP2872c [encoded by fabG5_2], MAP3523c [encoded by oxcA], MAP0187c [encoded by sodA], and the hypothetical proteins MAP3567 and MAP1168c) were identified as potential candidates for study of antibody- and cell-mediated immune responses within infected hosts. PMID:22496492

Factors affecting isolation and identification of Mycobacterium avium subsp. paratuberculosis from fecal and tissue samples in a liquid culture system.

PubMed

Whittington, Richard J

2009-03-01

Culture of Mycobacterium avium subsp. paratuberculosis is the definitive diagnostic test for Johne's disease, a chronic granulomatous enteropathy of animals. Compared to solid media, the identification of all strains of the organism in liquid media can be more difficult because the appearance of colonies and mycobactin dependence are not observable, and the growth of other organisms needs to be distinguished, commonly by PCR. Factors affecting the isolation rate of S strains and the contamination rate in modified Middlebrook 7H9 broth (Bactec 12B) and 7H10 agar were studied using 11,598 fecal samples and 2,577 tissue samples from sheep from 1,421 farms over 10 years. Minimization of contamination in Bactec cultures required the avoidance of the carryover of fecal particles from the first sedimentation step in the double-incubation centrifugation method, and contamination was reduced significantly by incubating the sample in a solution containing vancomycin, amphotericin B, and nalidixic acid for 3 days compared to 2 days. The growth of irrelevant microorganisms confounded the identification of M. avium subsp. paratuberculosis in liquid culture by inhibiting IS900 PCR and in solid medium culture by inhibiting the growth of M. avium subsp. paratuberculosis or obscuring colonies. The contamination of samples was clustered in certain laboratory submissions and was reduced by including ampicillin in Bactec medium without affecting the odds of isolation of M. avium subsp. paratuberculosis. The long-term contamination rate for fecal cultures was about 7%, and that for tissue cultures was <0.2%. Liquid medium was more sensitive than solid medium culture for M. avium subsp. paratuberculosis. The applicability of these findings for C strains is discussed.

Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus.

PubMed

Jensen, Anders; Scholz, Christian F P; Kilian, Mogens

2016-11-01

The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus. The recently described strains of the species Streptococcus dentisani includes one previously referred to as 'S. mitis biovar 2'. Together with S. oralis, S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.

Genetic Variability and Population Structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae) Based on AFLP Analysis

PubMed Central

Yu, Yi; Fan, Qiang; Shen, Rujiang; Guo, Wei; Jin, Jianhua; Cui, Dafang; Liao, Wenbo

2014-01-01

Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP) fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and “excess flowers production, but little fruit set”. It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible. PMID:25250583

Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988.

PubMed

Vancanneyt, M; Mengaud, J; Cleenwerck, I; Vanhonacker, K; Hoste, B; Dawyndt, P; Degivry, M C; Ringuet, D; Janssens, D; Swings, J

2004-03-01

Fourteen homofermentative lactic acid bacteria that were isolated from kefir grains and kefir fermented milks were assigned to either Lactobacillus kefiranofaciens or Lactobacillus kefirgranum, based on their characteristic morphotypes, phenotypic features and SDS-PAGE profiles of whole-cell proteins. Further genotypic analyses on representative strains from both taxa demonstrated that L. kefiranofaciens and L. kefirgranum share 100 % 16S rDNA sequence similarity and belong phylogenetically to the Lactobacillus acidophilus species group. DNA-DNA binding values of >79 % and analogous DNA G+C contents of 37-38 mol% showed that the strains studied belonged to one species: L. kefirgranum is a later synonym of L. kefiranofaciens. An emended description is proposed for L. kefiranofaciens. Due to the specific morphological and biochemical characteristics of these taxa in kefir grain formation, it is proposed that L. kefirgranum should be reclassified as L. kefiranofaciens subsp. kefirgranum subsp. nov.

Antioxidant Activity of the Essential Oils of Different Parts of Juniperus excelsa M. Bieb. subsp. excelsa and J. excelsa M. Bieb. subsp. polycarpos (K. Koch) Takhtajan (Cupressaceae)

PubMed Central

Emami, Sayyed Ahmad; Abedindo, Bibi Fatemeh; Hassanzadeh-Khayyat, Mohammad

2011-01-01

The essential oils of branchlets and fruits of Juniperus excelsa subsp. excelsa and Juniperus excelsa subsp. polycarpos were examined for their antioxidant activity. The compositions of the essential oils were studied by GC and GC-MS. To evaluation the antioxidants activity of the volatile oils, pure components and positive controls at different concentrations, thin-layer chromatography (TLC) screening methods, diphenylpicrylhydrazyl (DPPH) assay, deoxyribose degradation test and modified deoxyribose degradation test were employed. The results of the present study demonstrate some antioxidant activity for the tested essential oils obtained from various parts of both plants. It indicates that the use of these essential oils, in very low concentrations, may be useful as a natural preservative. However before any final conclusion, it is suggested that the antioxidant activity of these oils should also be evaluated by using lipid solvent system methods. PMID:24250416

New Type of Antimicrobial Protein Produced by the Plant Pathogen Clavibacter michiganensis subsp. michiganensis

PubMed Central

Liu, Zhanliang; Ma, Ping; Holtsmark, Ingrid; Skaugen, Morten; Eijsink, Vincent G. H.

2013-01-01

It has previously been shown that the tomato pathogen Clavibacter michiganensis subsp. michiganensis secretes a 14-kDa protein, C. michiganensis subsp. michiganensis AMP-I (CmmAMP-I), that inhibits growth of Clavibacter michiganensis subsp. sepedonicus, the causal agent of bacterial ring rot of potato. Using sequences obtained from tryptic fragments, we have identified the gene encoding CmmAMP-I and we have recombinantly produced the protein with an N-terminal intein tag. The gene sequence showed that CmmAMP-I contains a typical N-terminal signal peptide for Sec-dependent secretion. The recombinant protein was highly active, with 50% growth inhibition (IC50) of approximately 10 pmol, but was not toxic to potato leaves or tubers. CmmAMP-I does not resemble any known protein and thus represents a completely new type of bacteriocin. Due to its high antimicrobial activity and its very narrow inhibitory spectrum, CmmAMP-1 may be of interest in combating potato ring rot disease. PMID:23851100

Lymphoproliferative and Gamma Interferon Responses to Stress-Regulated Mycobacterium avium subsp. paratuberculosis Recombinant Proteins

PubMed Central

Gurung, Ratna B.; Begg, Douglas J.; Purdie, Auriol C.; de Silva, Kumudika; Bannantine, John P.

2014-01-01

Johne's disease in ruminants is a chronic infection of the intestines caused by Mycobacterium avium subsp. paratuberculosis. An important strategy to control disease is early detection, and a potentially efficient method for early detection is measurement of cell-mediated immune responses developed by the host in response to exposure or infection. One method is to measure lymphoproliferation and cytokine release from the host cells when exposed to the organism or parts of the organism. In this study, 10 recombinant M. avium subsp. paratuberculosis proteins known to be upregulated under in vitro stress conditions were evaluated by examining their ability to evoke memory as a result of exposure by vaccination or oral challenge with live Mycobacterium avium subsp. paratuberculosis. Out of 10 proteins, MAP2698c was found to induce higher cell-mediated immune responses in vaccinated and challenged sheep in comparison to healthy controls. The findings suggest that not all stress-regulated proteins have the diagnostic potential to detect cell-mediated immune responses in ovine paratuberculosis. PMID:24695774

Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils.

PubMed

Aanniz, Tarik; Ouadghiri, Mouna; Melloul, Marouane; Swings, Jean; Elfahime, Elmostafa; Ibijbijen, Jamal; Ismaili, Mohamed; Amar, Mohamed

2015-06-01

The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. subtilis (subsp. spizizenii (2) and subsp. inaquosurum (6)), B. amyloliquefaciens (subsp. amyloliquefaciens (4) and subsp. plantarum (4)), B. tequilensis (3), B. pumilus (3) and Bacillus sp. (19). Only six isolates (2.5%) belonged to the genus Aeribacillus represented by A. pallidus (4) and Aeribacillus sp. (2). In this study, B. aerius and B. tequilensis are described for the first time as thermophilic bacteria. Moreover, 71.25%, 50.41% and 5.41% of total strains exhibited high amylolytic, proteolytic or cellulolytic activity respectively.

Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils

PubMed Central

Aanniz, Tarik; Ouadghiri, Mouna; Melloul, Marouane; Swings, Jean; Elfahime, Elmostafa; Ibijbijen, Jamal; Ismaili, Mohamed; Amar, Mohamed

2015-01-01

The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. subtilis (subsp. spizizenii (2) and subsp. inaquosurum (6)), B. amyloliquefaciens (subsp. amyloliquefaciens (4) and subsp. plantarum (4)), B. tequilensis (3), B. pumilus (3) and Bacillus sp. (19). Only six isolates (2.5%) belonged to the genus Aeribacillus represented by A. pallidus (4) and Aeribacillus sp. (2). In this study, B. aerius and B. tequilensis are described for the first time as thermophilic bacteria. Moreover, 71.25%, 50.41% and 5.41% of total strains exhibited high amylolytic, proteolytic or cellulolytic activity respectively. PMID:26273259

Marked Differences in Mucosal Immune Responses Induced in Ileal versus Jejunal Peyer’s Patches to Mycobacterium avium subsp. paratuberculosis Secreted Proteins following Targeted Enteric Infection in Young Calves

PubMed Central

Facciuolo, Antonio; Gonzalez-Cano, Patricia; Napper, Scott; Griebel, Philip J.

2016-01-01

In cattle, Mycobacterium avium subsp. paratuberculosis infection is primarily mediated through M cells overlying Peyer’s patches (PP) in the ileum. The capacity of M. avium subsp. paratuberculosis to invade ileal PP (IPP) versus discrete PP in the jejunum (JPP) and subsequent differences in mucosal immune responses were investigated. Intestinal segments were surgically prepared in both mid-jejunum, containing two JPPs, and in terminal small intestine containing continuous IPP. M. avium subsp. paratuberculosis (109 CFU) was injected into the lumen of half of each intestinal segment when calves were 10–14 days-old and infection confirmed 1–2 months later by PCR and immunohistochemistry. Thirteen recombinant M. avium subsp. paratuberculosis proteins, previously identified as immunogenic, were used to analyze pathogen-specific B- and T-cell responses in PP and mesenteric lymph nodes. IgA plasma cell responses to 9 of 13 recombinant proteins were detected in JPP but not in IPP. Secretory IgA reacting in ELISA with 9 of the 13 recombinant proteins was detected in luminal contents from both jejunal and ileal segments. These observations support the conclusion that pathogen-specific IgA B cells were induced in JPP but not IPP early after a primary infection. The presence of secretory IgA in intestinal contents is consistent with dissemination of IgA plasma cells from the identified mucosa-associated immune induction sites. This is the first direct evidence for M. avium subsp. paratuberculosis uptake by bovine JPP and for local induction of pathogen-specific IgA plasma cell responses after enteric infection. We also provide evidence that bacterial invasion of IPP, a primary B lymphoid tissue, provides a novel strategy to evade induction of mucosal immune responses. Over 60% of PPs in the newborn calf small intestine is primary lymphoid tissue, which has significant implications when designing oral vaccines or diagnostic tests to detect early M. avium subsp. paratuberculosis infections. PMID:27387969

Bacterial symbionts, Buchnera, and starvation on wing dimorphism in English grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae)

USDA-ARS?s Scientific Manuscript database

Wing dimorphism in aphids can be affected by multiple cues including both biotic (nutrition, crowding, interspecific interactions, the presence of natural enemies, maternal and transgenerational effects, and alarm pheromone) and abiotic factors (temperature, humidity, and photoperiod). Virtually al...

Termination of cover crops using rollers/crimpers

USDA-ARS?s Scientific Manuscript database

An integral component of conservation agriculture systems is the use of a high-residue winter cover crop; however, terminating cover crops is an addition expense and planting into high-residue can be a challenge. An experiment was conducted using black oat (Avena strigosa Schreb.), rye (Secale cere...

Draft Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a Citrate-Fermenting Strain.

PubMed

Zuljan, Federico; Espariz, Martín; Blancato, Victor S; Esteban, Luis; Alarcón, Sergio; Magni, Christian

2016-02-04

We report the draft genome sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a natural strain isolated from artisanal cheese from northwest Argentina. L. lactis subsp. lactis bv. diacetylactis is one of the most important microorganisms used as starter culture around the world. The CRL264 strain constitutes a model microorganism in the studies on the generation of aroma compounds (diacetyl, acetoin, and 2,3-butanediol) by lactic acid bacteria. Our genome analysis shows similar genetic organization to other available genomes of L. lactis bv. diacetylactis strains. Copyright © 2016 Zuljan et al.

A Mycobacterium avium subsp. paratuberculosis predicted serine protease is associated with acid stress and intraphagosomal survival

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is an intracellular pathogen that persists inside host macrophages despite severe oxidative stress and nutrient deprivation. Intrabacterial pH homeostasis is vital to pathogenic mycobacteria to preserve cellular biological processes and stability of ...

Mycobacterium avium subsp. paratuberculosis infection, immunology and pathology of livestock

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) infection in ruminants leads to a chronic and progressive enteric disease (Johne’s disease) that results in loss of intestinal function, poor body condition, and eventual death. Transmission is primarily through a fecal-oral route in neonates but con...

Genome Sequence of Lactobacillus sakei subsp. sakei LS25, a Commercial Starter Culture Strain for Fermented Sausage.

PubMed

McLeod, Anette; Brede, Dag Anders; Rud, Ida; Axelsson, Lars

2013-07-11

Lactobacillus sakei is a lactic acid bacterium associated primarily with fermented meat and fish. Here, we present the draft genome sequence of L. sakei subsp. sakei strain LS25, a commercial starter culture strain for fermented sausage.

Experimental infection of dogs with Bartonella henselae and Bartonella vinsonii subsp. berkhoffii.

PubMed

Balakrishnan, Nandhakumar; Cherry, Natalie A; Linder, Keith E; Pierce, Eric; Sontakke, Neal; Hegarty, Barbara C; Bradley, Julie M; Maggi, Ricardo G; Breitschwerdt, Edward B

2013-11-15

The lack of a suitable infection model remains an important obstacle for the pathophysiological understanding of Bartonella spp. The following pilot study was designed to determine whether cell culture-grown Bartonella henselae SA2 and Bartonella vinsonii subsp. berkhoffii genotype III would cause persistent bacteremia in dogs. Pre-inoculation screening established that two laboratory-raised Golden retrievers were naturally-infected with Bartonella koehlerae. Despite prior infection, one dog each was inoculated subcutaneously with 5 × 10(4)B. henselae (SA2 strain) or 3 × 10(4)B. vinsonii subsp. berkhoffii genotype III. Dogs were bled weekly for serological testing and culture using Bartonella alpha proteobacteria growth medium (BAPGM) diagnostic platform. Dog 1 seroconverted to B. henselae and Dog 2 seroconverted to B. vinsonii subsp. berkhoffii genotype III. Throughout the study period, Bartonella spp. DNA was neither amplified nor isolated in ante-mortem BAPGM enrichment blood cultures. B. henselae SA2 was isolated from a postmortem bone marrow from Dog 1 and B. koehlerae DNA was amplified from postmortem lung from Dog 2 following BAPGM enrichment culture. Limitations include lack of uninfected controls, a potentially suboptimal B. vinsonii subsp. berkhoffii inoculum and a relatively short duration of study. We conclude that following intradermal infection, sequestration of Bartonella spp. in tissues may limit diagnostic detection of these bacteria in dog blood samples. Copyright © 2013 Elsevier B.V. All rights reserved.

Increased Production of Hydrogen Peroxide by Lactobacillus delbrueckii subsp. bulgaricus upon Aeration: Involvement of an NADH Oxidase in Oxidative Stress

PubMed Central

Marty-Teysset, C.; de la Torre, F.; Garel, J.-R.

2000-01-01

The growth of Lactobacillus delbrueckii subsp. bulgaricus (L. delbrueckii subsp. bulgaricus) on lactose was altered upon aerating the cultures by agitation. Aeration caused the bacteria to enter early into stationary phase, thus reducing markedly the biomass production but without modifying the maximum growth rate. The early entry into stationary phase of aerated cultures was probably related to the accumulation of hydrogen peroxide in the medium. Indeed, the concentration of hydrogen peroxide in aerated cultures was two to three times higher than in unaerated ones. Also, a similar shift from exponential to stationary phase could be induced in unaerated cultures by adding increasing concentrations of hydrogen peroxide. A significant fraction of the hydrogen peroxide produced by L. delbrueckii subsp. bulgaricus originated from the reduction of molecular oxygen by NADH catalyzed by an NADH:H2O2 oxidase. The specific activity of this NADH oxidase was the same in aerated and unaerated cultures, suggesting that the amount of this enzyme was not directly regulated by oxygen. Aeration did not change the homolactic character of lactose fermentation by L. delbrueckii subsp. bulgaricus and most of the NADH was reoxidized by lactate dehydrogenase with pyruvate. This indicated that NADH oxidase had no (or a very small) energetic role and could be involved in eliminating oxygen. PMID:10618234

Isolation of Bartonella henselae, Bartonella koehlerae subsp. koehlerae, Bartonella koehlerae subsp. bothieri and a new subspecies of B. koehlerae from free-ranging lions (Panthera leo) from South Africa, cheetahs (Acinonyx jubatus) from Namibia and captive cheetahs from California.

PubMed

Molia, S; Kasten, R W; Stuckey, M J; Boulouis, H J; Allen, J; Borgo, G M; Koehler, J E; Chang, C C; Chomel, B B

2016-11-01

Bartonellae are blood- and vector-borne Gram-negative bacteria, recognized as emerging pathogens. Whole-blood samples were collected from 58 free-ranging lions (Panthera leo) in South Africa and 17 cheetahs (Acinonyx jubatus) from Namibia. Blood samples were also collected from 11 cheetahs (more than once for some of them) at the San Diego Wildlife Safari Park. Bacteria were isolated from the blood of three (5%) lions, one (6%) Namibian cheetah and eight (73%) cheetahs from California. The lion Bartonella isolates were identified as B. henselae (two isolates) and B. koehlerae subsp. koehlerae. The Namibian cheetah strain was close but distinct from isolates from North American wild felids and clustered between B. henselae and B. koehlerae. It should be considered as a new subspecies of B. koehlerae. All the Californian semi-captive cheetah isolates were different from B. henselae or B. koehlerae subsp. koehlerae and from the Namibian cheetah isolate. They were also distinct from the strains isolated from Californian mountain lions (Felis concolor) and clustered with strains of B. koehlerae subsp. bothieri isolated from free-ranging bobcats (Lynx rufus) in California. Therefore, it is likely that these captive cheetahs became infected by an indigenous strain for which bobcats are the natural reservoir.

Laminaria japonica Extract, an Inhibitor of Clavibater michiganense Subsp. Sepedonicum

PubMed Central

Cai, Jin; Feng, Jia; Xie, Shulian; Wang, Feipeng; Xu, Qiufeng

2014-01-01

Bacterial ring rot of potato is one of the most serious potato plant and tuber diseases. Laminaria japonica extract was investigated for its antimicrobial activity against Clavibater michiganense subsp. sepedonicum (Spieckermann & Kotthoff) Davis et al., the causative agent of bacterial ring rot of potato. The results showed that the optimum extraction conditions of antimicrobial substances from L. japonica were an extraction temperature of 80°C, an extraction time of 12 h, and a solid to liquid ratio of 1∶25. Active compounds of L. japonica were isolated by solvent partition, thin layer chromatography (TLC) and column chromatography. All nineteen fractionations had antimicrobial activities against C. michiganense subsp. sepedonicum, while Fractionation three (Fr.3) had the highest (P<0.05) antimicrobial activity. Chemical composition analysis identified a total of 26 components in Fr.3. The main constituents of Fr.3 were alkanes (80.97%), esters (5.24%), acids (4.87%) and alcohols (2.21%). Antimicrobial activity of Fr.3 against C. michiganense subsp. sepedonicum could be attributed to its ability to damage the cell wall and cell membrane, induce the production of reactive oxygen species (ROS), increase cytosolic Ca2+ concentration, inhibit the glycolytic pathway (EMP) and tricarboxylic acid (TCA) cycle, inhibit protein and nucleic acid synthesis, and disrupt the normal cycle of DNA replication. These findings indicate that L. japonica extracts have potential for inhibiting C. michiganense subsp. sepedonicum. PMID:24714388

Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity

PubMed Central

Kienesberger, Sabine; Sprenger, Hanna; Wolfgruber, Stella; Halwachs, Bettina; Thallinger, Gerhard G.; Perez-Perez, Guillermo I.; Blaser, Martin J.; Zechner, Ellen L.; Gorkiewicz, Gregor

2014-01-01

Campylobacter fetus are important animal and human pathogens and the two major subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract of animals and humans. We report the complete genomic sequence of C. fetus subsp. venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40. Functional analysis of genes predicted to be involved in C. fetus virulence was performed. The two subspecies are highly syntenic with 92% sequence identity but C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element. Aside from apparent gene transfer agents and hypothetical proteins, the unique genes in both subspecies comprise two known functional groups: lipopolysaccharide production, and type IV secretion machineries. Analyses of lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to particular pathotypes, and mutational inactivation demonstrated their roles in regulating virulence and host range. The comparative analysis presented here broadens knowledge of the genomic basis of C. fetus pathogenesis and host specificity. It further highlights the importance of surface-exposed structures to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the fitness and host-adaptation of these pathogens. PMID:24416416

First identification of Francisella noatunensis subsp. orientalis causing mortality in Mexican tilapia Oreochromis spp.

PubMed

Ortega, Cesar; Mancera, Gerardo; Enríquez, Ricardo; Vargas, Augusto; Martínez, Simón; Fajardo, Raúl; Avendaño-Herrera, Ruben; Navarrete, María José; Romero, Alex

2016-08-09

Francisellosis, an emerging disease in tilapia Oreochromis spp., is caused by the facultative, intracellular bacterium Francisella noatunensis subsp. orientalis, which is present in various countries where tilapia farming is commercially important. We confirmed the presence of francisellosis in Mexican tilapia cultures in association with an outbreak during the second semester of 2012. Broodstock fish presented a mortality rate of approximately 40%, and disease was characterized by histologically classified granulomas, or whitish nodules, in different organs, mainly the spleen and kidney. Through DNA obtained from infected tissue and pure cultures in a cysteine heart medium supplemented with hemoglobin, F. noatunensis subsp. orientalis was initially confirmed through the amplification and analysis of the 16S rRNA gene and the internal transcribed spacer region. Phylogenetic analysis of these genes demonstrated close similarity with previously reported F. noatunensis subsp. orientalis sequences obtained from infected tilapia from various countries. The identification of this subspecies as the causative agent of the outbreak was confirmed using the iglC gene as a target sequence, which showed 99.5% identity to 2 F. noatunensis subsp. orientalis strains (Ethime-1 and Toba04). These findings represent the first documented occurrence of francisellosis in Mexican tilapia cultures, which highlights the importance of establishing preventative measures to minimize the spread of this disease within the Mexican aquaculture industry.

Whole-genome sequencing of Salmonella enterica subsp. enterica serovar Cubana strains isolated from agricultural sources

USDA-ARS?s Scientific Manuscript database

We report draft genomes of Salmonella enterica subsp. enterica Serovar Cubana strain CVM42234 isolated from chick feed in 2012 and Salmonella Cubana strain 76814 isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 base pairs, respectively....

Draft Genome Sequence of Bifidobacterium animalis subsp. lactis Strain CECT 8145, Able To Improve Metabolic Syndrome In Vivo.

PubMed

Chenoll, E; Codoñer, F M; Silva, A; Martinez-Blanch, J F; Martorell, P; Ramón, D; Genovés, S

2014-03-27

Bifidobacterium animalis subsp. lactis strain CECT 8145 is able to reduce body fat content and improve metabolic syndrome biomarkers. Here, we report the draft genome sequence of this strain, which may provide insights into its safety status and functional role.

Development of loop-mediated isothermal amplification for detection of Leifsonia xyli subsp. xyli in sugarcane

USDA-ARS?s Scientific Manuscript database

Ratoon stunt, caused by the xylem-limited coryneform bacterium Leifsonia xyli subsp. xyli (Lxx), is prevalent in most sugarcane-producing countries. Because the disease does not cause characteristic external symptoms, a laboratory-based technique is needed for accurate diagnosis. We developed a diag...

Development of loop-mediated isothermal amplification for detection of Leifsonia xyli subsp. xyli in sugarcane

USDA-ARS?s Scientific Manuscript database

Ratoon stunt, caused by the xylem-limited coryneform bacterium Leifsonia xyli subsp. xyli (Lxx), is prevalent in most sugarcane-planting countries. Because the disease does not cause characteristic external symptoms, a laboratory-based technique is needed for accurate diagnosis. Based on loop-mediat...

Geography of genetic differentiation in the barley wild relative Hordeum vulgare subsp. spontaneum in Jordan

USDA-ARS?s Scientific Manuscript database

Informed collecting, conservation, monitoring and utilization of genetic diversity require knowledge of the distribution and structure of genetic variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic...

Inferring biomarkers for Mycobacterium avium subsp. paratuberculosis infection and disease progression using experimental data

USDA-ARS?s Scientific Manuscript database

Available diagnostic assays for Mycobacterium avium subsp paratuberculosis (MAP) have poor sensitivities and cannot detect early stages of the infection, therefore, there is need to find new diagnostic markers for early infection detection and disease stages. We analyzed longitudinal IFN- gamma, ELI...

Environmental contamination with Mycobacterium avium subsp. paratuberculosis in endemically infected dairy herds

USDA-ARS?s Scientific Manuscript database

Environmental contamination with Mycobacterium avium subsp. paratuberculosis (MAP) is thought to be the primary source of infection for dairy cattle. The exact link between fecal shedding of MAP by individual cows and environmental contamination levels at the herd level was explored with a cross-se...

Reconstruction of the Strawberry, Fragaria × ananassa, Using Native Genotypes of F. virginiana and F. chiloensis

USDA-ARS?s Scientific Manuscript database

The germplasm base of strawberries is restricted. The major cultivated strawberry species, Fragaria ananassa, originated about 250 years ago when South American F. chiloensis subsp. chiloensis forma chiloensis and North American F. virginiana subsp. virginiana accidentally hybridized in European ga...

Comparison of fecal DNA extraction kits for the detection of Mycobacterium avium subsp. paratuberculosis

USDA-ARS?s Scientific Manuscript database

Fecal culture is considered the gold standard for the diagnostics of paratuberculosis, however, PCR for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) in fecal material is widely used today, having demonstrated great sensitivity and specificity. To insure the most efficient and r...

Comparison of fecal DNA extraction kits for the detection of Mycobacterium avium subsp. paratuberculosis

USDA-ARS?s Scientific Manuscript database

Fecal culture is considered the gold standard for the diagnosis of paratuberculosis, however, PCR for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) in fecal material is widely used today, having demonstrated great sensitivity and specificity. To insure the most efficient and rep...

Population Structure and Diversity in Finger Millet (Eleusine coracana) Germplasm.

USDA-ARS?s Scientific Manuscript database

A genotypic analysis of 79 finger millet accessions (E. coracana subsp. coracana) from 11 African and 5 Asian countries, plus 14 wild E. coracana subsp. africana lines collected in Uganda and Kenya was conducted with 45 SSR markers distributed across the finger millet genome. Phylogenetic and popula...

Detection of Mycobacterium avium subsp. paratuberculosis in Drinking Water and Biofilms Using Quantitative PCR

EPA Science Inventory

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s disease in domestic animals and has been implicated in Crohn’s disease in humans. Cows infected with Johne’s disease shed large quantities of MAP into soil. Further, MAP has been isolated from surface water, is resi...

Genetic analysis and antimicrobial susceptibility of Francisella noatunensis subsp. orientalis (sun. F. asiatica) isolates from fish

USDA-ARS?s Scientific Manuscript database

Francisella noatunensis subsp. orientalis (syn. F. asiatica) (Fno) is an emergent fish pathogen that causes acute to chronic disease in a wide variety of freshwater, brackish and marine fish. Due to the emergent nature of this bacterium, established protocols to measure antimicrobial susceptibility ...

Description of Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles

USDA-ARS?s Scientific Manuscript database

A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like isolates from humans (n=8) and reptiles (n=5). Phenotypic characterization, Genusgenus-specific and sap insertion-PCR initially identified all human isolates as type A Campylobacter fetus. Phylogenet...

Draft Genome Sequences of 18 Salmonella enterica subsp. enterica Serovar Oranienburg Strains Isolated from Rivers in Northwestern Mexico

PubMed Central

Casteñeda-Ruelas, Gloria M.; Carreón-Gaxiola, César; Castelán-Sánchez, Hugo G.; Acatzi-Silva, Abraham; Romero-Martínez, Salvador; García-Molina, Alejandra

2017-01-01

ABSTRACT Salmonella enterica subsp. enterica serovar Oranienburg is recognized as a foodborne pathogen widely distributed in the environment. Here, we report 18 draft genomes of S. Oranienburg strains isolated from rivers in the northwestern region of Mexico. PMID:28280020

Draft Genome Sequence of the Putrescine-Producing Strain Lactococcus lactis subsp. lactis 1AA59

PubMed Central

del Rio, Beatriz; Linares, Daniel M.; Fernandez, María; Mayo, Baltasar; Martín, M. Cruz

2015-01-01

We report here the 2,576,542-bp genome annotated draft assembly sequence of Lactococcus lactis subsp. lactis 1AA59. This strain—isolated from a traditional cheese—produces putrescine, one of the most frequently biogenic amines found in dairy products. PMID:26089428

Envelope protein complexes of Mycobacterium avium subsp. paratuberculosis and their antigenicity

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease, a chronic enteric disease of ruminant animals. In the present study, blue native PAGE electrophoresis and 2D SDS-PAGE were used to separate MAP envelope protein complexes, followed by mass spectrometry (MS) ...

Complete genome sequence of Clavibacter michiganensis subsp. insidiosus

USDA-ARS?s Scientific Manuscript database

Clavibacter michiganensis subsp. insidiosus (Cmi) causes bacterial wilt disease of alfalfa (Medicago sativa L.) and can also infect the model legume plant M. truncatula. The virulence mechanisms of Cmi are yet to be identified, hampered by the lack of efficient mutagenesis tools as well as by the la...

A SNP genotyping array for hexaploid oat

USDA-ARS?s Scientific Manuscript database

Recognizing a need in cultivated hexaploid oat (Avena sativa L.) for a reliable set of reference SNPs, we have developed a 6K BeadChip design containing 257 Infinium I and 5,486 Infinium II designs corresponding to 5,743 SNPs. Of those, 4,975 SNPs yielded successful assays after array manufacturing...

Chromosome-anchored QTL conferring aluminum tolerance in hexaploid oat

USDA-ARS?s Scientific Manuscript database

Abstract Aluminum (Al) toxicity is a major constraint on crop production in acid soils around the world. Hexaploid oat (Avena sativa L.) possesses signi'cant Al tolerance making it a good candidate for production in these environments. Genetic improvement for Al tolerance in oat has traditionally be...

7 CFR 810.1002 - Definition of other terms.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., rye, safflower, sorghum, soybeans, spelt, sunflower seed, sweet corn, triticale, and wheat. (e) Sieves... seeds. All matter that passes through a 5/64 triangular-hole sieve after sieving according to procedures...-damaged, or otherwise materially damaged. (g) Wild oats. Seeds of Avena fatua L. and A. sterillis L...

7 CFR 810.1002 - Definition of other terms.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., rye, safflower, sorghum, soybeans, spelt, sunflower seed, sweet corn, triticale, and wheat. (e) Sieves... seeds. All matter that passes through a 5/64 triangular-hole sieve after sieving according to procedures...-damaged, or otherwise materially damaged. (g) Wild oats. Seeds of Avena fatua L. and A. sterillis L...

Assembly and expression analysis of oat vitamin E biosynthesis gene homeologs during seed development

USDA-ARS?s Scientific Manuscript database

Among the cereal grains, hexaploid oats (Avena sativa L.) are particularly rich in vitamin E, an essential liposoluble vitamin that maintains membrane stability and possesses antioxidant and anti-inflammatory properties. To date, no gene sequences involved in vitamin E biosynthesis have been reporte...

Prey foraging by Hippodamia convergens for cereal aphids on wheat

USDA-ARS?s Scientific Manuscript database

We investigated predation by adult convergent lady beetle, Hippodamia convergens Guerin-Meneville, on English grain aphid, Sitobion avenae L., on wheat, Triticum aestivum L., plants in a laboratory arena, and developed a functional response model for the number of aphids eaten by an adult female con...

Field application of benzothiadiazole (BTH) to oats (Avena sativa): Effects on crown rust resistance and avenanthramide production

USDA-ARS?s Scientific Manuscript database

Plant defense activators such as benzothiadiazole (BTH) are known to elicit the biosynthesis of plant phytoalexins. In oat, BTH treatment was shown to up-regulate avenanthramide production in both the vegetative tissue and filling grain in greenhouse studies. Avenanthramides are phenolic antioxidant...

New Advances in Marker Assisted Selection for Winter Hardiness in Oats.

USDA-ARS?s Scientific Manuscript database

Oat (Avena sativa L.) breeding and genetics research has lagged behind other small grains, such as wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), in the development of PCR based markers and map construction due to fewer oat researchers and reduced research funding. As a result, marke...

Spectral analysis of winter wheat leaves for detection and differentiation of diseases and insects

USDA-ARS?s Scientific Manuscript database

Yellow rust (Puccinia striiformis f. sp. Tritici), powdery mildew (Blumeria graminis) and wheat aphid (Sitobion avenae F.) infestation are three serious conditions that have a severe impact on yield and grain quality of winter wheat worldwide. Discrimination among these three stressors is of practic...

Suppressors of oat crown rust resistance in interspecific oat crosses

USDA-ARS?s Scientific Manuscript database

Attempts to transfer disease resistance genes between related species may be hindered by suppression, or lack of expression, of the trait in the interspecific combination. In crosses of diploid oat Avena strigosa (Schreb.) accession CI6954SP with resistance to oat crown rust Puccinia coronata f. sp....

The correct name for a subspecies of Oenothera fruticosa L. (Onagraceae).

PubMed

Wagner, Warren L

2014-01-01

In 1978 when Straley adopted the name Oenothera fruticosa L. subsp. glauca (Michx.) Straley for one of the two recognized subspecies of O. fruticosa it was the correct name for this taxon; however, since that time the botanical code has changed so that now an autonym is treated as having priority over the name or names of the same date and rank that established it. This change means that since 1981 O. fruticosa subsp. glauca was no longer the correct name. The appropriate combination for it is made here as O. fruticosa L. subsp. tetragona (Roth) W.L. Wagner. Original material for the basionym, O. tetragona, is no longer extant so a neotype is designated.

Conditioned food aversion for control of poisoning by Ipomoea carnea subsp. fistulosa

USDA-ARS?s Scientific Manuscript database

Conditioned food aversion is a technique that can be used to train livestock to avoid ingestion of poisonous plants. This study tested the efficacy and durability of conditioned food aversion to eliminate goat’s consumption of Ipomoea carnea subsp. fistulosa. We used 14 young Moxotó goats, which wer...

Complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 using PacBio single-molecule real-time technology

USDA-ARS?s Scientific Manuscript database

We report the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 isolated in Minnesota, USA. The R1-1 genome, generated by de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies....

A comparative study of three detection techniques for Leifsonia xyli subsp. xyli, the causal pathogen of sugarcane ratoon stunting disease

USDA-ARS?s Scientific Manuscript database

Ratoon stunting disease (RSD), which is caused by the bacterium Leifsonia xyli subsp. xyli (Lxx), is now recognized worldwide as the most economically devastating disease impacting sugarcane. RSD causes significant yield losses and variety degradation. Diagnosis of RSD is challenging because it does...

Genome sequences of Salmonella enterica subsp. Kentucky ST152 isolated from dairy cows in the United States

USDA-ARS?s Scientific Manuscript database

Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from dairy cows in the United States, but is an infrequent cause of human salmonellosis. To investigate the genomic features of S. Kentucky strains isolated from these animals, genomes of eight isolates were sequenced and ad...

Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923

PubMed Central

Treangen, Todd J.; Maybank, Rosslyn A.; Enke, Sana; Friss, Mary Beth; Diviak, Lynn F.; Karaolis, David K. R.; Koren, Sergey; Ondov, Brian; Phillippy, Adam M.; Bergman, Nicholas H.

2014-01-01

Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used as a control strain for susceptibility testing to antibiotics and as a quality control strain for commercial products. We present the completed genome sequence for the strain, consisting of the chromosome and a 27.5-kb plasmid. PMID:25377701

Immunogenicity and protective efficacy of the Mycobacterium avium subsp. paratuberculosis attenuated mutants against challenge in a mouse model

USDA-ARS?s Scientific Manuscript database

Johne’s disease (JD), caused by Mycobacterium avium subsp. paratuberculosis (MAP), results in serious economic losses worldwide especially in cattle, sheep and goats. To control the impact of JD on the animal industry, an effective vaccine with minimal adverse effects is urgently required. In order ...

Mediation of host immune responses after immunization of neonatal calves with a heat-killed Mycobacterium avium subsp. paratuberculosis vaccine

USDA-ARS?s Scientific Manuscript database

A major drawback of current whole-cell vaccines for Mycobacterium avium subsp. paratuberculosis(MAP) is the interference with diagnostic tests for bovine tuberculosis and paratuberculosis. The current study was designed to explore effects of immunization with a heat-killed whole cell vaccine (Mycop...

Optimization of methods for the detection of Mycobacterium avium subsp. paratuberculosis in milk and colostrum of naturally infected dairy cows

USDA-ARS?s Scientific Manuscript database

Two decontamination chemicals, hexadecylpyridinium choride (HPC) and N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH), were compared for their efficacy of reducing the growth of non-specific microorganisms in milk while minimally affecting the recovery of Mycobacterium avium subsp. paratuberculosis ...

Evaluation of Control Points in Youngstock and Adult Dairy Cow Management to Control Transmission of Mycobacterium avium subsp. paratuberculosis

USDA-ARS?s Scientific Manuscript database

Goal Complete a series of controlled on-farm trials to critically evaluate the efficacy and cost-benefit of commonly recommended management practices for reducing the transmission of Mycobacterium avium subsp. paratuberculosis (Map) in infected herds. Objective 1. Evaluate the effect of maternity...

Peritonitis in a llama caused by Streptococcus equi subsp. zooepidemicus.

PubMed Central

Hewson, J; Cebra, C K

2001-01-01

A 7-month-old, male llama was diagnosed with peritonitis caused by Streptococcus equi subsp. zooepidemicus. Clinical findings, medical treatment, and case outcome are described. Hematogenous dissemination from suspected pneumonia is proposed as the route of infection in this case. Possible transmission of the organism through contact with horses is discussed. PMID:11424579

Divergent cellular responses during asymptomatic subclinical and clinical states of disease in cows naturally infected with Mycobacterium avium subsp. paratuberculosis

USDA-ARS?s Scientific Manuscript database

Infection of the host with Mycobacterium avium subsp. paratuberculosis (MAP) results in a chronic and progressive enteritis that traverses both subclinical and clinical stages. The mechanism(s) for the shift from asymptomatic subclinical disease state to advanced clinical disease are not fully under...

Occurrence of transgenic feral alfalfa (Medicago sativa subsp. sativa L.) in alfalfa seed production areas in the United States

USDA-ARS?s Scientific Manuscript database

Genetically-engineered glyphosate-resistant alfalfa (Medicago sativa subsp. sativa) was commercialized in 2011. The potential risk of transgene dispersal into the environment is not clearly understood for alfalfa, a perennial crop that is cross-pollinated by insects. We gathered data on feral and tr...

Selection of single chain variable fragments (scFv) against Xylella fastidiosa subsp. pauca by phage display

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa is a gram-negative member of the gamma proteobacteria. Xylella fastidiosa subsp pauca causes citrus variegated chlorosis in Brazil and enjoys ‘select agent’ status in the United States. Antibody based detection assays are commercially available for Xylella fastidiosa, and are ef...

Development of single chain variable fragment (scFv) antibodies against Xylella fastidiosa subsp. pauca by phage display

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Xylella fastidiosa subsp pauca causes citrus variegat...

Stawamycin analog, JBIR-11 from Streptomyces viridochromogenes subsp. sulfomycini NBRC 13830.

PubMed

Izumikawa, Miho; Komaki, Hisayuki; Hashimoto, Junko; Takagi, Motoki; Shin-ya, Kazuo

2008-05-01

A stawamycin analog, JBIR-11 (1) was isolated from mycelium of Streptomyces viridochromogenes subsp. sulfomycini NBRC 13830. The structure was determined on the basis of the spectroscopic data. Compound 1 exhibited growth inhibitory effect against human fibrosarcoma HT1080 cells with an IC50 value of 25 microM.

Comparison of fecal DNA extraction kits for the detection of Mycobacterium avium subsp. paratuberculosis by polymerase chain reaction

USDA-ARS?s Scientific Manuscript database

Culture of Mycobacterium avium subsp. paratuberculosis (MAP) from feces has been considered the gold standard for the diagnosis of paratuberculosis for many years. However, direct fecal PCR is becoming more widely used today, demonstrating similar sensitivity and specificity to culture. To ensure ef...

Lymphoproliferative and gamma interferon responses to stress-regulated Mycobacterium avium subsp. paratuberculosis recombinant proteins

USDA-ARS?s Scientific Manuscript database

Johne’s disease in ruminants is a chronic infection of the intestines caused by Mycobacterium avium subsp. paratuberculosis. Economic losses associated with Johne’s disease arise due to premature culling, reduced production of milk and wool and mortalities. The disease is characterised by a long inc...

Efficacy of florfenicol for control of mortality with Francisella noatunensis subsp. orientalis in Nile tilapia, oreochromis niloticus (L.)

USDA-ARS?s Scientific Manuscript database

Francisella noatunensis subsp. orientalis (Fno) (syn. F. asiatica) is an emergent Gram-negative facultative intracellular bacterium. Although it is considered one of the most pathogenic bacteria in fish, there are no commercially available treatments of vaccines. The objective of this project was ...

Genome Sequence of the Cheese-Starter Strain Lactobacillus delbrueckii subsp. lactis CRL 581.

PubMed

Hebert, Elvira María; Raya, Raúl R; Brown, Lucía; Font de Valdez, Graciela; Savoy de Giori, Graciela; Taranto, María Pía

2013-08-08

We report the genome sequence of Lactobacillus delbrueckii subsp. lactis CRL 581 (1,911,137 bp, GC 49.7%), a proteolytic strain isolated from a homemade Argentinian hard cheese which has a key role in bacterial nutrition and releases bioactive health-beneficial peptides from milk proteins.

Antigenicity of recombinant maltose binding protein-Mycobacterium avium subsp. paratuberculosis fusion proteins with and without factor Xa cleaving

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp paratuberculosis (MAP) causes Johne’s disease (JD) in ruminants. Proteomic studies have shown that MAP expresses certain proteins when exposed to in vitro physiological stress conditions similar to the conditions experienced within a host during natural infection. Such prot...

Complete genome sequence of salmonella enterica subsp. enterica Serovar Thompson Strain RM6836

USDA-ARS?s Scientific Manuscript database

Salmonella enterica subsp. enterica serovar Thompson (S. Thompson) strain RM6836 was isolated from lettuce in 2002. We report the complete sequence and annotation of the genome of S. Thompson strain RM6836. This is the first reported complete genome sequence for S. Thompson and will provide a point ...

Production and Evaluation of an Improved Mycobacterium avium subsp. paratuberculosis Purified Protein Derivative for Use in In-Vivo and In-Vitro Diagnostic Testing

USDA-ARS?s Scientific Manuscript database

Purified protein derivatives (PPD’s) were prepared from the cultured filtrate of Mycobacterium avium subsp. paratuberculosis (MAP) ATCC strain 19698. Production of PPD has historically been problematic for maintaining optimal floating cultures yielding defined immunogenic components. To obtain mor...

Complete genomic sequence of campylobacter jejuni subsp. jejuni HS:19 penner reference strain

USDA-ARS?s Scientific Manuscript database

Campylobacter jejuni subsp. jejuni (Cjj) infections are a leading cause of foodborne gastroenteritis and the most prevalent antecedent to Guillain-Barré syndrome (GBS). Capsular type Penner HS:19 is among several capsule types shown to be markers for GBS. This study describes the genome of Cjj HS:19...

[The occurrence of campylobacter fetus subsp. jejuni and Salmonella bacteria in some wild birds (author's transl)].

PubMed

Rosef, O

1981-12-01

An investigation was carried out into the occurrence of Campylobacter fetus subsp. jejuni and Salmonella species in some wild birds. A total of 129 birds was examined, consisting of 71 pigeons, 54 seagulls, three crows and one raven. Campylobacter bacteria were isolated from 32 birds (24.8%), of which three were pigeons, 27 seagulls and two were crows. Of the 27 Campylobacter strains isolated from seagulls, four had the biochemical characteristics of the NARTC biotype described by Skirrow and Benjamin, seven were grouped as Campylobacter coli biotype and 16 as the biotype of Campylobacter jejuni. All the strains isolated from crows and pigeons had the biochemical characteristics of Campylobacter jejuni biotypes. Salmonella bacteria were isolated from the intestinal contents of two of the 54 seagulls (3.7%), and were identified serologically as Salmonella indiana and Salmonella typhimurium. One seagull was found to be a carrier of both Campylobacter fetus subsp. jejuni and Salmonella typhimurium. A correlation could not be demonstrated between the occurrence of Salmonella bacteria and Campylobacter fetus subsp. jejuni.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan.

PubMed

Thormann, Imke; Reeves, Patrick; Reilley, Ann; Engels, Johannes M M; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.

Prevalence of American foulbrood in asymptomatic apiaries of Kurdistan, Iran

PubMed Central

Khezri, M.; Moharrami, M.; Modirrousta, H.; Torkaman, M.; Rokhzad, B.; Khanbabaie, H.

2018-01-01

Aim: Paenibacillus larvae subsp. larvae is the etiological agent of American foulbrood (AFB), the most virulent bacterial disease of honey bee brood worldwide. In many countries, AFB is a notifiable disease since it is highly contagious, in most cases incurable, and able to kill affected colonies. The aim of this study was to determine the prevalence of P. larvae subsp. larvae in Kurdistan province apiaries by polymerase chain reaction (PCR) technique. Materials and Methods: A total of 100 samples were randomly purchased from apiaries in Kurdistan, Iran. Apiaries were randomly sampled in accordance with the instructions of the veterinary organization from different provinces and were tested using PCR method and an exclusive primer of 16S rRNA for the presence of P. larvae subsp. larvae. Results: The results of this study indicated a low level of contamination with P. larvae subsp. larvae in the Kurdistan province. The number of positive samples obtained by PCR was 2%. Conclusion: Therefore, monitoring programs for this honeybee disease in Kurdistan should be developed and implemented to ensure that it is detected early and managed. PMID:29657417

Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray

PubMed Central

Shin, Hwa Hui; Hwang, Byeong Hee; Seo, Jeong Hyun

2014-01-01

It is important to rapidly and selectively detect and analyze pathogenic Salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of Salmonella infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carB gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three S. enterica subsp. enterica serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target Salmonella serotype from a bacterial mixture. Therefore, these results demonstrated that our novel carB-based oligonucleotide microarray can be used as an effective and specific detection system for S. enterica subsp. enterica serotypes. PMID:24185846

Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray.

PubMed

Shin, Hwa Hui; Hwang, Byeong Hee; Seo, Jeong Hyun; Cha, Hyung Joon

2014-01-01

It is important to rapidly and selectively detect and analyze pathogenic Salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of Salmonella infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carB gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three S. enterica subsp. enterica serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target Salmonella serotype from a bacterial mixture. Therefore, these results demonstrated that our novel carB-based oligonucleotide microarray can be used as an effective and specific detection system for S. enterica subsp. enterica serotypes.

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meincke, Linda; Copeland, A; Lapidus, Alla L.

2012-01-01

Polynucleobacter necessarius subsp. asymbioticus Hahn et al. 2009 is one of currently two subspecies of P. necessarius. While P. necessarius subsp. asymbioticus is a free-living bacterium, the closely related second subspecies, P. necessarius subsp. necessarius is an obligate endosymbiont living in the cytoplasm of freshwater ciliates of the genus Euplotes aediculatus. The two P. necessarius subspecies were the closest thus far reported phylogenetic neighbors that differ in their lifestyle as obligately free-living vs. obligate endosymbiontic, and they are the only members of the genus Polynucleobacter with completely sequenced genomes. The genome-sequenced strain represents a group of closely related strains notmore » distinguishable by 16S rRNA, 16S-23S ITS or glnA sequences, which is persistent in the home habitat of the strain and frequently contributes > 10% of total bacterial numbers in water samples of the habitat. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.« less

Lactobacillus delbrueckii subsp. bulgaricus CRL 454 cleaves allergenic peptides of β-lactoglobulin.

PubMed

Pescuma, Micaela; Hébert, Elvira M; Haertlé, Thomas; Chobert, Jean-Marc; Mozzi, Fernanda; Font de Valdez, Graciela

2015-03-01

Whey, a cheese by-product used as a food additive, is produced worldwide at 40.7 million tons per year. β-Lactoglobulin (BLG), the main whey protein, is poorly digested and is highly allergenic. We aimed to study the contribution of Lactobacillus delbrueckii subsp. bulgaricus CRL 454 to BLG digestion and to analyse its ability to degrade the main allergenic sequences of this protein. Pre-hydrolysis of BLG by L. delbrueckii subsp. bulgaricus CRL 454 increases digestion of BLG assayed by an in vitro simulated gastrointestinal system. Moreover, peptides from hydrolysis of the allergenic sequences V41-K60, Y102-R124, C121-L140 and L149-I162 were found when BLG was hydrolysed by this strain. Interestingly, peptides possessing antioxidant, ACE inhibitory, antimicrobial and immuno-modulating properties were found in BLG degraded by both the Lactobacillus strain and digestive enzymes. To conclude, pre-hydrolysis of BLG by L. delbrueckii subsp. bulgaricus CRL 454 has a positive effect on BLG digestion and could diminish allergenic reactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Lymphoproliferative and gamma interferon responses to stress-regulated Mycobacterium avium subsp. paratuberculosis recombinant proteins.

PubMed

Gurung, Ratna B; Begg, Douglas J; Purdie, Auriol C; de Silva, Kumudika; Bannantine, John P; Whittington, Richard J

2014-06-01

Johne's disease in ruminants is a chronic infection of the intestines caused by Mycobacterium avium subsp. paratuberculosis. An important strategy to control disease is early detection, and a potentially efficient method for early detection is measurement of cell-mediated immune responses developed by the host in response to exposure or infection. One method is to measure lymphoproliferation and cytokine release from the host cells when exposed to the organism or parts of the organism. In this study, 10 recombinant M. avium subsp. paratuberculosis proteins known to be upregulated under in vitro stress conditions were evaluated by examining their ability to evoke memory as a result of exposure by vaccination or oral challenge with live Mycobacterium avium subsp. paratuberculosis. Out of 10 proteins, MAP2698c was found to induce higher cell-mediated immune responses in vaccinated and challenged sheep in comparison to healthy controls. The findings suggest that not all stress-regulated proteins have the diagnostic potential to detect cell-mediated immune responses in ovine paratuberculosis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

An introgressed wing pattern acts as a mating cue.

PubMed

Sánchez, Angela P; Pardo-Diaz, Carolina; Enciso-Romero, Juan; Muñoz, Astrid; Jiggins, Chris D; Salazar, Camilo; Linares, Mauricio

2015-06-01

Heliconius butterflies provide good examples of both homoploid hybrid speciation and ecological speciation. In particular, examples of adaptive introgression have been detected among the subspecies of Heliconius timareta, which acquired red color pattern elements from H. melpomene. We tested whether the introgression of red wing pattern elements into H. timareta florencia might also be associated with incipient reproductive isolation (RI) from its close relative, H. timareta subsp. nov., found in the eastern Andes. No choice experiments show a 50% reduction in mating between females of H. t. subsp. nov. and males of H .t. florencia, but not in the reciprocal direction. In choice experiments using wing models, males of H. timareta subsp. nov. approach and court red phenotypes less than their own, whereas males of H. t. florencia prefer models with a red phenotype. Intrinsic postzygotic isolation was not detected in crosses between these H. timareta races. These results suggest that a color pattern trait gained by introgression is triggering RI between H. timareta subsp. nov. and H. t. florencia. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Prevalence of American foulbrood in asymptomatic apiaries of Kurdistan, Iran.

PubMed

Khezri, M; Moharrami, M; Modirrousta, H; Torkaman, M; Rokhzad, B; Khanbabaie, H

2018-03-01

Paenibacillus larvae subsp. larvae is the etiological agent of American foulbrood (AFB), the most virulent bacterial disease of honey bee brood worldwide. In many countries, AFB is a notifiable disease since it is highly contagious, in most cases incurable, and able to kill affected colonies. The aim of this study was to determine the prevalence of P. larvae subsp . larvae in Kurdistan province apiaries by polymerase chain reaction (PCR) technique. A total of 100 samples were randomly purchased from apiaries in Kurdistan, Iran. Apiaries were randomly sampled in accordance with the instructions of the veterinary organization from different provinces and were tested using PCR method and an exclusive primer of 16S rRNA for the presence of P. larvae subsp . larvae . The results of this study indicated a low level of contamination with P. larvae subsp . larvae in the Kurdistan province. The number of positive samples obtained by PCR was 2%. Therefore, monitoring programs for this honeybee disease in Kurdistan should be developed and implemented to ensure that it is detected early and managed.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan

PubMed Central

Reeves, Patrick; Reilley, Ann; Engels, Johannes M. M.; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M.

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum. PMID:27513459

Comparison of the acidifying activity of Lactococcus lactis subsp. lactis strains isolated from goat's milk and Valdeteja cheese.

PubMed

Alonso-Calleja, C; Carballo, J; Capita, R; Bernardo, A; García-López, M L

2002-01-01

This work was carried out to study the acid production by Lactococcus lactis subsp. lactis strains isolated from goat's milk and goat cheese (Valdeteja variety) in order to select a suitable starter culture for industrial goat cheese manufacturing. The titrable acidity of 45 Lactococcus lactis subsp. lactis strains isolated from a home-made batch of Valdeteja cheese with excellent sensory characteristics was measured over a period of 18 h. The strains were divided into two groups depending on the acid production rate: 20 fast acid producer (F) strains and 25 slow acid producer (S) strains. The kinetic parameters (lag phase, maximum acid production rate and value of upper asymptote curve) of the acid production curves for F and S strains were significantly (P < 0.001) different. Significant (P < 0.001) differences between titrable acidity of F and S strains were observed after the second hour of incubation. An F strain acetoin producer (Lactococcus lactis subsp. lactis 470Ch2) was selected as autochthonous starter culture for industrial Valdeteja goat cheese manufacturing.

Chemical composition and in vitro antioxidant activity of hydro-ethanolic extracts from Bauhinia forficata subsp. pruinosa and B. variegata.

PubMed

Sayago, Carla T M; Camargo, Vanessa B; Barbosa, F; Gularte, Cláudia; Pereira, Geovana; Miotto, Silvia; Cechinel Filho, V; Luiz Puntel, R; Folmer, V; Mendez, A

2013-03-01

Bauhinia species are known to have hypoglycemiant and antioxidant activities. Here, hydro-ethanolic leaf extracts from Bauhinia forficata subsp. pruinosa and Bauhinia variegata, collected in a Pampa biome region of Brazil, were investigated to characterize their chromatographic profile, flavonoid content and in vitro antioxidant activity (TBARS and DPH assays). The extracts were obtained from dried and fresh leaves. The total flavonoid content was assessed by spectrophotometric determination, and the results ranged between 572.08 and 1,102.99 μg mL-1. Moreover, flavonoids were more predominant in B. variegata than in B. forficata subsp. pruinosa. HPLC analysis detected a complex profile of phenolic compounds, being the flavonoid kaempferitrin founded B. forficata subsp. pruinosa; in addition, other kaempferol and quercetin derivatives were present. In vitro antioxidant assays demonstrated a different behavior depending on the species, leaf treatment and extract concentration. In general, B. variegata extracts obtained from fresh material presented higher antioxidant potential, which can be attributed to the predominance of flavonoids in their chemical composition.

In vitro evaluation of the probiotic and functional potential of Lactobacillus strains isolated from fermented food and human intestine.

PubMed

Ren, Dayong; Li, Chang; Qin, Yanqing; Yin, Ronglan; Du, Shouwen; Ye, Fei; Liu, Cunxia; Liu, Hongfeng; Wang, Maopeng; Li, Yi; Sun, Yang; Li, Xiao; Tian, Mingyao; Jin, Ningyi

2014-12-01

This study aims to evaluate the functional and probiotic characteristics of eight indigenous Lactobacillus strains in vitro. The selected lactobacilli include strains of Lactobacillus casei subsp. casei, Lactobacillus salivarius subsp. salicinius, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus delbrueckii subsp. lactis, Lactobacillus delbrueckii subsp. bulgaricus, and Lactobacillus rhamnosus. All strains tolerated both pH 2 for 3 h and 1% bile salt for 24 h. The strains CICC 23174 and CGMCC 1.557 were the most adhesive strains producing the highest quantity of EPS. Although a wide variation in the ability of the eight strains to deplete cholesterol and nitrite, antagonize pathogens, scavenge free radical, and stimulate innate immune response were observed, the strains CICC 23174 and CGMCC 1.557 showed the widest range of these useful traits. Taken together, the strains CICC 23174 and CGMCC 1.557 exhibited the best probiotic properties with the potential for use in the production of probiotic fermented foods. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effective heat inactivation of Mycobacterium avium subsp. paratuberculosis in raw milk contaminated with naturally infected feces.

PubMed

Rademaker, Jan L W; Vissers, Marc M M; Te Giffel, Meike C

2007-07-01

The effectiveness of high-temperature, short holding time (HTST) pasteurization and homogenization with respect to inactivation of Mycobacterium avium subsp. paratuberculosis was evaluated quantitatively. This allowed a detailed determination of inactivation kinetics. High concentrations of feces from cows with clinical symptoms of Johne's disease were used to contaminate raw milk in order to realistically mimic possible incidents most closely. Final M. avium subsp. paratuberculosis concentrations varying from 10(2) to 3.5 x 10(5) cells per ml raw milk were used. Heat treatments including industrial HTST were simulated on a pilot scale with 22 different time-temperature combinations, including 60 to 90 degrees C at holding (mean residence) times of 6 to 15 s. Following 72 degrees C and a holding time of 6 s, 70 degrees C for 10 and 15 s, or under more stringent conditions, no viable M. avium subsp. paratuberculosis cells were recovered, resulting in >4.2- to >7.1-fold reductions, depending on the original inoculum concentrations. Inactivation kinetic modeling of 69 quantitative data points yielded an E(a) of 305,635 J/mol and an lnk(0) of 107.2, corresponding to a D value of 1.2 s at 72 degrees C and a Z value of 7.7 degrees C. Homogenization did not significantly affect the inactivation. The conclusion can be drawn that HTST pasteurization conditions equal to 15 s at > or =72 degrees C result in a more-than-sevenfold reduction of M. avium subsp. paratuberculosis.

Effective Heat Inactivation of Mycobacterium avium subsp. paratuberculosis in Raw Milk Contaminated with Naturally Infected Feces▿

PubMed Central

Rademaker, Jan L. W.; Vissers, Marc M. M.; te Giffel, Meike C.

2007-01-01

The effectiveness of high-temperature, short holding time (HTST) pasteurization and homogenization with respect to inactivation of Mycobacterium avium subsp. paratuberculosis was evaluated quantitatively. This allowed a detailed determination of inactivation kinetics. High concentrations of feces from cows with clinical symptoms of Johne's disease were used to contaminate raw milk in order to realistically mimic possible incidents most closely. Final M. avium subsp. paratuberculosis concentrations varying from 102 to 3.5 × 105 cells per ml raw milk were used. Heat treatments including industrial HTST were simulated on a pilot scale with 22 different time-temperature combinations, including 60 to 90°C at holding (mean residence) times of 6 to 15 s. Following 72°C and a holding time of 6 s, 70°C for 10 and 15 s, or under more stringent conditions, no viable M. avium subsp. paratuberculosis cells were recovered, resulting in >4.2- to >7.1-fold reductions, depending on the original inoculum concentrations. Inactivation kinetic modeling of 69 quantitative data points yielded an Ea of 305,635 J/mol and an lnk0 of 107.2, corresponding to a D value of 1.2 s at 72°C and a Z value of 7.7°C. Homogenization did not significantly affect the inactivation. The conclusion can be drawn that HTST pasteurization conditions equal to 15 s at ≥72°C result in a more-than-sevenfold reduction of M. avium subsp. paratuberculosis. PMID:17496131

Bacillus amyloliquefaciens subsp. plantarum GR53, a potent biocontrol agent resists Rhizoctonia disease on Chinese cabbage through hormonal and antioxidants regulation.

PubMed

Kang, Sang-Mo; Radhakrishnan, Ramalingam; Lee, In-Jung

2015-10-01

The fungus Rhizoctonia solani is one of the causal agents of numerous diseases that affect crop growth and yield. The aim of this present investigation was to identify a biocontrol agent that acts against R. solani and to determine the agent's protective effect through phytohormones and antioxidant regulation in experimentally infected Chinese cabbage plants. Four rhizospheric soil bacterial isolates GR53, GR169, GR786, and GR320 were tested for their antagonistic activity against R. solani. Among these isolates, GR53 significantly suppressed fungal growth. GR53 was identified as Bacillus amyloliquefaciens subsp. plantarum by phylogenetic analysis of the 16S rDNA sequence. The biocontrol activity of B. amyloliquefaciens subsp. plantarum GR53 was tested in Chinese cabbage plants under controlled conditions. Results showed that R. solani inhibited plant growth (length, width, fresh and dry weight of leaves) by reducing chlorophyll and total phenolic content, as well as by increasing the levels of salicylic acid, jasmonic acid, abscisic acid, and DPPH scavenging activity. By regulating the levels of these compounds, the co-inoculation of B. amyloliquefaciens subsp. plantarum GR53 heightened induced systemic resistance in infected Chinese cabbage, effectively mitigating R. solani-induced damaging effects and improving plant growth. The results obtained from this study suggest that B. amyloliquefaciens subsp. plantarum GR53 is an effective biocontrol agent to prevent the damage caused by R. solani in Chinese cabbage plants.

Comparative genome analysis of two Streptococcus phocae subspecies provides novel insights into pathogenicity.

PubMed

Bethke, J; Avendaño-Herrera, R

2017-02-01

Streptococcus phocae is a beta-hemolytic, Gram-positive bacterium that was first isolated in Norway from clinical specimens of harbor seal (Phoca vitulina) affected by pneumonia or respiratory infection, and in 2005, this bacterium was identified from disease outbreaks at an Atlantic salmon farm. A recent comparative polyphasic study reclassified Streptococcus phocae as subsp. phocae and subsp. salmonis, and there are currently two S. phocae NCBI sequencing projects for the type strains ATCC 51973 T and C-4 T . The present study compared these genome sequences to determine shared properties between the pathogenic mammalian and fish S. phocae subspecies. Both subspecies presented genomic islands, prophages, CRISPRs, and multiple gene activator and RofA regulator regions that could play key roles in the pathogenesis of streptococcal species. Likewise, proteins possibly influencing immune system evasion and virulence strategies were identified in both genomes, including Streptokinases, Streptolysin S, IgG endopeptidase, Fibronectin binding proteins, Daunorubicin, and Penicillin resistance proteins. Comparative differences in phage, non-phage, and genomic island sequences may form the genetic basis for the virulence, pathogenicity, and ability of S. phocae subsp. salmonis to infect and cause disease in Atlantic salmon, in contrast to S. phocae subsp. phocae. This comparative genomic study between two S. phocae subsp. provides novel insights into virulence factors and pathogenicity, offering important information that will facilitate the development of preventive and treatment measures against this pathogen. Copyright © 2016 Elsevier B.V. All rights reserved.

Bioprocessing of some agro-industrial residues for endoglucanase production by the new subsp.; Streptomyces albogriseolus subsp. cellulolyticus strain NEAE-J

PubMed Central

El-Naggar, Noura El-Ahmady; Abdelwahed, Nayera A.M.; Saber, Wesam I.A.; Mohamed, Asem A.

2014-01-01

The use of low cost agro-industrial residues for the production of industrial enzymes is one of the ways to reduce significantly production costs. Cellulase producing actinomycetes were isolated from soil and decayed agricultural wastes. Among them, a potential culture, strain NEAE-J, was selected and identified on the basis of morphological, cultural, physiological and chemotaxonomic properties, together with 16S rDNA sequence. It is proposed that strain NEAE-J should be included in the species Streptomyces albogriseolus as a representative of a novel sub-species, Streptomyces albogriseolus subsp. cellulolyticus strain NEAE-J and sequencing product was deposited in the GenBank database under accession number JN229412. This organism was tested for its ability to produce endoglucanase and release reducing sugars from agro-industrial residues as substrates. Sugarcane bagasse was the most suitable substrate for endoglucanase production. Effects of process variables, namely incubation time, temperature, initial pH and nitrogen source on production of endoglucanase by submerged fermentation using Streptomyces albogriseolus subsp. cellulolyticus have been studied. Accordingly optimum conditions have been determined. Incubation temperature of 30 °C after 6 days, pH of 6.5, 1% sugarcane bagasse as carbon source and peptone as nitrogen source were found to be the optimum for endoglucanase production. Optimization of the process parameters resulted in about 2.6 fold increase in the endoglucanase activity. Therefore, Streptomyces albogriseolus subsp. cellulolyticus coud be potential microorganism for the intended application. PMID:25242966

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea

PubMed Central

Godornes, Charmie; Giacani, Lorenzo; Barry, Alyssa E.; Mitja, Oriol

2017-01-01

Background Yaws is a neglected tropical disease, caused by Treponema pallidum subsp. pertenue. The disease causes chronic lesions, primarily in young children living in remote villages in tropical climates. As part of a global yaws eradication campaign initiated by the World Health Organization, we sought to develop and evaluate a molecular typing method to distinguish different strains of T. pallidum subsp. pertenue for disease control and epidemiological purposes. Methods and principal findings Published genome sequences of strains of T. pallidum subsp. pertenue and pallidum were compared to identify polymorphic genetic loci among the strains. DNA from a number of existing historical Treponema isolates, as well as a subset of samples from yaws patients collected in Lihir Island, Papua New Guinea, were analyzed using these targets. From these data, three genes (tp0548, tp0136 and tp0326) were ultimately selected to give a high discriminating capability among the T. pallidum subsp. pertenue samples tested. Intragenic regions of these three target genes were then selected to enhance the discriminating capability of the typing scheme using short readily amplifiable loci. This 3-gene multilocus sequence typing (MLST) method was applied to existing historical human yaws strains, the Fribourg-Blanc simian isolate, and DNA from 194 lesion swabs from yaws patients on Lihir Island, Papua New Guinea. Among all samples tested, fourteen molecular types were identified, seven of which were found in patient samples and seven among historical isolates or DNA. Three types (JG8, TD6, and SE7) were predominant on Lihir Island. Conclusions This MLST approach allows molecular typing and differentiation of yaws strains. This method could be a useful tool to complement epidemiological studies in regions where T. pallidum subsp. pertenue is prevalent with the overall goals of improving our understanding of yaws transmission dynamics and helping the yaws eradication campaign to succeed. PMID:29281641

Differential effects of the essential oils of Lavandula luisieri and Eryngium duriaei subsp. juresianum in cell models of two chronic inflammatory diseases.

PubMed

Rufino, Ana T; Ferreira, Isabel; Judas, Fernando; Salgueiro, Lígia; Lopes, M Celeste; Cavaleiro, Carlos; Mendes, Alexandrina F

2015-08-01

Effective drugs to treat osteoarthritis (OA) and inflammatory bowel disease (IBD) are needed. To identify essential oils (EOs) with anti-inflammatory activity in cell models of OA and IBD. EOs from Eryngium duriaei subsp. juresianum (M. Laínz) M. Laínz (Apiaceae), Laserpitium eliasii subsp. thalictrifolium Sennen & Pau (Apiaceae), Lavandula luisieri (Rozeira) Rivas-Martínez (Lamiaceae), Othantus maritimus (L.) Hoff. & Link (Asteraceae), and Thapsia villosa L. (Apiaceae) were analyzed by GC and GC/MS. The anti-inflammatory activity of EOs (5-200 μg/mL) was evaluated by measuring inducible nitric oxide synthase (iNOS) and nuclear factor-κB (NF-κB) activation (total and phosphorylated IκB-α), in primary human chondrocytes and the intestinal cell line, C2BBe1, stimulated with interleukin-1β (IL-1β) or interferon-γ (IFN-γ), IL-1β and tumor necrosis factor-α (TNF-α), respectively. The EO of L. luisieri significantly reduced iNOS (by 54.9 and 81.0%, respectively) and phosphorylated IκB-α (by 87.4% and 62.3%, respectively) in both cell models. The EO of E. duriaei subsp. juresianum caused similar effects in human chondrocytes, but was inactive in intestinal cells, even at higher concentrations. The EOs of L. eliasii subsp. thalictrifolium and O. maritimus decreased iNOS expression by 45.2 ± 8.7% and 45.2 ± 6.2%, respectively, in C2BBe1 cells and were inactive in chondrocytes. The EO of T. villosa was inactive in both cell types. This is the first study showing anti-inflammatory effects of the EOs of L. luisieri and E. duriaei subsp. juresianum. These effects are specific of the cell type and may be valuable to develop new therapies or as sources of active compounds with improved efficacy and selectivity towards OA and IBD.

Bis-indolic compounds as potential new therapeutic alternatives for tularaemia

PubMed Central

Caspar, Yvan; Sutera, Vivien; Boisset, Sandrine; Denis, Jean-Noël; Maurin, Max

2014-01-01

Francisella tularensis is the etiological agent of tularaemia and a CDC class A biological threat agent. Few antibiotic classes are currently useful in treating tularaemia, including the aminoglycosides gentamicin and streptomycin, fluoroquinolones, and tetracyclines. However, treatment failures and relapses remain frequent and F. tularensis strains resistant to antibiotics have been easily selected in vitro. In this study, we evaluated the activity of new synthetic bis-indole derivatives against this pathogen. Minimum inhibitory concentrations (MICs) of four compounds (dcm01 to dcm04) were determined for the reference strains F. tularensis subsp. holarctica LVS NCTC10857, F. tularensis subsp. novicida CIP56.12 and F. philomiragia ATCC25015, and for 41 clinical strains of F. tularensis subsp. holarctica isolated in France. Minimal bactericidal concentrations (MBCs) were determined for the dcm02 and dcm04 compounds for the LVS and two clinical strains. Killing curves were also determined for the same three strains exposed to dcm04. All tested bis-indole compounds were bacteriostatic against F. tularensis subsp. holarctica strains, with a MIC90 of 8 μg/mL for dcm01, dcm02, and dcm03, and 2 μg/mL for dcm04. Only one strain was resistant to both dcm01 and dcm03, with MICs > 32 μg/mL. In contrast, F. tularensis subsp. novicida was resistant to all derivatives and F. philomiragia was only susceptible to dcm02 and dcm04, with MICs of 16 and 4 μg/mL, respectively. MBC and killing curve experiments revealed significant bactericidal activity (i.e., 3-log reduction of the bacterial inoculum) of the dcm02 and dcm04 compounds only for the LVS strain. In conclusion, we have identified novel synthetic bis-indole compounds that are active against F. tularensis subsp. holarctica. They may be drug candidates for the development of new therapeutic alternatives for tularaemia treatment. Their further characterization is needed, especially identification of their bacterial targets. PMID:24579066

Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively

PubMed Central

Mikalová, Lenka; Strouhal, Michal; Oppelt, Jan; Grange, Philippe Alain; Janier, Michel; Benhaddou, Nadjet; Dupin, Nicolas; Šmajs, David

2017-01-01

Background Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). An unusual human TEN 11q/j isolate was obtained from a syphilis-like primary genital lesion from a patient that returned to France from Pakistan. Methodology/Principal findings The TEN 11q/j isolate was characterized using nested PCR followed by Sanger sequencing and/or direct Illumina sequencing. Altogether, 44 chromosomal regions were analyzed. Overall, the 11q/j isolate clustered with TEN strains Bosnia A and Iraq B as expected from previous TEN classification of the 11q/j isolate. However, the 11q/j sequence in a 505 bp-long region at the TP0488 locus was similar to Treponema pallidum subsp. pallidum (TPA) strains, but not to TEN Bosnia A and Iraq B sequences, suggesting a recombination event at this locus. Similarly, the 11q/j sequence in a 613 bp-long region at the TP0548 locus was similar to Treponema pallidum subsp. pertenue (TPE) strains, but not to TEN sequences. Conclusions/Significance A detailed analysis of two recombinant loci found in the 11q/j clinical isolate revealed that the recombination event occurred just once, in the TP0488, with the donor sequence originating from a TPA strain. Since TEN Bosnia A and Iraq B were found to contain TPA-like sequences at the TP0548 locus, the recombination at TP0548 took place in a treponeme that was an ancestor to both TEN Bosnia A and Iraq B. The sequence of 11q/j isolate in TP0548 represents an ancestral TEN sequence that is similar to yaws-causing treponemes. In addition to the importance of the 11q/j isolate for reconstruction of the TEN phylogeny, this case emphasizes the possible role of TEN strains in development of syphilis-like lesions. PMID:28263990

Bis-indolic compounds as potential new therapeutic alternatives for tularaemia.

PubMed

Caspar, Yvan; Sutera, Vivien; Boisset, Sandrine; Denis, Jean-Noël; Maurin, Max

2014-01-01

Francisella tularensis is the etiological agent of tularaemia and a CDC class A biological threat agent. Few antibiotic classes are currently useful in treating tularaemia, including the aminoglycosides gentamicin and streptomycin, fluoroquinolones, and tetracyclines. However, treatment failures and relapses remain frequent and F. tularensis strains resistant to antibiotics have been easily selected in vitro. In this study, we evaluated the activity of new synthetic bis-indole derivatives against this pathogen. Minimum inhibitory concentrations (MICs) of four compounds (dcm01 to dcm04) were determined for the reference strains F. tularensis subsp. holarctica LVS NCTC10857, F. tularensis subsp. novicida CIP56.12 and F. philomiragia ATCC25015, and for 41 clinical strains of F. tularensis subsp. holarctica isolated in France. Minimal bactericidal concentrations (MBCs) were determined for the dcm02 and dcm04 compounds for the LVS and two clinical strains. Killing curves were also determined for the same three strains exposed to dcm04. All tested bis-indole compounds were bacteriostatic against F. tularensis subsp. holarctica strains, with a MIC90 of 8 μg/mL for dcm01, dcm02, and dcm03, and 2 μg/mL for dcm04. Only one strain was resistant to both dcm01 and dcm03, with MICs > 32 μg/mL. In contrast, F. tularensis subsp. novicida was resistant to all derivatives and F. philomiragia was only susceptible to dcm02 and dcm04, with MICs of 16 and 4 μg/mL, respectively. MBC and killing curve experiments revealed significant bactericidal activity (i.e., 3-log reduction of the bacterial inoculum) of the dcm02 and dcm04 compounds only for the LVS strain. In conclusion, we have identified novel synthetic bis-indole compounds that are active against F. tularensis subsp. holarctica. They may be drug candidates for the development of new therapeutic alternatives for tularaemia treatment. Their further characterization is needed, especially identification of their bacterial targets.

Trophic Interactions of Infant Bifidobacteria and Eubacterium hallii during L-Fucose and Fucosyllactose Degradation

PubMed Central

Schwab, Clarissa; Ruscheweyh, Hans-Joachim; Bunesova, Vera; Pham, Van Thanh; Beerenwinkel, Niko; Lacroix, Christophe

2017-01-01

Fucosyllactoses (2′- or 3′-FL) account for up to 20% of human milk oligosaccharides (HMOs). Infant bifidobacteria, such as Bifidobacterium longum subsp. infantis, utilize the lactose moiety to form lactate and acetate, and metabolize L-fucose to 1,2-propanediol (1,2-PD). Eubacterium hallii is a common member of the adult gut microbiota that can produce butyrate from lactate and acetate, and convert 1,2-PD to propionate. Recently, a Swiss cohort study identified E. hallii as one of the first butyrate producers in the infant gut. However, the global prevalence of E. hallii and its role in utilization of HMO degradation intermediates remains unexplored. Fecal 16S rRNA gene libraries (n = 857) of humans of all age groups from Venezuela, Malawi, Switzerland, and the USA were screened for the occurrence of E. hallii. Single and co-culture experiments of B. longum subsp. infantis and E. hallii were conducted in modified YCFA containing acetate and glucose, L-fucose, or FL. Bifidobacterium spp. (n = 56) of different origin were screened for the ability to metabolize L-fucose. Relative abundance of E. hallii was low (10−5–10−3%) during the first months but increased and reached adult levels (0.01–10%) at 5–10 years of age in all four populations. In single culture, B. longum subsp. infantis grew in the presence of all three carbohydrates while E. hallii was metabolically active only with glucose. In co-culture E. hallii also grew with L-fucose or FL. In co-cultures grown with glucose, acetate, and glucose were consumed and nearly equimolar proportions of formate and butyrate were formed. B. longum subsp. infantis used L-fucose and produced 1,2-PD, acetate and formate in a ratio of 1:1:1, while 1,2-PD was used by E. hallii to form propionate. E. hallii consumed acetate, lactate and 1,2-PD released by B. longum subsp. infantis from FL, and produced butyrate, propionate, and formate. Beside B. longum subsp. infantis, Bifidobacterium breve, and a strain of B. longum subsp. suis were able to utilize L-fucose. This study identified a trophic interaction of infant bifidobacteria and E. hallii during L-fucose degradation, and pointed at E. hallii as a metabolically versatile species that occurs in infants and utilizes intermediates of bifidobacterial HMO fermentation. PMID:28194144

Trophic Interactions of Infant Bifidobacteria and Eubacterium hallii during L-Fucose and Fucosyllactose Degradation.

PubMed

Schwab, Clarissa; Ruscheweyh, Hans-Joachim; Bunesova, Vera; Pham, Van Thanh; Beerenwinkel, Niko; Lacroix, Christophe

2017-01-01

Fucosyllactoses (2'- or 3'-FL) account for up to 20% of human milk oligosaccharides (HMOs). Infant bifidobacteria, such as Bifidobacterium longum subsp. infantis , utilize the lactose moiety to form lactate and acetate, and metabolize L-fucose to 1,2-propanediol (1,2-PD). Eubacterium hallii is a common member of the adult gut microbiota that can produce butyrate from lactate and acetate, and convert 1,2-PD to propionate. Recently, a Swiss cohort study identified E. hallii as one of the first butyrate producers in the infant gut. However, the global prevalence of E. hallii and its role in utilization of HMO degradation intermediates remains unexplored. Fecal 16S rRNA gene libraries ( n = 857) of humans of all age groups from Venezuela, Malawi, Switzerland, and the USA were screened for the occurrence of E. hallii . Single and co-culture experiments of B. longum subsp. infantis and E. hallii were conducted in modified YCFA containing acetate and glucose, L-fucose, or FL. Bifidobacterium spp. ( n = 56) of different origin were screened for the ability to metabolize L-fucose. Relative abundance of E. hallii was low (10 -5 -10 -3 %) during the first months but increased and reached adult levels (0.01-10%) at 5-10 years of age in all four populations. In single culture, B. longum subsp. infantis grew in the presence of all three carbohydrates while E. hallii was metabolically active only with glucose. In co-culture E. hallii also grew with L-fucose or FL. In co-cultures grown with glucose, acetate, and glucose were consumed and nearly equimolar proportions of formate and butyrate were formed. B. longum subsp. infantis used L-fucose and produced 1,2-PD, acetate and formate in a ratio of 1:1:1, while 1,2-PD was used by E. hallii to form propionate. E. hallii consumed acetate, lactate and 1,2-PD released by B. longum subsp. infantis from FL, and produced butyrate, propionate, and formate. Beside B. longum subsp. infantis, Bifidobacterium breve , and a strain of B. longum subsp. suis were able to utilize L-fucose. This study identified a trophic interaction of infant bifidobacteria and E. hallii during L-fucose degradation, and pointed at E. hallii as a metabolically versatile species that occurs in infants and utilizes intermediates of bifidobacterial HMO fermentation.

Aerosol and Surface Deposition Characteristics of Two Surrogates for Bacillus anthracis Spores

PubMed Central

Stapleton, Helen L.

2016-01-01

ABSTRACT Spores of an acrystalliferous derivative of Bacillus thuringiensis subsp. kurstaki, termed Btcry−, are morphologically, aerodynamically, and structurally indistinguishable from Bacillus anthracis spores. Btcry− spores were dispersed in a large, open-ended barn together with spores of Bacillus atrophaeus subsp. globigii, a historically used surrogate for Bacillus anthracis. Spore suspensions (2 × 1012 CFU each of B. atrophaeus subsp. globigii and Btcry−) were aerosolized in each of five spray events using a backpack misting device incorporating an air blower; a wind of 4.9 to 7.6 m s−1 was also flowing through the barn in the same direction. Filter air samplers were situated throughout the barn to assess the aerosol density of the spores during each release. Trays filled with a surfactant in aqueous buffer were placed on the floor near the filter samplers to assess spore deposition. Spores were also recovered from arrays of solid surfaces (concrete, aluminum, and plywood) that had been laid on the floor and set up as a wall at the end of the barn. B. atrophaeus subsp. globigii spores were found to remain airborne for significantly longer periods, and to be deposited on horizontal surfaces at lower densities, than Btcry− spores, particularly near the spray source. There was a 6-fold-higher deposition of Btcry− spores than of B. atrophaeus subsp. globigii spores on vertical surfaces relative to the surrounding airborne density. This work is relevant for selecting the best B. anthracis surrogate for the prediction of human exposure, hazard assessment, and hazard management following a malicious release of B. anthracis. IMPORTANCE There is concern that pathogenic bacteria could be maliciously disseminated in the air to cause human infection and disruption of normal life. The threat from spore-forming organisms, such as the causative agent of anthrax, is particularly serious. In order to assess the extent of this risk, it is important to have a surrogate organism that can be used to replicate the dispersal characteristics of the threat agent accurately. This work compares the aerosol dispersal and deposition behaviors of the surrogates Btcry− and B. atrophaeus subsp. globigii. Btcry− spores remained in the air for a shorter time, and were markedly more likely to adhere to vertical surfaces, than B. atrophaeus subsp. globigii spores. PMID:27613681

Investigation of bovine venereal campyloacteriosis in beef cow herds in New Zealand.

PubMed

McFadden, A M; Heuer, C; Jackson, R; West, D M; Parkinson, T J

2005-02-01

To determine regional prevalences of beef cow herds in New Zealand positive for Campylobacter fetus subsp venerealis antibodies in samples of vaginal mucus tested using an immunoglobulin (Ig) A enzyme-linked immunosorbent assay (ELISA), and to examine the suitability of the IgA ELISA for detecting infection with C. fetus subsp venerealis under field conditions in New Zealand. Vaginal mucus samples (n=1,230) collected from beef cow herds (n=125) throughout New Zealand (approximately 10 samples/herd) were tested for antibodies to C. fetus subsp venerealis using an IgA ELISA. Test results were compared between herds classified as having low, medium and high fertility based on pregnancy test results interpreted in relation to the duration of the mating period used. In addition, a small number of samples were collected from dairy cows that were mated using artificial insemination (AI) and had no contact with breeding bulls. The influence of putative risk factors for the spread of venereal disease and the effect of sample quality on the status of herds according to test results was assessed using multivariate logistical regression. Preputial washings from 54 bulls from nine herds classified as low fertility in which mucus samples from > or =3 cows were IgA antibody-positive were cultured for the presence of Campylobacter spp, and isolates of C. fetus subspecies were characterised using a polymerase chain reaction (PCR) test. One or more mucus samples was positive to the IgA ELISA in 70% of all herds tested. The prevalence of IgA antibody- positive individuals was >20% in most regions of New Zealand and did not differ significantly for cows from herds classified as high, medium or low fertility (28%, 26% and 23%, respectively; p=0.39). No relationship was found between mucus antibody status and age of breeding group, herd size, herd fertility, number of herds that female replacements or breeding bulls were sourced from, whether a serving ability test (SAT) was used to assess bulls, or the quality of samples submitted to the laboratory. Campylobacter fetus subsp venerealis was not cultured from any of the 54 bulls sampled. Four other species of Campylobacter and related organisms were cultured, viz Arcobacter cryaerophilus, Campylobacter jejuni, Campylobacter fetus subsp fetus and Helicobacter cinaedi. The specificity of the IgA ELISA as a diagnostic test for C. fetus subsp venerealis was found to be unsatisfactory under New Zealand conditions. It is possible that an immunological response by cows to Campylobacter species other than C. fetus subsp venerealis caused cross-reactivity in the IgA ELISA. The results do not support the hypothesis that C. fetus subsp venerealis is widespread in New Zealand.

Foraging by Hippodamia convergens for cereal aphids on wheat plants in the laboratory

USDA-ARS?s Scientific Manuscript database

We investigated predation by adult Hippodamia convergens Guerin-Meneville on the English grain aphid, Sitobion avenae L., on wheat plants in a laboratory arena. A model relating beetle hunger to starvation time was developed and was used to calculate initial hunger for beetles used in predation obs...

Genetic diversity and crown rust resistance of oat landraces from various locations throughout Turkey

USDA-ARS?s Scientific Manuscript database

A diversity study was carried out to identify the origin of 375 oat landraces (Avena sativa L. and A. byzantina C. Koch.) collected from Turkey and maintained in various gene banks. New assays interrogating oat-based microsatellite and single-nucleotide polymorphism loci were used to characterize t...

Prey foraging movements by Hippodamia convergens in wheat are influenced by hunger and aphids

USDA-ARS?s Scientific Manuscript database

We investigated foraging movements by adult female convergent lady beetles, Hippodamia convergens Guerin-Meneville, on English grain aphids, Sitobion avenae L., on wheat, Triticum aestivum L., growing in 1.8 x 1.8 m plantings in a greenhouse with a soil floor. The wheat was planted to simulate whea...

A gene expression atlas of developing oat seeds for enhancing nutritional composition

USDA-ARS?s Scientific Manuscript database

Oat (Avena sativa L.) genome resources are less abundant than for wheat and barley, but next generation sequencing (NGS) technologies have great potential to accelerate new genome information for oat in a cost-effective manner. We are employing RNA-Seq to develop a gene expression atlas of developin...

A comparative study between nonlinear regression and artificial neural network approaches for modelling wild oat (Avena fatua) field emergence

USDA-ARS?s Scientific Manuscript database

Non-linear regression techniques are used widely to fit weed field emergence patterns to soil microclimatic indices using S-type functions. Artificial neural networks present interesting and alternative features for such modeling purposes. In this work, a univariate hydrothermal-time based Weibull m...

Black oat cover crop management in watermelon production systems

USDA-ARS?s Scientific Manuscript database

Black oats (Avena strigosa Schreb.) were sown as a cover crop near Weslaco, Texas (Lat. 26 deg N) in Fall 2010. The cover crop was allowed to senesce naturally and was planted to watermelons in both the spring and in the fall of 2011. Watermelon transplants planted in the spring into mowed black o...

Response of Pinus ponderosa Seedlings to Stylet-Bearing Nematodes

PubMed Central

Viglierchio, D. R.

1979-01-01

Of 12 stylet-bearing nematodes used for inoculations, Pratylenchus penetrans, P. brachyurus, P. vulnus, Ditylenchus destructor, Meloidogyne incognita, M. javanica, and M. hapla reproduced on Pinus ponderosa, while Xiphinema index, Aphelenchus avenae, Paratylenehus neoamblycephalus, Tylenchulus semipenetrans, and Macroposthonia xenoplax did not. P. vulnus, P. brachyurus, P. penetrans, A. avenae, D. destructor, T. semipenetrans, and P. neoamblycephalus significantly suppressed both the shoot and root wet weights of ponderosa pine seedlings obtained from stands in five different locations. X. index significantly suppressed root wet weights, M. xenoplax siguificantly suppressed shoot wet weight, and M. incognita, M. javanica, and M. hapla suppressed neither at the inoculation levels used. Injurious nematodes tended to suppress root growth more than shoot growth. Seedlings from two locations produced greater shoot growth wet weight than did seedlings from the other three locations. The more injurious nematodes tended to cause an increase in the water content of shoots. Frequency analyses of seedling population shoot-root ratios indicated that ponderosa pine seedlings could be selected for better shoot-root ratios as well as for resistance to several pathogenic nematodes. PMID:19300659

Gravitropic responses of the Avena coleoptile in space and on clinostats. I. Gravitropic response thresholds

NASA Technical Reports Server (NTRS)

Brown, A. H.; Chapman, D. K.; Johnsson, A.; Heathcote, D.

1995-01-01

We conducted a series of gravitropic experiments on Avena coleoptiles in the weightlessness environment of Spacelab. The purpose was to test the threshold stimulus, reciprocity rule and autotropic reactions to a range of g-force stimulations of different intensities and durations The tests avoided the potentially complicating effects of earth's gravity and the interference from clinostat ambiguities. Using slow-speed centrifuges, coleoptiles received transversal accelerations in the hypogravity range between 0.l and 1.0 g over periods that ranged from 2 to 130 min. All responses that occurred in weightlessness were compared to clinostat experiments on earth using the same apparatus. Characteristic gravitropistic response patterns of Atuena were not substantially different from those observed in ground-based experiments. Gravitropic presentation times were extrapolated. The threshold at 1.0 g was less than 1 min (shortest stimulation time 2 min), in agreement with values obtained on the ground. The least stimulus tested, 0.1 g for 130 min, produced a significant response. Therefore the absolute threshold for a gravitropic response is less than 0.1 g.

[A sudden rise in INR due to combination of Tribulus terrestris, Avena sativa, and Panax ginseng (Clavis Panax)].

PubMed

Turfan, Murat; Tasal, Abdurrahman; Ergun, Fatih; Ergelen, Mehmet

2012-04-01

Warfarin sodium is an antithrombin agent used in patients with prosthetic valve and atrial fibrillation. However, there are many factors that can change the effectiveness of the drug. Today, herbal mixtures promoted through targeted print and visual media can lead to sudden activity changes in patients using warfarin. In this case report we will present two cases with a sudden rise in INR due to using combination of Tribulus terrestris, Avena sativa and Panax ginseng (Panax Clavis). Two patients who used warfarin due to a history of aortic valve replacement (case 1) and atrial fibrillation (case 2) were admitted to the hospital due very high levels of INR detected during routine follow-up. Both patients had used an herbal medicine called ''Panax'' during the last month. The patients gave no indication regarding a change in diet or the use of another agent that might interact with warfarin. In cases where active bleeding could not be determinated, we terminated the use of the drug and re-evaluated dosage of warfarin before finally discharging the patient.

Ozone suppression of oat crown rust uredia development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heagle, A.S.

1969-01-01

First foliage leaves of 10-day-old crown rust differential varieties of Avena sativa were inoculated with urediospores of race 264 of Puccinia coronata var. avenae and placed for 16 hr in a mist chamber at 23 C. Infected plants were then placed in two separate chambers at 25C, 80% relative humidity, 3000 ft-c, and a 16-hr photoperiod. Plants in one chamber were exposed to 10 pphm ozone (KI corrected Mast value) for 6 hr daily in the light for 10 days. Plants in the other chamber were not exposed to ozone. Visible ozone injury was restricted to minor flecking. In severalmore » varieties, a slight reddening appeared on inoculated leaves near the end of the experiment. The reaction to rust on ozone-exposed plants of all varieties was resistant, whereas the reaction on nonexposed plants of all differentials except 8, 9, and 10 was susceptible. The level of ozone used in this experiment is often surpassed in rural areas near urban centers, indicating that air pollution can influence rust development in the field.« less

Genome-Wide Association Mapping of Barley Yellow Dwarf Virus Tolerance in Spring Oat (Avena sativa L.)

PubMed Central

Foresman, Bradley J.; Oliver, Rebekah E.; Jackson, Eric W.; Chao, Shiaoman; Arruda, Marcio P.; Kolb, Frederic L.

2016-01-01

Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD) and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance. A genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C (Mrg17) and 18D (Mrg04). This is the first report of BYDV tolerance QTL on chromosome 3C (Mrg17) and 18D (Mrg04). Haplotypes using the two QTL were evaluated and distinct classes for tolerance were identified based on the number of favorable alleles. A large number of lines carrying both favorable alleles were observed in the panel. PMID:27175781

Theoretical study of the acid-base properties of the montmorillonite/electrolyte interface: influence of the surface heterogeneity and ionic strength on the potentiometric titration curves.

PubMed

Zarzycki, Piotr; Thomas, Fabien

2006-10-15

The parallel shape of the potentiometric titration curves for montmorillonite suspension is explained using the surface complexation model and taking into account the surface heterogeneity. The homogeneous models give accurate predictions only if they assume unphysically large values of the equilibrium constants for the exchange process occurring on the basal plane. However, the assumption that the basal plane is energetically heterogeneous allows to fit the experimental data (reported by Avena and De Pauli [M. Avena, C.P. De Pauli, J. Colloid Interface Sci. 202 (1998) 195-204]) for reasonable values of exchange equilibrium constant equal to 1.26 (suggested by Fletcher and Sposito [P. Fletcher, G. Sposito, Clay Miner. 24 (1989) 375-391]). Moreover, we observed the typical behavior of point of zero net proton charge (pznpc) as a function of logarithm of the electrolyte concentration (log[C]). We showed that the slope of the linear dependence, pznpc=f(log[C]), is proportional to the number of isomorphic substitutions in the crystal phase, which was also observed in the experimental studies.

Identification and Quantification of Avenanthramides and Free and Bound Phenolic Acids in Eight Cultivars of Husked Oat ( Avena sativa L) from Finland.

PubMed

Multari, Salvatore; Pihlava, Juha-Matti; Ollennu-Chuasam, Priscilla; Hietaniemi, Veli; Yang, Baoru; Suomela, Jukka-Pekka

2018-03-21

Finland is the second largest oat producer in Europe. Despite the existing knowledge of phenolics in oat, there is little information on the phenolic composition of oats from Finland. The aim of the study was to investigate the concentrations of free and bound phenolic acids, as well as avenanthramides in eight Finnish cultivars of husked oat ( Avena sativa L.). Seven phenolic acids and one phenolic aldehyde were identified, including, in decreasing order of abundance: p-coumaric, ferulic, cinnamic, syringic, vanillic, 2,4-dihydroxybenzoic, and o-coumaric acids and syringaldehyde. Phenolic acids were mostly found as bound compounds. Significant varietal differences ( p < 0.05) were observed in the cumulative content of phenolic acids, with the lowest level found in cv. 'Viviana' (1202 ± 52.9 mg kg -1 ) and the highest in cv. 'Akseli' (1687 ± 80.2 mg kg -1 ). Avenanthramides (AVNs) 2a, 2p, and 2f were the most abundant. Total AVNs levels ranged from 26.7 ± 1.44 to 185 ± 12.5 mg kg -1 in cv. 'Avetron' and 'Viviana', respectively.

Metabonomic strategy for the investigation of the mode of action of the phytotoxin (5S,8R,13S,16R)-(-)-pyrenophorol using 1H nuclear magnetic resonance fingerprinting.

PubMed

Aliferis, Konstantinos A; Chrysayi-Tokousbalides, Maria

2006-03-08

The biochemical mode of action of (5S,8R,13S,16R)-(-)-pyrenophorol isolated from a Drechslera avenae pathotype was investigated by using metabolic fingerprinting. (1)H NMR spectra of crude leaf extracts from untreated Avena sterilis seedlings and A. sterilis seedlings treated with pyrenophorol were compared with those obtained from treatments with the herbicides diuron, glyphosate, mesotrione, norflurazon, oxadiazon, and paraquat. Multivariate analysis was carried out to group treatments according to the mode of action of the phytotoxic substances applied. Analysis results revealed that none of the herbicide treatments fitted the pyrenophorol model and indicate that the effect of the phytotoxin on A. sterilis differs than those caused by glyphosate, mesotrione, norflurazon, oxadiazon, paraquat, and diuron, which inhibit 5-enolpyruvylshikimate-3-phosphate synthase, 4-hydroxyphenyl-pyruvate-dioxygenase, phytoene desaturase, protoporphyrinogen oxidase, photosystem I, and photosystem II, respectively. The method applied, combined with appropriate data preprocessing and analysis, was found to be rapid for the screening of phytotoxic substances for metabolic effects.

Genotypic and phenotypic changes in wild barley (Hordeum vulgare subsp. spontaneum) during a period of climate change in Jordan

USDA-ARS?s Scientific Manuscript database

Climate change and other anthropogenic disturbances can lead to the loss of genetic variation and thereby affect evolutionary potential and survival of plant populations in the wild. We examined these predictions in the primary wild relative of barley, Hordeum vulgare L. subsp. spontaneum (K. Koch) ...

First report of bacterial blight of crucifers caused by Pseudomonas cannabina pv. alisalensis in Minnesota on arugula (Eruca vesicaria subsp. sativa)

USDA-ARS?s Scientific Manuscript database

In 2011, bacterial blight of arugula (Eruca vesicaria subsp. sativa; cv. Roquette) was observed in organically grown plants under overhead irrigation near Delano, MN. Approximately 80 to 100% of each planting was affected. Blue-green fluorescent pseudomonads were isolated consistently on King’s Medi...

Analysis of the Immune Response to a Major Membrane Protein of Mycobacterium avium subsp. paratuberculosis in Experimentally and Naturally Infected Cattle

USDA-ARS?s Scientific Manuscript database

The 35 kDa major membrane protein (MMP) of Mycobacterium avium subsp. paratuberculosis (Map) is implicated in the pathogenesis of paratuberculosis (Ptb) in cattle. Understanding the immune response to MMP could reveal how Map evades immune elimination and provide information needed for developing a ...

Rocket Immunoelectrophoresis of the Entomocidal Parasporal Crystal of Bacillus thuringiensis subsp. kurstaki†

PubMed Central

Andrews, R. E.; Iandolo, J. J.; Campbell, B. S.; Davidson, L. I.; Bulla, L. A.

1980-01-01

Rocket immunoelectrophoresis was used to quantitate the soluble parasporal crystal of Bacillus thuringiensis subsp. kurstaki. The method described is rapid, reliable, specific, and extremely accurate, and it can be used to measure crystal toxin in commercial microbial insecticides that contain a mixture of spores, vegetative cells, and carrier materials. Images PMID:16345656

Comparison of nine PCR primer sets designed to detect Pantoea stewartii subsp. stewartii in maize

USDA-ARS?s Scientific Manuscript database

Pantoea stewartii subsp. stewartii, the causal agent of Stewart's bacterial wilt of maize, is a major quarantine pest in maize seed. Verifying freedom from P. stewartii remains a significant hurdle in exporting corn seed from the U.S. Several PCR primer sets have been developed and suggested as bein...

Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.

PubMed

Treangen, Todd J; Maybank, Rosslyn A; Enke, Sana; Friss, Mary Beth; Diviak, Lynn F; Karaolis, David K R; Koren, Sergey; Ondov, Brian; Phillippy, Adam M; Bergman, Nicholas H; Rosovitz, M J

2014-11-06

Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used as a control strain for susceptibility testing to antibiotics and as a quality control strain for commercial products. We present the completed genome sequence for the strain, consisting of the chromosome and a 27.5-kb plasmid. Copyright © 2014 Treangen et al.

Chemical decontamination with n-acetyl-l-cysteine-sodium hydroxide improves recovery of viable Mycobacterium avium subsp. paratuberculosis organisms from cultured milk

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is shed into milk and feces of cows with advanced Johne’s disease, allowing transmission of MAP among animals. The objective of this study was to formulate an optimized protocol for the isolation of MAP from milk. Parameters investigated included che...

Sensitivity of mycobacterium avium subsp paratuberculosis, escherichia coli and salmonella enterica serotype typhimurium to low pH, high organic acids and ensiling

USDA-ARS?s Scientific Manuscript database

The ability of Mycobacterium avium subsp paratuberculosis (M. paratuberculosis), Salmonella enterica serotype Typhimurium (S. Typhimurium) and a commensal Escherichia coli (E. coli) isolate to persist under low pH and high organic acid conditions was determined. Die-off rates were calculated followi...

Analysis of Mycobacterium avium subsp. paratuberculosis mutant libraries reveals loci-dependent transcription biases and strategies to novel mutant discovery

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in ruminants and it has been implicated as a cause of Crohn’s disease in humans. The generation of comprehensive random mutant banks by transposon mutagenesis is a fundamental wide genomic technology utilized...

Bartonella vinsonii subsp. berkhoffii endocarditis in a dog from Saskatchewan

PubMed Central

Cockwill, Ken R.; Taylor, Susan M.; Philibert, Helene M.; Breitschwerdt, Edward B.; Maggi, Ricardo G.

2007-01-01

A dog referred for lameness was diagnosed with culture-negative endocarditis. Antibodies to Bartonella spp. were detected. Antibiotic treatment resulted in transient clinical improvement, but the dog developed cardiac failure and was euthanized. Bartonella vinsonii subsp. berkhoffii genotype IV was identified within the aortic heart valve lesions by PCR amplification and DNA sequencing. PMID:17824328

Identification of quantitative trait loci for Goss’s wilt of maize caused by Clavibacter michiganensis subsp. nebraskensis

USDA-ARS?s Scientific Manuscript database

Since its discovery in 1969, Goss’s wilt, a vascular disease caused by the gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn), has emerged as one of the top four diseases of maize in the United States and Ontario, Canada. No source of complete resistance has been described f...

Mycobacterium avium subsp. paratuberculosis PPE Protein MAP1152 and Conserved Protein MAP1156 are Antigenic in Experimentally and Naturally Infected Cattle

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s Disease (JD) in ruminants resulting in significant production losses. An insertion mutation upstream from the MAP1152-MAP1156 region causes a change in colony morphotype and results in an attenuated phenotype in bovine monocyte derive...

Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology

PubMed Central

Lu, You; Samac, Deborah A.; Glazebrook, Jane

2015-01-01

We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies. PMID:25953184

Wind speed effects on the quantity of Xanthomonas citri subsp. citri dispersed downwind from canopies of grapefruit trees infected with citrus canker

USDA-ARS?s Scientific Manuscript database

The epidemic of citrus canker (Xanthomonas citri subsp. citri, Xcc) in Florida continues to expand since termination of the eradication program in 2006. Storms are known to be associated with disease spread, but little information exists on the interaction of fundamental physical and biological proc...

Splenic Abscess Caused by Streptococcus gallolyticus subsp. pasteurianus as Presentation of a Pancreatic Cancer

PubMed Central

Su, Yanli; Miao, Bin; Wang, Hong; Wang, Chao

2013-01-01

Splenic abscesses caused by Streptococcus bovis are rarely reported in the literature and are mainly seen in patients with endocarditis and associated colonic neoplasia/carcinoma. We report the first case of splenic abscess caused by Streptococcus gallolyticus subsp. pasteurianus (Streptococcus bovis biotype II/2) as presentation of a pancreatic cancer. PMID:24025909

Evaluation of the association between fecal excretion of Mycobacterium avium subsp paratuberculosis and detection in colostrum and on teat skin surfaces of dairy cows

USDA-ARS?s Scientific Manuscript database

Objective—To evaluate the association between fecal excretion of Mycobacterium avium subsp paratuberculosis (MAP) by dairy cows in the periparturient period and detection of MAP DNA in colostrum specimens and on teat skin surfaces. Design—Cross-sectional study. Animals—112 Holstein cows. Procedures—...

Evaluation of two mutants of Mycobacterium avium subsp. paratuberculosis as candidates for a live attenuated vaccine for Johne's disease

USDA-ARS?s Scientific Manuscript database

Efforts to control Johne’s disease (JD), caused by Mycobacterium avium subsp. paratuberculosis (Map), has been difficult because of a lack of an effective vaccine. To address this problem we examined the potential of targeted gene disruption as a method to develop candidate vaccines with impaired c...

Draft Genome Sequences of 18 Salmonella enterica subsp. enterica Serovar Oranienburg Strains Isolated from Rivers in Northwestern Mexico.

PubMed

Casteñeda-Ruelas, Gloria M; Carreón-Gaxiola, César; Castelán-Sánchez, Hugo G; Acatzi-Silva, Abraham; Romero-Martínez, Salvador; García-Molina, Alejandra; Jiménez-Edeza, Maribel

2017-03-09

Salmonella enterica subsp. enterica serovar Oranienburg is recognized as a foodborne pathogen widely distributed in the environment. Here, we report 18 draft genomes of S  Oranienburg strains isolated from rivers in the northwestern region of Mexico. Copyright © 2017 Casteñeda-Ruelas et al.

The correct name for a subspecies of Oenothera fruticosa L. (Onagraceae)

PubMed Central

Wagner, Warren L.

2014-01-01

Abstract In 1978 when Straley adopted the name Oenothera fruticosa L. subsp. glauca (Michx.) Straley for one of the two recognized subspecies of O. fruticosa it was the correct name for this taxon; however, since that time the botanical code has changed so that now an autonym is treated as having priority over the name or names of the same date and rank that established it. This change means that since 1981 O. fruticosa subsp. glauca was no longer the correct name. The appropriate combination for it is made here as O. fruticosa L. subsp. tetragona (Roth) W.L. Wagner. Original material for the basionym, O. tetragona, is no longer extant so a neotype is designated. PMID:24596489

Tripartite Interactions of Barley Yellow Dwarf Virus, Sitobion avenae and Wheat Varieties

PubMed Central

Liu, Xiao-Feng; Hu, Xiang-Shun; Keller, Mike A.; Zhao, Hui-Yan; Wu, Yun-Feng; Liu, Tong-Xian

2014-01-01

The tripartite interactions in a pathosystem involving wheat (Triticum aestivum L.), the Barley yellow dwarf virus (BYDV), and the BYDV vector aphid Sitobion avenae were studied under field conditions to determine the impact of these interactions on aphid populations, virus pathology and grain yield. Wheat varietal resistance to BYDV and aphids varied among the three wheat varieties studied over two consecutive years. The results demonstrated that (1) aphid peak number (APN) in the aphid + BYDV (viruliferous aphid) treatment was greater and occurred earlier than that in the non-viruliferous aphid treatment. The APN and the area under the curve of population dynamics (AUC) on a S. avenae-resistant variety 98-10-30 was significantly lower than on two aphid-susceptible varieties Tam200(13)G and Xiaoyan6. (2) The production of alatae (PA) was greater on the variety 98-10-30 than on the other varieties, and PA was greater in the aphid + BYDV treatment on 98-10-30 than in the non-viruliferous aphid treatment, but this trend was reversed on Tam200(13)G and Xiaoyan6. (3) The BYDV disease incidence (DIC) on the variety 98-10-30 was greater than that on the other two varieties in 2012, and the disease index (DID) on Tam200(13)G was lower than on the other varieties in the aphid + BYDV and BYDV treatments in 2012, but not in 2011 when aphid vector numbers were generally lower. (4) Yield loss in the aphid + BYDV treatment tended to be greater than that in the aphid or BYDV alone treatments across varieties and years. We suggested that aphid population development and BYDV transmission tend to promote each other under field conditions. The aphids + BYDV treatment caused greater yield reductions than non-viruliferous aphids or virus treatment. Wheat varietal resistance in 98-10-30 affects the aphid dispersal, virus transmission and wheat yield loss though inhibits aphid populations from increasing. PMID:25184214

Discrimination of plant-parasitic nematodes from complex soil communities using ecometagenetics.

PubMed

Porazinska, Dorota L; Morgan, Matthew J; Gaspar, John M; Court, Leon N; Hardy, Christopher M; Hodda, Mike

2014-07-01

Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens-known and unknown, indigenous, and experimentally added-were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.

Puccinia coronata f. sp. avenae: a threat to global oat production.

PubMed

Nazareno, Eric S; Li, Feng; Smith, Madeleine; Park, Robert F; Kianian, Shahryar F; Figueroa, Melania

2018-05-01

Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/. © 2017 BSPP AND JOHN WILEY & SONS LTD.

Characterization of Three Novel Fatty Acid- and Retinoid-Binding Protein Genes (Ha-far-1, Ha-far-2 and Hf-far-1) from the Cereal Cyst Nematodes Heterodera avenae and H. filipjevi.

PubMed

Qiao, Fen; Luo, Lilian; Peng, Huan; Luo, Shujie; Huang, Wenkun; Cui, Jiangkuan; Li, Xin; Kong, Lingan; Jiang, Daohong; Chitwood, David J; Peng, Deliang

2016-01-01

Heterodera avenae and H. filipjevi are major parasites of wheat, reducing production worldwide. Both are sedentary endoparasitic nematodes, and their development and parasitism depend strongly on nutrients obtained from hosts. Secreted fatty acid- and retinol-binding (FAR) proteins are nematode-specific lipid carrier proteins used for nutrient acquisition as well as suppression of plant defenses. In this study, we obtained three novel FAR genes Ha-far-1 (KU877266), Ha-far-2 (KU877267), Hf-far-1 (KU877268). Ha-far-1 and Ha-far-2 were cloned from H. avenae, encoding proteins of 191 and 280 amino acids with molecular masses about 17 and 30 kDa, respectively and sequence identity of 28%. Protein Blast in NCBI revealed that Ha-FAR-1 sequence is 78% similar to the Gp-FAR-1 protein from Globodera pallida, while Ha-FAR-2 is 30% similar to Rs-FAR-1 from Radopholus similis. Only one FAR protein Hf-FAR-1was identified in H. filipjevi; it had 96% sequence identity to Ha-FAR-1. The three proteins are alpha-helix-rich and contain the conserved domain of Gp-FAR-1, but Ha-FAR-2 had a remarkable peptide at the C-terminus which was random-coil-rich. Both Ha-FAR-1 and Hf-FAR-1 had casein kinase II phosphorylation sites, while Ha-FAR-2 had predicted N-glycosylation sites. Phylogenetic analysis showed that the three proteins clustered together, though Ha-FAR-1 and Hf-FAR-1 adjoined each other in a plant-parasitic nematode branch, but Ha-FAR-2 was distinct from the other proteins in the group. Fluorescence-based ligand binding analysis showed the three FAR proteins bound to a fluorescent fatty acid derivative and retinol and with dissociation constants similar to FARs from other species, though Ha-FAR-2 binding ability was weaker than that of the two others. In situ hybridization detected mRNAs of Ha-far-1 and Ha-far-2 in the hypodermis. The qRT-PCR results showed that the Ha-far-1and Ha-far-2 were expressed in all developmental stages; Ha-far-1 expressed 70 times more than Ha-far-2 in all stages. The highest expression level of Ha-far-1 was observed in fourth-stage juvenile (J4), whereas the highest expression level of Ha-far-2 occurred in second-stage juvenile (J2). In conclusion, we have identified two novel far genes from H. avenae and one from H. filipjevi and have provided further indication that nematode far genes are present in a variety of nematode species, where the FAR proteins share similar basic structure, expression pattern and biochemical activities.

Quorum sensing in the plant pathogen Erwinia carotovora subsp. carotovora: the role of expR(Ecc).

PubMed

Andersson, R A; Eriksson, A R; Heikinheimo, R; Mäe, A; Pirhonen, M; Kõiv, V; Hyytiäinen, H; Tuikkala, A; Palva, E T

2000-04-01

The production of the main virulence determinants of the plant pathogen Erwinia carotovora subsp. carotovora, the extracellular cell wall-degrading enzymes, is partly controlled by the diffusible signal molecule N-(3-oxohexanoyl)-L-homoserine lactone (OHHL). OHHL is synthesized by the product of the expI/carI gene. Linked to expI we found a gene encoding a putative transcriptional regulator of the LuxR-family. This gene, expR(Ecc), is transcribed convergently to the expI gene and the two open reading frames are partially overlapping. The ExpR(Ecc) protein showed extensive amino acid sequence similarity to the repressor EsaR from Pantoea stewartii subsp. stewartii (formerly Erwinia stewartii subsp. stewartii) and to the ExpR(Ech) protein of Erwinia chrysanthemi. Inactivation of the E. carotovora subsp. carotovora expR(Ecc) gene caused no decrease in virulence or production of virulence determinants in vitro. In contrast, there was a slight increase in the maceration capacity of the mutant strain. The effects of ExpR(Ecc) were probably mediated by changes in OHHL levels. Inactivation of expR(Ecc) resulted in increased OHHL levels during early logarithmic growth. In addition, overexpression of expR(Ecc) caused a clear decrease in the production of virulence determinants and part of this effect was likely to be caused by OHHL binding to ExpR(Ecc). ExpR(Ecc) did not appear to exhibit transcriptional regulation of expI, but the effect on OHHL was apparently due to other mechanisms.

Production of Buttery-Odor Compounds and Transcriptome Response in Leuconostoc gelidum subsp. gasicomitatum LMG18811T during Growth on Various Carbon Sources

PubMed Central

Vesterinen, Sanna; Parshintsev, Jevgeni; Johansson, Per; Riekkola, Marja-Liisa; Björkroth, Johanna

2014-01-01

Leuconostoc gelidum subsp. gasicomitatum is a common spoilage bacterium in meat products packaged under oxygen-containing modified atmospheres. Buttery off-odors related to diacetyl/acetoin formation are frequently associated with the spoilage of these products. A whole-genome microarray study, together with gas chromatography (GC)-mass spectrometry (MS) analyses of the pathway end products, was performed to investigate the transcriptome response of L. gelidum subsp. gasicomitatum LMG18811T growing on semidefined media containing glucose, ribose, or inosine, which are essential carbon sources in meat. Generally, the gene expression patterns with ribose and inosine were quite similar, indicating that catabolism of ribose and nucleosides is closely linked. Diacetyl/acetoin concentrations as high as 110 or 470 μM were measured when growth was based on inosine or ribose, respectively. The gene expression results for pyruvate metabolism (upregulation of α-acetolactate synthase, downregulation of l-lactate dehydrogenase and pyruvate dehydrogenase) were as expected when diacetyl and acetoin were the end products. No diacetyl production (<7.5 μM) was detected with the glucose-containing medium, even though the cell counts of LMG18811T was 6 or 10 times higher than that on inosine or ribose, respectively. Although glucose was the most effective carbon source for the growth of L. gelidum subsp. gasicomitatum, utilization of inosine and ribose resulted in the production of the unwanted buttery-odor compounds. These results increase our understanding of which compounds are likely to enhance the formation of buttery odors during meat spoilage caused by L. gelidum subsp. gasicomitatum. PMID:25548057

Antibacterial activities of naturally occurring compounds against Mycobacterium avium subsp. paratuberculosis.

PubMed

Wong, Stella Y Y; Grant, Irene R; Friedman, Mendel; Elliott, Christopher T; Situ, Chen

2008-10-01

The antibacterial activities of 18 naturally occurring compounds (including essential oils and some of their isolated constituents, apple and green tea polyphenols, and other plant extracts) against three strains of Mycobacterium avium subsp. paratuberculosis (a bovine isolate [NCTC 8578], a raw-milk isolate [806R], and a human isolate [ATCC 43015]) were evaluated using a macrobroth susceptibility testing method. M. avium subsp. paratuberculosis was grown in 4 ml Middlebrook 7H9 broth containing 10% oleic acid-albumin-dextrose-catalase, 0.05% Tween 80 (or 0.2% glycerol), and 2 microg/ml mycobactin J supplemented with five concentrations of each test compound. The changes in the optical densities of the cultures at 600 nm as a measure of CFU were recorded at intervals over an incubation period of 42 days at 37 degrees C. Six of the compounds were found to inhibit the growth of M. avium subsp. paratuberculosis. The most effective compound was trans-cinnamaldehyde, with a MIC of 25.9 microg/ml, followed by cinnamon oil (26.2 microg/ml), oregano oil (68.2 microg/ml), carvacrol (72.2 microg/ml), 2,5-dihydroxybenzaldehyde (74 microg/ml), and 2-hydroxy-5-methoxybenzaldehyde (90.4 microg/ml). With the exception of carvacrol, a phenolic compound, three of the four most active compounds are aldehydes, suggesting that the structure of the phenolic group or the aldehyde group may be important to the antibacterial activity. No difference in compound activity was observed between the three M. avium subsp. paratuberculosis strains studied. Possible mechanisms of the antimicrobial effects are discussed.

The Complex Biogeography of the Plant Pathogen Xylella fastidiosa: Genetic Evidence of Introductions and Subspecific Introgression in Central America

PubMed Central

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A.; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa. PMID:25379725

The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

PubMed

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

Antibacterial Activities of Naturally Occurring Compounds against Mycobacterium avium subsp. paratuberculosis▿

PubMed Central

Wong, Stella Y. Y.; Grant, Irene R.; Friedman, Mendel; Elliott, Christopher T.; Situ, Chen

2008-01-01

The antibacterial activities of 18 naturally occurring compounds (including essential oils and some of their isolated constituents, apple and green tea polyphenols, and other plant extracts) against three strains of Mycobacterium avium subsp. paratuberculosis (a bovine isolate [NCTC 8578], a raw-milk isolate [806R], and a human isolate [ATCC 43015]) were evaluated using a macrobroth susceptibility testing method. M. avium subsp. paratuberculosis was grown in 4 ml Middlebrook 7H9 broth containing 10% oleic acid-albumin-dextrose-catalase, 0.05% Tween 80 (or 0.2% glycerol), and 2 μg/ml mycobactin J supplemented with five concentrations of each test compound. The changes in the optical densities of the cultures at 600 nm as a measure of CFU were recorded at intervals over an incubation period of 42 days at 37°C. Six of the compounds were found to inhibit the growth of M. avium subsp. paratuberculosis. The most effective compound was trans-cinnamaldehyde, with a MIC of 25.9 μg/ml, followed by cinnamon oil (26.2 μg/ml), oregano oil (68.2 μg/ml), carvacrol (72.2 μg/ml), 2,5-dihydroxybenzaldehyde (74 μg/ml), and 2-hydroxy-5-methoxybenzaldehyde (90.4 μg/ml). With the exception of carvacrol, a phenolic compound, three of the four most active compounds are aldehydes, suggesting that the structure of the phenolic group or the aldehyde group may be important to the antibacterial activity. No difference in compound activity was observed between the three M. avium subsp. paratuberculosis strains studied. Possible mechanisms of the antimicrobial effects are discussed. PMID:18676709

A zinc, copper and citric acid biocomplex shows promise for control of Xylella fastidiosa subsp. pauca in olive trees in Apulia region (southern Italy)

USDA-ARS?s Scientific Manuscript database

The bacterium Xylella fastidiosa subsp. pauca is associated with the “olive quick decline syndrome” in the Apulia region of southern Italy. To investigate control of this phytopathogen, a compound containing zinc and copper complexed with citric-acid hydracids (Dentamet®) was evaluated for in vitro ...

Depletion of CD4 T Lymphocytes at the time of infection with M. avium subsp. paratuberculosis does not accelerate disease progression

USDA-ARS?s Scientific Manuscript database

A calf model was used to determine if the depletion of CD4 T cells prior to inoculation of Mycobacterium avium subsp. paratuberculosis (Map) would delay development of an immune response to Map and accelerate disease progression. Ileal cannulas were surgically implanted in 5 bull calves at two month...

Analysis of the genetic diversity and structure of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia regions.

USDA-ARS?s Scientific Manuscript database

Background: The mountainous region between the Caucasus and China is considered to be the center of diversity for many temperate fruit crops including grapevine (Vitis vinifera subsp. sativa L). The wild forms of the subsp. Vitis vinifera spp. sylvestris, cultivated and ancient local varieties, were...

Complete genomic sequences of two salmonella enterica subsp. enterica serogroup C2 (O:6,8) strains from central California

USDA-ARS?s Scientific Manuscript database

Salmonella enteric subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype 6,8:-:e,n,z15, were isolated from environmental sampling in Central California in 2009. We report the complete genome sequences and annotation of these two strains. These genomic sequences are distinct and wi...

Draft Genome Sequence of Staphylococcus cohnii subsp. urealyticus Isolated from a Healthy Dog

PubMed Central

Wigmore, Sarah M.; Wareham, David W.

2017-01-01

ABSTRACT   Staphylococcus cohnii subsp. urealyticus strain SW120 was isolated from the ear swab of a healthy dog. The isolate is resistant to methicillin and fusidic acid. The SW120 draft genome is 2,805,064 bp and contains 2,667 coding sequences, including 58 tRNAs and nine complete rRNA coding regions. PMID:28209829

Survivability of Mycobacterium avium subsp paratuberculosis in grass silage after fermentation and exposure to low pH and high organic acids

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp paratuberculosis (Map) is a pathogen of concern in dairy production due to its ability to withstand harsh conditions and cause new infections. Infection is a result of ingesting Map cells from contaminated feed, water, or manure. The goal of this research was to evaluate th...

WC1+ gamma delta T cells from cattle naturally infected with Mycobacterium avium subsp. paratuberculosis respond differentially to stimulation with PPD-J.

USDA-ARS?s Scientific Manuscript database

A role for gamma delta T cells in protection against mycobacterial infections including Johne’s disease (JD) has been suggested. In neonatal calves where the risk to infection with Mycobacterium avium subsp. paratuberculosis (MAP) is high, the majority of circulating CD3+ lymphocytes are gamma delta...

Immunogenicity and reactivity of novel Mycobacterium avium subsp. paratuberculosis PPE MAP1152 and conserved MAP1156 proteins with sera from experimentally and naturally infected animals

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s Disease (JD) in ruminants. Development of genetic tools and completion of the MAP genome sequencing project expanded opportunities for antigen discovery. In this study, we determined the seroreactivity of two proteins encoded for at th...

Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Infantis Strain SPE101, Isolated from a Chronic Human Infection

PubMed Central

Iriarte, Andrés; Giner-Lamia, Joaquín; Betancor, Laura; Astocondor, Lizeth; Cestero, Juan J.; Ochoa, Theresa; García, Coralith; Puente, José L.; Chabalgoity, José A.

2017-01-01

ABSTRACT We report a 4.99-Mb draft genome sequence of Salmonella enterica subsp. enterica serovar Infantis strain SPE101, isolated from feces of a 5-month-old breast-fed female showing diarrhea associated with severe dehydration and malnutrition. The infection prolonged for 6 months despite antibiotic treatment. PMID:28729277

Hydrolyzable tannins, the active constituents of three Greek Cytinus taxa against several tumor cell lines.

PubMed

Magiatis, P; Pratsinis, H; Kalpoutzakis, E; Konstantinidou, A; Davaris, P; Skaltsounis, A L

2001-06-01

Hydrolyzable tannins were found to be the active cytotoxic constituents of three Greek Cytinus taxa: Cytinus ruber, Cytinus hypocistis subsp. hypocistis and Cytinus hypocistis subsp. orientalis. The cytotoxic activity was evaluated against a broad spectrum of cancer cell lines. The structure of the active compounds was investigated with NMR and electrospray-MS/MS techniques.

Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology.

PubMed

Lu, You; Samac, Deborah A; Glazebrook, Jane; Ishimaru, Carol A

2015-05-07

We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies. Copyright © 2015 Lu et al.

Inhibitory activities of venom alkaloids of Red Imported Fire Ant against Clavibacter michiganensis subsp. michiganensis in vitro and the application of piperidine alkaloids to manage symptom development..

USDA-ARS?s Scientific Manuscript database

Bacterial canker of tomato caused by Clavibacter michiganensis subsp. michiganensis (CMM) is a highly destructive disease and has caused major economic losses in tomato production worldwide. There are limited methods available to manage this disease. In searching for disease management alternatives,...

Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp plantarum and ‘Bacillus oryzicola’ are later heterotypic synonyms of Bacillus

USDA-ARS?s Scientific Manuscript database

The rhizosphere isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of comm...

Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

PubMed

Fazal, Mohammed-Abbas; Alexander, Sarah; Burnett, Edward; Deheer-Graham, Ana; Oliver, Karen; Holroyd, Nancy; Parkhill, Julian; Russell, Julie E

2016-11-03

Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939. © Crown copyright 2016.

Herbivores and pathogens on Alnus viridis subsp. fruticosa in interior Alaska: effects of leaf, tree, and neighbour characteristics on damage levels

Treesearch

Christa P.H. Mulder; Bitty A. Roy; Sabine Gusewell

2008-01-01

Parasite damage strongly affects dynamics of boreal forests. Damage levels may be affected by climate change, either directly or indirectly through changes in properties of host trees. We examined how herbivore and pathogen damage in Alnus viridis subsp. fruticosa (Rupr.) Nym. depend on leaf morphology and chemistry, tree size...

Complete genomic sequence of Campylobacter jejuni subsp. jejuni HS:19 strain RM1285 that was isolated from packaged chicken

USDA-ARS?s Scientific Manuscript database

Poultry products serve as the main source of Campylobacter jejuni subsp. jejuni (Cjj) infections in humans. Cjj infections are a leading cause of foodborne gastroenteritis and are a prevalent antecedent to Guillain-Barré syndrome (GBS). This study describes the genome of Cjj HS:19 strain RM1285 isol...

Genome Sequence of Streptococcus phocae subsp. salmonis Strain C-4T, Isolated from Atlantic Salmon (Salmo salar)

PubMed Central

Suarez, Rudy; Lazo, Eduardo; Bravo, Diego; Llegues, Katerina O.; Romalde, Jesús L.; Godoy, Marcos G.

2014-01-01

Streptococcus phocae subsp. salmonis is a fish pathogen that has an important impact on the Chilean salmon industry. Here, we report the genome sequence of the type strain C-4T isolated from Atlantic salmon (Salmo salar), showing a number of interesting features and genes related to its possible virulence factors. PMID:25502668

Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov., a thermophilic bacterium isolated from a hot spring in Batman.

PubMed

Gul-Guven, Reyhan; Guven, Kemal; Poli, Annarita; Nicolaus, Barbara

2008-12-01

A new thermophilic spore-forming strain KG8(T) was isolated from the mud of Taslidere hot spring in Batman. Strain KG8(T) was aerobe, Gram-positive, rod-shaped, motile, occurring in pairs or filamentous. Growth was observed from 35-65 degrees C (optimum 55 degrees C) and at pH 5.5-9.5 (optimum pH 7.5). It was capable of utilizing starch, growth was observed until 3% NaCl (w/v) and it was positive for nitrate reduction. On the basis of 16S rRNA gene sequence similarity, strain KG8(T) was shown to be related most closely to Anoxybacillus species. Chemotaxonomic data (major isoprenoid quinone-menaquinone-7; major fatty acid-iso-C15:0 and iso-C17:0) supported the affiliation of strain KG8(T) to the genus Anoxybacillus. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain KG8(T). Based on these results we propose assigning a novel subspecies of Anoxybacillus kamchatkensis, to be named Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov. with the type strain KG8(T) (DSM 18475(T)=CIP 109280(T)).

Acetylcholinesterase and butyrylcholinesterase inhibitory activity of Pinus species essential oils and their constituents.

PubMed

Bonesi, Marco; Menichini, Federica; Tundis, Rosa; Loizzo, Monica R; Conforti, Filomena; Passalacqua, Nicodemo G; Statti, Giancarlo A; Menichini, Francesco

2010-10-01

This study aimed to investigate the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory activity of the essential oils from Pinus nigra subsp. nigra, P. nigra var. calabrica, and P. heldreichii subsp. leucodermis. This activity is relevant to the treatment of Alzheimer's disease (AD), since cholinesterase drugs are currently the only drugs available to treat AD. P. heldreichii subsp. leucodermis exhibited the most promising activity, with IC(50) values of 51.1 and 80.6 microg/mL against AChE and BChE, respectively. An interesting activity against AChE was also observed with P. nigra subsp. nigra essential oil, with an IC(50) value of 94.4 microg/mL. Essential oils were analyzed by GC and GC-MS with the purpose of investigating their relationships with the observed activities. Among the identified constituents, terpinolene, beta-phellandrene, linalyl acetate, trans-caryophyllene, and terpinen-4-ol were tested. trans-Caryophyllene and terpinen-4-ol inhibited BChE with IC(50) values of 78.6 and 107.6 microg/mL, respectively. beta-Phellandrene was selective against AChE (IC(50) value of 120.2 microg/mL).

Co-culturing of Lactobacillus paracasei subsp. paracasei with a Lactobacillus delbrueckii subsp. delbrueckii mutant to make high cell density for increased lactate productivity from cassava bagasse hydrolysate.

PubMed

John, Rojan Pappy; Nampoothiri, K Madhavan

2011-03-01

To increase the productivity of lactic acid, a co-culture of lactobacilli was made by mixing 1:1 ratio of Lactobacillus paracasei subsp. paracasei and a fast growing L. delbrueckii subsp. delbrueckii mutant. The culture was embedded on to polyurethane foam (PUF) cubes as a biofilm and used for fermentation. In order to prevent the cell leakage, the PUF cubes were further entrapped in calcium cross-linked alginate. The maximum lactic acid production using a high cell density free culture was >38 g l(-1) from ~40 g l(-1) of reducing sugar within 12 h of fermentation. Using PUF biofilms, the same yield of lactic acid attained after 24 h. When the cubes were further coated with alginate it took 36 h for the maximum yield. Even though, the productivity is slightly lesser with the alginate coating, cell leakage was decreased and cubes were reused without much decrease in production in repeated batches. Using a conventional control inoculum (3%, w/v), it took 120 h to yield same amount of lactic acid.

Proteolysis in goat "coalho" cheese supplemented with probiotic lactic acid bacteria.

PubMed

Bezerra, Taliana Kênia Alves; de Araujo, Ana Rita Ribeiro; do Nascimento, Edilza Santos; de Matos Paz, José Eduardo; Gadelha, Carlos Alberto; Gadelha, Tatiane Santi; Pacheco, Maria Teresa Bertoldo; do Egypto Queiroga, Rita de Cássia Ramos; de Oliveira, Maria Elieidy Gomes; Madruga, Marta Suely

2016-04-01

This study aimed to analyse the proteolytic effects of adding isolated and combined probiotic strains to goat "coalho" cheese. The cheeses were: QS - with culture Start, composed by Lactococcus lactis subsp. lactis and L. lactis subsp. cremoris (R704); QLA - with Lactobacillus acidophilus (LA-5); QLP - with Lactobacillus paracasei subsp. paracasei (L. casei 01); QB - with Bifidobacterium animalis subsp. lactis (BB 12); and QC, co-culture with the three probiotic microorganisms. The cheeses were analysed during 28 days of storage at 10°C. The probiotic cell count was higher than 6.5 and 7 log colony-forming units (CFU) g(-1) of cheese at the 1st and 28th days of storage, respectively. The addition of co-culture influenced (p<0.01) proteolysis in the cheese and resulted in a higher content of soluble protein and release of amino acids at the 1st day after processing. However, over all 28 days, the cheese supplemented with Bifidobacterium lactis in its isolated form showed the highest proteolytic activity, particularly in the hydrolysis of the alpha-s2 and kappa-casein fractions. Copyright © 2015 Elsevier Ltd. All rights reserved.

A taxonomic revision of small neotropical saurian Malarias allied to Plasmodium minasense.

PubMed

Telford, S R

1979-01-01

Saurian malaria species which produce schizonts smaller than normal erythrocyte nuclei, with 4-8 merozoietes and gametocytes equal to or smaller than erythrocyte nuclei in size, parasitizing hosts of the lizard families Scincidae, Iguanidae and Teiidae in the Neotropics are considered to be Plasmodium minasense Carini and Rudolph, 1912. Subspecific designations are given to distinctive populations parasitizing different host species: P. minasense minasense is recognized from the type host, Mabuya mabouya of Brasil; P. minasense carinii Leger and Mouzels, 1917 from Iguana iguana of coastal South America; P. minasense anolisi subsp. nov. from Anolis limifrons of Panama; P. minasense capitoi subsp. nov. from Anolis capito of Panama; P. minasense plicae subsp. nov. from Plica umbra of Guyana; P. minasense tegui subsp. nov. from Tupinambis teguixin of Venezuela; and P. minasense diminutivum Telford, 1973, new combination, from Ameiva ameiva of Panama. Plasmodium rhadinurum Thompson and Huff, 1944 is recognized as a distinct species at present on the basis of possessing schizonts of different shape, asexual stages with filamentous projections in most portions of its range, and larger gametocytes, as well as apparent sympatry with P. minasense carinii in some areas.

Detection of Olea europaea subsp. cuspidata and Juniperus procera in the dry Afromontane forest of northern Ethiopia using subpixel analysis of Landsat imagery

NASA Astrophysics Data System (ADS)

Hishe, Hadgu; Giday, Kidane; Neka, Mulugeta; Soromessa, Teshome; Van Orshoven, Jos; Muys, Bart

2015-01-01

Comprehensive and less costly forest inventory approaches are required to monitor the spatiotemporal dynamics of key species in forest ecosystems. Subpixel analysis using the earth resources data analysis system imagine subpixel classification procedure was tested to extract Olea europaea subsp. cuspidata and Juniperus procera canopies from Landsat 7 enhanced thematic mapper plus imagery. Control points with various canopy area fractions of the target species were collected to develop signatures for each of the species. With these signatures, the imagine subpixel classification procedure was run for each species independently. The subpixel process enabled the detection of O. europaea subsp. cuspidata and J. procera trees in pure and mixed pixels. Total of 100 pixels each were field verified for both species. An overall accuracy of 85% was achieved for O. europaea subsp. cuspidata and 89% for J. procera. A high overall accuracy level of detecting species at a natural forest was achieved, which encourages using the algorithm for future species monitoring activities. We recommend that the algorithm has to be validated in similar environment to enrich the knowledge on its capability to ensure its wider usage.

A highly efficient transposon mutagenesis system for the tomato pathogen Clavibacter michiganensis subsp. michiganensis.

PubMed

Kirchner, O; Gartemann, K H; Zellermann, E M; Eichenlaub, R; Burger, A

2001-11-01

A transposon mutagenesis system for Clavibacter michiganensis subsp. michiganensis was developed based on antibiotic resistance transposons that were derived from the insertion element IS1409 from Arthrobacter sp. strain TM1 NCIB12013. As a prerequisite, the electroporation efficiency was optimized by using unmethylated DNA and treatment of the cells with glycine such that about 5 x 10(6) transformants per microg of DNA were generally obtained. Electroporation of C. michiganensis subsp. michiganensis with a suicide vector carrying transposon Tn1409C resulted in approximately 1 x 10(3) transposon mutants per pg of DNA and thus is suitable for saturation mutagenesis. Analysis of Tn1409C insertion sites suggests a random mode of transposition. Transposition of Tn1409C was also demonstrated for other subspecies of C. michiganensis.

Six-Month Multicenter Study on Invasive Infections Due to Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis in Argentina

PubMed Central

Lopardo, Horacio A.; Vidal, Patricia; Sparo, Monica; Jeric, Paola; Centron, Daniela; Facklam, Richard R.; Paganini, Hugo; Pagniez, N. Gaston; Lovgren, Marguerite; Beall, Bernard

2005-01-01

During a 6-month period, 95 invasive infections due to Streptococcus pyogenes and group C or group G Streptococcus dysgalactiae subsp. equisimilis were recorded from 40 centers of 16 cities in Argentina. We describe here epidemiologic data available for 55 and 19 patients, respectively, associated with invasive infections due to S. pyogenes and S. dysgalactiae subsp. equisimilis. The associated isolates and 58 additional pharyngeal isolates were genotyped and subjected to serologic and/or antibiotic susceptibility testing. Group A streptococcal emm type distribution and strain association with toxic shock appeared to differ somewhat from results found within the United States; however, serologic characterization and sof sequence typing suggested that emm types found in both countries are reflective of shared clonal types. PMID:15695683

Quantification of betaglucans, lipid and protein contents in whole oat groats (Avena sativa L.) using near infrared reflectance spectroscopy

USDA-ARS?s Scientific Manuscript database

Whole oat has been described as an important healthy food for humans due to its beneficial nutritional components. Near infrared reflectance spectroscopy (NIRS) is a powerful, fast, accurate and non-destructive analytical tool that can be substituted for some traditional chemical analysis. A total o...

Quantitative trait loci from two genotypes of oat (Avena sativa L.) conditioning resistance to Puccinia coronata

USDA-ARS?s Scientific Manuscript database

Developing oat cultivars with partial resistance to crown rust would be beneficial for disease management. Two recombinant inbred line (RIL) populations were derived by crossing the susceptible cultivar ‘Provena’ with two partially resistant sources, ‘CDC Boyer’ and breeding line 94197A1-9-2-2-2-5. ...

Genome-wide association mapping of crown rust resistance in oat elite germplasm

USDA-ARS?s Scientific Manuscript database

Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat production in many parts of the world. In this first comprehensive multi-environment genome-wide association map of oat crown rust, we used 2,972 SNPs genotyped on 631 oat lines for association mapping of quantit...

Studies on the control of cell wall extension. Yearly progress report, September 1, 1978-August 31, 1979

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleland, R. E.

Research has been centered around the question as to how plant cell enlargement is controlled and regulated at the cellular level. Progress is reported on the following projects: proton permeability of plant cuticles; the control of osmoregulation in Avena coleoptiles; an analysis of the acid-extension curves. (ACR)

Vulnerability of grain crops and croplands in the Midwest to climatic variability and adaptation strategies

USDA-ARS?s Scientific Manuscript database

Maize (Zea mays L.) and soybean (Gylcine max (L.) Merr.) are the dominant grain crops across the Midwest and are grown on 75% of the arable land with wheat (Triticum aestivum L.) and oats (Avena sativa L.) small but economically important crops. Historically there have been variations in annual yiel...

Evolution of the Oat Genetic Road Map: From Tetraploid to Hexaploid

USDA-ARS?s Scientific Manuscript database

The development of a genetic linkage map for hexaploid oat (Avena sativa L. 2n = 6 x = 42) that defines all 21 chromosomes has been hindered due to the lack of oat-based markers and the size and complexity of the oat genome. Recent efforts in oat DArT, SSR, and SNP marker development should improve...

Comparative Genomic Analysis of a Clinical Isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil

PubMed Central

Nicolás, Marisa F.; Ramos, Pablo Ivan Pereira; Marques de Carvalho, Fabíola; Camargo, Dhian R. A.; de Fátima Morais Alves, Carlene; Loss de Morais, Guilherme; Almeida, Luiz G. P.; Souza, Rangel C.; Ciapina, Luciane P.; Vicente, Ana C. P.; Coimbra, Roney S.; Ribeiro de Vasconcelos, Ana T.

2018-01-01

The aim of this study was to unravel the genetic determinants responsible for multidrug (including carbapenems) resistance and virulence in a clinical isolate of Klebsiella quasipneumoniae subsp. similipneumoniae by whole-genome sequencing and comparative analyses. Eighty-three clinical isolates initially identified as carbapenem-resistant K. pneumoniae were collected from nosocomial infections in southeast Brazil. After RAPD screening, the KPC-142 isolate, showing the most divergent DNA pattern, was selected for complete genome sequencing in an Illumina HiSeq 2500 instrument. Reads were assembled into scaffolds, gaps between scaffolds were resolved by in silico gap filling and extensive bioinformatics analyses were performed, using multiple comparative analysis tools and databases. Genome sequencing allowed to correct the classification of the KPC-142 isolate as K. quasipneumoniae subsp. similipneumoniae. To the best of our knowledge this is the first complete genome reported to date of a clinical isolate of this subspecies harboring both class A beta-lactamases KPC-2 and OKP-B-6 from South America. KPC-142 has one 5.2 Mbp chromosome (57.8% G+C) and two plasmids: 190 Kbp pKQPS142a (50.7% G+C) and 11 Kbp pKQPS142b (57.3% G+C). The 3 Kbp region in pKQPS142b containing the blaKPC−2 was found highly similar to that of pKp13d of K. pneumoniae Kp13 isolated in Southern Brazil in 2009, suggesting the horizontal transfer of this resistance gene between different species of Klebsiella. KPC-142 additionally harbors an integrative conjugative element ICEPm1 that could be involved in the mobilization of pKQPS142b and determinants of resistance to other classes of antimicrobials, including aminoglycoside and silver. We present the completely assembled genome sequence of a clinical isolate of K. quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 beta-lactamases producer and discuss the most relevant genomic features of this important resistant pathogen in comparison to several strains belonging to K. quasipneumoniae subsp. similipneumoniae (phylogroup II-B), K. quasipneumoniae subsp. quasipneumoniae (phylogroup II-A), K. pneumoniae (phylogroup I), and K. variicola (phylogroup III). Our study contributes to the description of the characteristics of a novel K. quasipneumoniae subsp. similipneumoniae strain circulating in South America that currently represent a serious potential risk for nosocomial settings. PMID:29503635

The effect of wind on dispersal of splash-borne Xanthomonas citri subsp citri at different heights and distances downwind of canker-infected grapefruit trees

USDA-ARS?s Scientific Manuscript database

Xanthomonas citri subsp citri (Xcc), which causes citrus canker, is a major pathogen of grapefruit and other canker-susceptible citrus species and cultivars grown in Florida and elsewhere. It is dispersed by rain splash, and wind promotes the dispersal of the pathogen. The aim of this study was to e...

Short distance dispersal of splashed bacteria of Xanthomonas citri subsp. citri from canker-infected grapefruit tree canopies in turbulent wind

USDA-ARS?s Scientific Manuscript database

Citrus canker (Xanthomonas citri subsp citri [Xcc]) can result in yield loss and market restrictions. The pathogen is dispersed in rain splash and spread is promoted by wind. The goal of this study was to gain some insight into the behavior of the downwind plume of Xcc from ~1.5 m-tall canker-affect...

Chemical composition, larvicidal, and biting deterrent activity of essential oils of two subspecies of Tanacetum argenteum (Asterales: Asteraceae) and individual constituents against Aedes aegypti (Diptera: Culicidae)

USDA-ARS?s Scientific Manuscript database

Water distilled essential oils from the air dried aerial parts of Tanacetum argenteum (Lam.) Willd. subsp. argenteum (Lam.) and T. argenteum (Lam.) Willd. subsp. canum (C. Koch) Grierson were analyzed by gas chromatography (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Twenty-seven and 3...

Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil.

PubMed

Seribelli, Amanda Aparecida; Frazão, Miliane Rodrigues; Gonzales, Júlia Cunha; Cao, Guojie; Leon, Maria Sanchez; Kich, Jalusa Deon; Allard, Marc William; Falcão, Juliana Pfrimer

2018-04-19

Salmonellosis is a disease with a high incidence worldwide, and Salmonella enterica subsp. enterica serovar Typhimurium is one of the most clinically important serovars. We report here the draft genome sequences of 20 S. Typhimurium strains isolated from swine in Santa Catarina, Brazil. These draft genomes will improve our understanding of S. Typhimurium in Brazil.

De Novo whole genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 from blueberry in Georgia, USA

USDA-ARS?s Scientific Manuscript database

This study reports a de novo assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp with a G+C content of 51.8% and 2,943 open reading frames (ORFs) and 48 RNA genes....

Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources

PubMed Central

Labbé, Geneviève; Ziebell, Kim; Bekal, Sadjia; Parmley, E. Jane; Agunos, Agnes; Desruisseau, Andrea; Daignault, Danielle; Slavic, Durda; Hoang, Linda; Ramsay, Danielle; Pollari, Frank; Robertson, James; Nash, John H. E.

2016-01-01

Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian S. Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes. PMID:27635008

Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources.

PubMed

Labbé, Geneviève; Ziebell, Kim; Bekal, Sadjia; Macdonald, Kimberley A; Parmley, E Jane; Agunos, Agnes; Desruisseau, Andrea; Daignault, Danielle; Slavic, Durda; Hoang, Linda; Ramsay, Danielle; Pollari, Frank; Robertson, James; Nash, John H E; Johnson, Roger P

2016-09-15

Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian S Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes. © Crown copyright 2016.

Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham.

PubMed

Müller, Anne; Huptas, Christopher; Wenning, Mareike; Schmidt, Herbert; Weiss, Agnes

2015-05-14

Staphylococcus carnosus is used as a starter culture in meat fermentation, where it contributes to color formation and produces aromatic compounds. Here, we report the first draft genome sequence of an S. carnosus subsp. utilis strain, LTH 7013, isolated from South Tyrolean ham, with potential application as a starter culture. Copyright © 2015 Müller et al.

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.

PubMed

Urshev, Zoltan; Hajo, Karima; Lenoci, Leonardo; Bron, Peter A; Dijkstra, Annereinou; Alkema, Wynand; Wels, Michiel; Siezen, Roland J; Minkova, Svetlana; van Hijum, Sacha A F T

2016-10-06

Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 originates from homemade Bulgarian yogurt and was selected for its ability to form a strong association with Streptococcus thermophilus The genome sequence will facilitate elucidating the genetic background behind the contribution of LBB.B5 to the taste and aroma of yogurt and its exceptional protocooperation with S. thermophilus. Copyright © 2016 Urshev et al.

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

PubMed

Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

2016-03-03

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. Copyright © 2016 Meneghel et al.

Lancefield group G Streptococcus dysgalactiae subsp. equisimilis: an unusual aetiology of perianal streptococcal dermatitis acquired from heterosexual oral-anal intercourse.

PubMed

Abdolrasouli, A; Hemmati, Y; Amin, A; Roushan, A; Butler, I

2012-12-01

Perianal streptococcal dermatitis (PSD) is an uncommon superficial cutaneous infection of the perianal area, almost exclusively described in children and mainly caused by group A streptococci. We report here a case of PSD caused by Streptococcus dysgalactiae subsp. equisimilis, Lancefield group G, in an adult man due to heterosexual oral-anal sexual contact.

Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Infantis Strain SPE101, Isolated from a Chronic Human Infection.

PubMed

Iriarte, Andrés; Giner-Lamia, Joaquín; Silva, Claudia; Betancor, Laura; Astocondor, Lizeth; Cestero, Juan J; Ochoa, Theresa; García, Coralith; Puente, José L; Chabalgoity, José A; García-Del Portillo, Francisco

2017-07-20

We report a 4.99-Mb draft genome sequence of Salmonella enterica subsp. enterica serovar Infantis strain SPE101, isolated from feces of a 5-month-old breast-fed female showing diarrhea associated with severe dehydration and malnutrition. The infection prolonged for 6 months despite antibiotic treatment. Copyright © 2017 Iriarte et al.

Clonal relationship and differentiation among Mycobacterium abscessus isolates as determined using the semiautomated repetitive extragenic palindromic sequence PCR-based DiversiLab system.

PubMed

Mougari, Faiza; Raskine, Laurent; Ferroni, Agnes; Marcon, Estelle; Sermet-Gaudelus, Isabelle; Veziris, Nicolas; Heym, Beate; Gaillard, Jean-Louis; Nassif, Xavier; Cambau, Emmanuelle

2014-06-01

Mycobacterium abscessus is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episodes, we evaluated the discriminatory power of the semiautomated DiversiLab (DL) repetitive extragenic palindromic sequence PCR (REP-PCR) test for M. abscessus genotyping. Since M. abscessus was shown to be composed of subspecies (M. abscessus subsp. massiliense, M. abscessus subsp. bolletii, and M. abscessus subsp. abscessus), we also evaluated the ability of this technique to differentiate subspecies. The technique was applied to two collections of clinical isolates, (i) 83 M. abscessus original isolates (43 M. abscessus subsp. abscessus, 12 M. abscessus subsp. bolletii, and 28 M. abscessus subsp. massiliense) from infected patients and (ii) 35 repeated isolates obtained over 1 year from four cystic fibrosis patients. The DL REP-PCR test was standardized for DNA extraction, DNA amplification, and electrophoresis pattern comparisons. Among the isolates from distinct patients, 53/83 (62%) isolates showed a specific pattern, and 30 were distributed in 11 clusters and 6 patterns, with 2 to 4 isolates per pattern. The clusters and patterns did not fully correlate with multilocus sequence typing (MLST) analysis results. This revealed a high genomic diversity between patients, with a discriminatory power of 98% (Simpson's diversity index). However, since some isolates shared identical patterns, this raises the question of whether it is due to transmission between patients or a common reservoir. Multiple isolates from the same patient showed identical patterns, except for one patient infected by two strains. Between the M. abscessus subspecies, the indexes were <70%, indicating that the DL REP-PCR test is not an accurate tool for identifying organisms to the subspecies level. REP-PCR appears to be a rapid genotyping method that is useful for investigating epidemics of M. abscessus infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Three new insertion sequence elements ISLdl2, ISLdl3, and ISLdl4 in Lactobacillus delbrueckii: isolation, molecular characterization, and potential use for strain identification.

PubMed

Ravin, Victor; Alatossava, Tapani

2003-05-01

A group of new insertion sequence (IS) elements, ISLdl2, ISLdl3, and ISLdl4, from Lactobacillus delbrueckii subsp. lactis ATCC 15808 was isolated, characterized, and used for strain identification together with ISLdl1, recently characterized as an L. delbrueckii IS element belonging to the ISL3 family. ISLdl2 was 1367 bp in size and had a 24 bp IR and an 8 bp DR. The single ORF of ISLdl2 encoded a protein of 392 aa similar to transposases of the IS256 family. ISLdl3 had a single ORF encoding a protein of 343 aa similar to transposases of the IS30 family. Finally, ISLdl4 had a single ORF encoding a protein of 406 aa and displayed homology to the transposases of the IS110 family. ISLdl4 was only slight different from ISL4 (Accession No. AY040213). ISLdl1, ISLdl2, and ISLdl4 were present in all of the 10 L. delbrueckii subsp. lactis and subsp. delbrueckii strains tested, as well as in three of the 11 L. delbrueckii subsp. bulgaricus strains tested. ISLdl3 was present only in four closely related strains of L. delbrueckii subsp. lactis. These IS elements were not observed in Lactobacillus rhamnosus, Lactobacillus acidophilus, Lactobacillus helveticus, or Lactobacillus plantarum. A cluster of IS elements, ISLdl1, ISLdl2, ISLdl3, ISLdl4, and ISL6, was observed in L. delbrueckii subsp. lactis strain ATCC 15808. Within this cluster, ISLdl4 was inserted into ISLdl1 between the left IR and the start codon of ORF455, encoding a putative transposase. Most of the integration sites of the IS elements were strain-specific. We have observed that IS elements can migrate from one strain to another as integral parts of bacterial DNA by using phage LL-H as a vehicle. We demonstrate for the first time that inverse PCR and vectorette PCR methods with primers based on sequences of the IS elements could be used for identification of L. delbrueckii strains.

Vascular plant biodiversity of the lower Coppermine River valley and vicinity (Nunavut, Canada): an annotated checklist of an Arctic flora

PubMed Central

Bull, Roger D.

2017-01-01

The Coppermine River in western Nunavut is one of Canada’s great Arctic rivers, yet its vascular plant flora is poorly known. Here, we report the results of a floristic inventory of the lower Coppermine River valley and vicinity, including Kugluk (Bloody Falls) Territorial Park and the hamlet of Kugluktuk. The study area is approximately 1,200 km2, extending from the forest-tundra south of the treeline to the Arctic coast. Vascular plant floristic data are based on a review of all previous collections from the area and more than 1,200 new collections made in 2014. Results are presented in an annotated checklist, including citation of all specimens examined, comments on taxonomy and distribution, and photographs for a subset of taxa. The vascular plant flora comprises 300 species (311 taxa), a 36.6% increase from the 190 species documented by previous collections made in the area over the last century, and is considerably more diverse than other local floras on mainland Nunavut. We document 207 taxa for Kugluk (Bloody Falls) Territorial Park, an important protected area for plants on mainland Nunavut. A total of 190 taxa are newly recorded for the study area. Of these, 14 taxa (13 species and one additional variety) are newly recorded for Nunavut (Allium schoenoprasum, Carex capitata, Draba lonchocarpa, Eremogone capillaris subsp. capillaris, Sabulina elegans, Eleocharis quinqueflora, Epilobium cf. anagallidifolium, Botrychium neolunaria, Botrychium tunux, Festuca altaica, Polygonum aviculare, Salix ovalifolia var. arctolitoralis, Salix ovalifolia var. ovalifolia and Stuckenia pectinata), seven species are newly recorded for mainland Nunavut (Carex gynocrates, Carex livida, Cryptogramma stelleri, Draba simmonsii, Festuca viviparoidea subsp. viviparoidea, Juncus alpinoarticulatus subsp. americanus and Salix pseudomyrsinites) and 56 range extensions are reported. The psbA-trnH and rbcL DNA sequence data were used to help identify the three Botrychium taxa recorded in the study area. Three new combinations are proposed: Petasites frigidus subsp. sagittatus (Banks ex Pursh) Saarela, Carex petricosa subsp. misandroides (Fernald) Saarela and Carex simpliciuscula subsp. subholarctica (T. V. Egorova) Saarela. PMID:28194307

Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru.

PubMed

Finster, Kai W; Kjeldsen, Kasper U

2010-03-01

Two deltaproteobacterial sulfate reducers, designated strain I.8.1(T) and I.9.1(T), were isolated from the oxygen minimum zone water column off the coast of Peru at 400 and 500 m water depth. The strains were Gram-negative, vibrio-shaped and motile. Both strains were psychrotolerant, grew optimally at 20 degrees C at pH 7.0-8.0 and at 2.5-3.5% NaCl (w/v). The strains grew by utilizing hydrogen/acetate, C(3-4) fatty acids, amino acids and glycerol as electron acceptors for sulfate reduction. Fumarate, lactate and pyruvate supported fermentative growth. Sulfate, sulfite, thiosulfate and taurin supported growth as electron acceptors. Both strains were catalase-positive and highly oxygen-tolerant, surviving 24 days of exposure to atmospheric concentrations. MK6 was the only respiratory quinone. The most prominent cellular fatty acid was iso-17:1-omega9c (18%) for strain I.8.1(T) and iso-17:0-omega9c (14%) for strain I.9.1(T). The G+C contents of their genomic DNA were 45-46 mol%. Phylogenetic analysis of 16S rRNA and dsrAB gene sequences showed that both strains belong to the genus Desulfovibrio. Desulfovibrio acrylicus DSM 10141(T) and Desulfovibrio marinisediminis JCM 14577(T) represented their closest validly described relatives with pairwise 16S rRNA gene sequence identities of 98-99%. The level of DNA-DNA hybridization between strains I.8.1(T) and I.9.1(T) was 30-38%. The two strains shared 10-26% DNA-DNA relatedness with D. acrylicus. Based on a polyphasic investigation it is proposed that strains I.8.1(T) and I.9.1(T) represent a novel species for which the name Desulfovibrio oceani sp. nov. is proposed with the two subspecies D. oceani subsp. oceani (type strain, I.8.1(T) = DSM 21390(T) = JCM 15970(T)) and D. oceani subsp. galateae (type strain, I.9.1(T) = DSM 21391(T) = JCM 15971(T)).

In Vitro Antiproliferative Activity of Extracts of Carlina acaulis subsp. caulescens and Carlina acanthifolia subsp. utzka

PubMed Central

Strzemski, Maciej; Wojnicki, Kamil; Sowa, Ireneusz; Wojas-Krawczyk, Kamila; Krawczyk, Paweł; Kocjan, Ryszard; Such, Justyna; Latalski, Michał; Wnorowski, Artur; Wójciak-Kosior, Magdalena

2017-01-01

Various species of the Carlina genus have been used in traditional medicine in many countries to treat numerous skin disorders, including cancer. The objective of this work was to assess the anticancer properties of root and leaf extracts from Carlina acaulis subsp. caulescens and C. acanthifolia subsp. utzka. Anti-tumor properties of the extracts were explored using a tetrazolium-based cell viability assay and flow cytometric apoptosis analysis, followed by immunodetection of phosphoactive ERK1/2 in UACC-903, C32, and UACC-647 human melanoma cell lines. Normal human fibroblasts were used as a control. Leaf extracts inhibited the viability of all tested melanoma cell lines in a dose-dependent fashion while the fibroblasts were less sensitive to such extract. The root extracts inhibited the proliferation of UACC-903 and UACC-647 cells only at the highest doses (300 μg/mL). However, the C32 and fibroblast cells exhibited an increase in the cellular proliferation rate and no caspase activity was observed in response to the root extracts (100 μg/mL). An increase in caspase activity was observed in melanoma cells treated with the leaf extracts of both Carlina species. Leaf extracts from C. acaulis subsp. caulescens (100 μg/mL) inhibited proliferatory ERK1/2 in UACC-903 and C32 cells, as demonstrated by the decrease in ERK1/2 phosphorylation. No reduction in phospho-ERK1/2 was observed in the tested cell lines treated with the root extracts, apart from UACC-647 after incubation with the C. acanthifolia subsp. utzka root extract (100 μg/mL). There was no change in ERK1/2 phosphorylation in the fibroblasts. The extracts from the leaves and roots were analyzed by HPLC and the analysis showed the presence of triterpenes and phenolic acids as the main extract components. The research demonstrated that the extracts from the leaves of the plants were cytotoxic against the human melanoma line and induced apoptosis of the cells. The triterpene fraction present in the tested extracts may be responsible for this activity. PMID:28659804

Genomic Diversity of Erwinia carotovora subsp. carotovora and Its Correlation with Virulence

PubMed Central

Yap, Mee-Ngan; Barak, Jeri D.; Charkowski, Amy O.

2004-01-01

We used genetic and biochemical methods to examine the genomic diversity of the enterobacterial plant pathogen Erwinia carotovora subsp. carotovora. The results obtained with each method showed that E. carotovora subsp. carotovora strains isolated from one ecological niche, potato plants, are surprisingly diverse compared to related pathogens. A comparison of 23 partial mdh sequences revealed a maximum pairwise difference of 10.49% and an average pairwise difference of 2.13%, values which are much greater than the maximum variation (1.81%) and average variation (0.75%) previously reported for Escherichia coli. Pulsed-field gel electrophoresis analysis of I-CeuI-digested genomic DNA revealed seven rrn operons in all E. carotovora subsp. carotovora strains examined except strain WPP17, which had only six copies. We identified 26 I-CeuI restriction fragment length polymorphism patterns and observed significant polymorphism in fragment sizes ranging from 100 to 450 kb for all strains. We detected large plasmids in two strains, including the model strain E. carotovora subsp. carotovora 71. The two least virulent strains had an unusual chromosomal structure, suggesting that a particular pulsotype is correlated with virulence. To compare chromosomal organization of multiple enterobacterial genomes, several genes were mapped onto I-CeuI fragments. We identified portions of the genome that appear to be conserved across enterobacteria and portions that have undergone genome rearrangements. We found that the least virulent strain, WPP17, failed to oxidize cellobiose and was missing several hrp and hrc genes. The unexpected variability among isolates obtained from clonal hosts in one region and in one season suggests that factors other than the host plant, potato, drive the evolution of this common environmental bacterium and key plant pathogen. PMID:15128563

Prophage Lysin Ply30 Protects Mice from Streptococcus suis and Streptococcus equi subsp. zooepidemicus Infections

PubMed Central

Tang, Fang; Li, Dezhi; Wang, Haojin; Ma, Zhe; Lu, Chengping

2015-01-01

Streptococcus suis and Streptococcus equi subsp. zooepidemicus are capable of infecting humans and various animals, causing significant problems for the worldwide swine industry. As antibiotic resistance has increased, lysosomal enzymes encoded by phages have shown potential for use against pathogenic bacteria. In this study, a novel bacteriophage lysin, Ply30, encoded by the S. suis prophage phi30c, was recombinantly expressed and purified. Ply30 showed high bacteriolysis activity on S. suis and S. equi subsp. zooepidemicus in vitro. The ratio of the optical density at 600 nm (OD600) with treatment versus the OD600 with no treatment for most tested S. suis and S. equi subsp. zooepidemicus strains decreased from 1 to <0.3 and <0.5, respectively, within 1 h. The results of plate viability assays showed that treated bacteria suffered a 1- to 2-log decrease in CFU within 1 h. The optimal concentration of Ply30 was 50 μg/ml, and the optimal pH was 7. Moreover, Ply30 maintained high activity over a wide pH range (pH 6 to 10). The MICs of Ply30 against Streptococcus strains ranged from 16 to 512 μg/ml. In vivo, a 2-mg dose of Ply30 protected 90% (9/10 mice) of mice from infection with S. equi subsp. zooepidemicus and 80% (8/10 mice) of mice from infection with S. suis. Seven days after lysin Ply30 treatment, bacterial loads were significantly decreased in all tested organs and blood compared with those at 1 h postinfection without Ply30 treatment. Ply30 showed in vitro and in vivo antimicrobial efficiency and protected mice against two kinds of bacterial infections, indicating that Ply30 may be an effective therapeutic against streptococci. PMID:26253669

Monograph of Diplachne (Poaceae, Chloridoideae, Cynodonteae)

PubMed Central

Snow, Neil; Peterson, Paul M.; Romaschenko, Konstantin; Simon, Bryan K.

2018-01-01

Abstract Diplachne P. Beauv. comprises two species with C4 (NAD-ME) photosynthesis. Diplachne fusca has a nearly pantropical-pantemperate distribution with four subspecies: D. fusca subsp. fusca is Paleotropical with native distributions in Africa, southern Asia and Australia; the widespread Australian endemic D. f. subsp. muelleri; and D. f. subsp. fascicularis and D. f. subsp. uninervia occurring in the New World. Diplachne gigantea is known from a few widely scattered, older collections in east-central and southern Africa, and although Data Deficient clearly is of conservation concern. A discussion of previous taxonomic treatments is provided, including molecular data supporting Diplachne in its newer, restricted sense. Many populations of Diplachne fusca are highly tolerant of saline substrates and most prefer seasonally moist to saturated soils, often in disturbed areas. Some populations of Diplachne fusca in southern Asia combine nitrogen-fixation, high salinity tolerance and palatibilty to livestock, which should be pursued with further research for purposes of soil reclamation. Diplachne fusca subsp. uninervia is the most invasive of the subspecies and is becoming weedy in some non-native areas, including in the Old World. This monograph provides detailed descriptions of all taxa, a key to the species and subspecies, geographic distributions and information on the anatomy of leaves, stems, lemmatal micromorphology and discussions of the chromosome numbers. Lectotypes are designated for: Atropis carinata Grisb.; Diplachne acuminata Nash; Diplachne capensis (Nees) Nees var. concinna Nees; Diplachne capensis (Nees) Nees var. obscura Nees, Diplachne capensis (Nees) Nees var. prolifera subvar. minor Nees, Diplachne halei Nash, Diplachne maritima E.P. Bicknel, Diplachne muelleri Benth., Diplachne reverchonii Vasey, Diplachne tectoneticola Backer, Leptochloa imbricata Thurb., Leptochloa neuroglossa Peter, Leptochloa uninervia var. typica fo. abbreviata Parodi, Triodia ambigua R. Br. and Triodia parviflora R. Br. PMID:29416413

Characterization of two nisin-producing Lactococcus lactis subsp. lactis strains isolated from a commercial sauerkraut fermentation.

PubMed Central

Harris, L J; Fleming, H P; Klaenhammer, T R

1992-01-01

Two Lactococcus lactis subsp. lactis strains, NCK400 and LJH80, isolated from a commercial sauerkraut fermentation were shown to produce nisin. LJH80 was morphologically unstable and gave rise to two stable, nisin-producing (Nip+) derivatives, NCK318-2 and NCK318-3. NCK400 and derivatives of LJH80 exhibited identical morphological and metabolic characteristics, but could be distinguished on the basis of plasmid profiles and genomic hybridization patterns to a DNA probe specific for the iso-ISS1 element, IS946. NCK318-2 and NCK318-3 harbored two and three plasmids, respectively, which hybridized with IS946. Plasmid DNA was not detected in NCK400, and DNA from this strain failed to hybridize with IS946. Despite the absence of detectable plasmid DNA in NCK400, nisin-negative derivatives (NCK402 and NCK403) were isolated after repeated transfer in broth at 37 degrees C. Nisin-negative derivatives concurrently lost the ability to ferment sucrose and became sensitive to nisin. A 4-kbp HindIII fragment containing the structural gene for nisin (spaN), cloned from L. lactis subsp. lactis ATCC 11454, was used to probe genomic DNA of NCK318-2, NCK318-3, NCK400, and NCK402 digested with EcoRI or HindIII. The spaN probe hybridized to an 8.8-kbp EcoRI fragment and a 10-kbp HindIII fragment in the Nip+ sauerkraut isolates, but did not hybridize to the Nip- derivative, NCK402. A different hybridization pattern was observed when the same probe was used against Nip+ L. lactis subsp. lactis ATCC 11454 and ATCC 7962. These phenotypic and genetic data confirmed that unique Nip+ L. lactis subsp. lactis strains were isolated from fermenting sauerkraut. Images PMID:1622214

Development and Validation of a Liquid Medium (M7H9C) for Routine Culture of Mycobacterium avium subsp. paratuberculosis To Replace Modified Bactec 12B Medium

PubMed Central

Whittington, Ann-Michele; Waldron, Anna; Begg, Douglas J.; de Silva, Kumi; Purdie, Auriol C.; Plain, Karren M.

2013-01-01

Liquid culture of Mycobacterium avium subsp. paratuberculosis from clinical samples, such as feces, is the most sensitive antemortem test for the diagnosis of Johne's disease in ruminants. In Australia, New Zealand, the United States, and some other countries, the Bactec 460 system with modified Bactec 12B medium (Becton, Dickinson) has been the most commonly used liquid culture system, but it was discontinued in 2012. In this study, a new liquid culture medium, M7H9C, was developed. It consists of a Middlebrook 7H9 medium base with added Casitone, albumin, dextrose, catalase, egg yolk, mycobactin J, and a cocktail of antibiotics. We found that polyoxyethylene stearate (POES) was not essential for the cultivation of M. avium subsp. paratuberculosis in either the Bactec 12B or the M7H9C medium. The limit of detection determined using pure cultures of the C and S strains of M. avium subsp. paratuberculosis was 7 bacilli per 50 μl inoculum in the two media. The new medium was validated using 784 fecal and tissue samples from sheep and cattle, >25% of which contained viable M. avium subsp. paratuberculosis. Discrepant results for the clinical samples between the two media were mostly associated with samples that contained <10 viable bacilli per gram, but these results were relatively uncommon, and the performances of the two media were not significantly different. M7H9C medium was less than half the cost of the Bactec 12B medium and did not require regular examination during incubation, but a confirmatory IS900 PCR test had to be performed on every culture after the predetermined incubation period. PMID:24048541