scholarly journals Ralstonia solanacearum Virulence Increased Following Large Interstrain Gene Transfers by Natural Transformation

2011 ◽  
Vol 24 (4) ◽  
pp. 497-505 ◽  
Author(s):  
Bénédicte Coupat-Goutaland ◽  
Dominique Bernillon ◽  
Alice Guidot ◽  
Philippe Prior ◽  
Xavier Nesme ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Natural Transformation ◽  
Comparative Genomic ◽  
Type Iii Effectors ◽  
New Genes ◽  
Tomato Isolate ◽  
Polymerase Chain ◽  
Genomic Regions ◽  
The Impact ◽  
Reaction Sequencing

Horizontal gene transfer (HGT) is a major driving force of evolution and is also likely to play an important role in the threatening emergence of novel pathogens, especially if it involves distantly related strains with substantially different pathogenicity. In this study, the impact of natural transformation on pathogenicity in six strains belonging to the four phylotypes of the plant-pathogenic bacterium Ralstonia solanacearum was investigated. The study focused on genomic regions that vary between donor and recipient strains and that carry genes involved in pathogenicity such as type III effectors. First, strains from R. solanacearum species complex were naturally transformed with heterologous genomic DNA. Transferred DNA regions were then determined by comparative genomic hybridization and polymerase chain reaction sequencing. We identified three transformant strains that acquired large DNA regions of up to 80 kb. In one case, strain Psi07 (phylotype IV tomato isolate) acquired 39.4 kb from GMI1000 (phylotype I tomato isolate). Investigations revealed that i) 24.4 kb of the acquired region contained 20 new genes, ii) an allelic exchange of 12 genes occurred, and iii) 27 genes (33.4 kb) formerly present in Psi07 were lost. Virulence tests with the three transformants revealed a significant increase in the aggressiveness of BCG20 over its Psi07 parent on tomato. These findings demonstrate the potential importance of HGT in the pathogenic evolution of R. solanacearum strains and open new avenues for studying pathogen emergence.

scholarly journals Towards the Identification of Type III Effectors Associated with Ralstonia solanacearum Virulence on Tomato and Eggplant

2015 ◽  
Vol 105 (12) ◽  
pp. 1529-1544 ◽  
Author(s):  
Flora Pensec ◽  
Aurore Lebeau ◽  
M. C. Daunay ◽  
Frédéric Chiroleu ◽  
Alice Guidot ◽  
...  
Keyword(s):  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Evolutionary Dynamics ◽  
Allelic Diversity ◽  
Chain Reaction ◽  
Field Collection ◽  
Type Iii Effectors ◽  
Type Iii ◽  
Dna Microarray Data ◽  
Polymerase Chain

For the development of pathogen-informed breeding strategies, identifying the microbial genes involved in interactions with the plant is a critical step. To identify type III effector (T3E) repertoires associated with virulence of the bacterial wilt pathogen Ralstonia solanacearum on Solanaceous crops, we used an original association genetics approach combining DNA microarray data and pathogenicity data on resistant eggplant, pepper, and tomato accessions. From this first screen, 25 T3Es were further full-length polymerase chain reaction-amplified within a 35-strain field collection, to assess their distribution and allelic diversity. Six T3E repertoire groups were identified, within which 11 representative strains were chosen to challenge the bacterial wilt-resistant eggplants ‘Dingras multiple Purple’ and ‘AG91-25’, and tomato Hawaii7996. The virulence or avirulence phenotypes could not be explained by specific T3E repertoires, but rather by individual T3E genes. We identified seven highly avirulence-associated genes, among which ripP2, primarily referenced as conferring avirulence to Arabidopsis thaliana. Interestingly, no T3E was associated with avirulence to both eggplants. Highly virulence-associated genes were also identified: ripA5_2, ripU, and ripV2. This study should be regarded as a first step toward investigating both avirulence and virulence function of the highlighted genes, but also their evolutionary dynamics in natural R. solanacearum populations.

scholarly journals Specific Genes from the Potato Brown Rot Strains of Ralstonia solanacearum and Their Potential Use for Strain Detection

2009 ◽  
Vol 99 (9) ◽  
pp. 1105-1112 ◽  
Author(s):  
A. Guidot ◽  
M. Elbaz ◽  
Sébastien Carrère ◽  
M. I. Siri ◽  
M. J. Pianzzola ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Crop Production ◽  
Brown Rot ◽  
Potato Industry ◽  
Genomic Islands ◽  
Detection Methods ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Polymerase Chain ◽  
Potato Brown Rot

Ralstonia solanacearum is the agent of bacterial wilt infecting >200 different plant species covering >50 botanical families. The genus R. solanacearum can be classified into four phylotypes and each phylotype can be further subdivided into sequevars. The potato brown rot strains of R. solanacearum from phylotype IIB, sequevar 1 (IIB1), historically known as race 3, biovar 2 strains, are responsible for important economic losses to the potato industry and threaten ornamental crop production worldwide. Sensitive and specific detection methods are required to control this pathogen. This article provides a list of 70 genes and 15 intergenes specific to the potato brown rot strains of R. solanacearum from phylotype IIB1. This list was identified by comparative genomic hybridization on microarray and subsequent polymerase chain reaction validation with 14 IIB1 strains against 45 non-IIB1 strains that covered the known genetic diversity in R. solanacearum. The microarray used consisted of the previously described microarray representative of the phylotype I strain GMI1000, to which were added 660 70-mer oligonucleotides representative of new genomic islands detected in the phylotype IIB1 strain IPO1609. The brown rot strain-specific genes thus identified were organized in nine clusters covering 2 to 29 genes within the IPO1609 genome and 6 genes isolated along the genome. Of these specific genes, 29 were parts of mobile genetic elements. Considering the known instability of the R. solanacearum genome, we believe that multiple probes are required to consistently detect all IIB1 strains and we recommend the use of probes which are not part of genetic mobile elements.

Trends in Genomic Analysis of the Cardiovascular System

2002 ◽  
Vol 126 (3) ◽  
pp. 310-316
Author(s):  
Leni Moldovan ◽  
Nicanor I. Moldovan
Keyword(s):  
Additional Data ◽  
Meta Analysis ◽  
Genomic Analysis ◽  
Cardiovascular Research ◽  
Oligonucleotide Arrays ◽  
Genomic Technologies ◽  
New Genes ◽  
On Line ◽  
Polymerase Chain ◽  
The Impact

Abstract Objective.—To evaluate the opportunities afforded cardiovascular medicine by the comprehensive and integrative approaches of genomics in cellular physiology. We present a meta-analysis of recently reported results obtained by means of high-throughput technologies (complementary DNA and oligonucleotide arrays, serial analysis of gene expression [SAGE]), as well as more traditional molecular biology approaches (real-time polymerase chain reaction, differential display, and others). Data Sources.—Newly published articles identified on PubMed and additional data provided by authors on-line (where available). Conclusions.—The impact of genomic analysis on cardiovascular research is already visible. New genes of cardiovascular interest have been discovered, while a number of known genes have been found to be changed in unexpected contexts. The patterns in the variation of expression of many genes correlate well with the models currently used to explain the pathogenesis of cardiovascular diseases. Much more work has yet to be done, however, for the full exploitation of the immense informative potential still dormant in the genomic technologies.

Lymphocyte predominance Hodgkin disease is characterized by recurrent genomic imbalances

Blood ◽  
2001 ◽  
Vol 97 (6) ◽  
pp. 1845-1853 ◽  
Author(s):  
Sabine Franke ◽  
Iwona Wlodarska ◽  
Brigitte Maes ◽  
Peter Vandenberghe ◽  
Jan Delabie ◽  
...  
Keyword(s):  
Hodgkin Disease ◽  
Chromosome 17 ◽  
Comparative Genomic ◽  
Non Hodgkin Lymphoma ◽  
Genomic Imbalances ◽  
Degenerate Oligonucleotide ◽  
Chromosome Arm ◽  
Polymerase Chain ◽  
Genomic Regions

Single-cell polymerase chain reaction (PCR) has been used as a tool to demonstrate clonality and B-cell origin of Reed-Sternberg (RS) cells in Hodgkin disease (HD). An analogous approach was used to investigate genomic imbalances in a (cyto)genetically poorly characterized subentity: lymphocyte predominance Hodgkin disease (LPHD). Nineteen cases of LPHD were selected for a comparative genomic hybridization (CGH) study. CGH was performed with degenerate oligonucleotide primed–PCR (DOP-PCR)–amplified DNA from 4-5 microdissected CD20+ malignant cells. All analyzed cases revealed a high number of genomic imbalances (average 10.8 per case), involving all chromosomes but the excluded 19, 22, and Y, indicating a high complexity of LPHD. The majority of detected aberrations were recurrent. Gain of 1, 2q, 3, 4q, 5q, 6, 8q, 11q, 12q, and X, and loss of chromosome 17 were identified in 36.8% to 68.4% of the analyzed cases. Some of them have also been found in non-Hodgkin lymphoma (NHL), and possibly represent secondary changes associated with disease progression. Gain of 2q, 4q, 5q, 6, 11q, however, are much more rarely observed in NHL and could be more specifically associated with LPHD. Particularly interesting is a frequent overrepresentation of chromosome arm 6q, a region usually deleted in NHL. Rearrangement of theBCL6 gene (3q27) demonstrated by cytogenetics and fluorescence in situ hybridization in 2 cases in this study suggests its contribution in pathogenesis of LPHD. In conclusion, the data show a consistent occurrence of genomic alterations in LPHD and highlight genomic regions that might be relevant for development and/or progression of this lymphoma entity.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

scholarly journals Identification of RD5-EncodedMycobacterium tuberculosisProteins As B-Cell Antigens Used for Serodiagnosis of Tuberculosis

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Miao-Miao Zhang ◽  
Jun-Wei Zhao ◽  
Zhan-Qiang Sun ◽  
Jun Liu ◽  
Xiao-Kui Guo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Detection Sensitivity ◽  
Comparative Genomic ◽  
Healthy Controls ◽  
Specific Diagnosis ◽  
Pulmonary Tb ◽  
Genomic Studies ◽  
Immunodominant Antigens ◽  
Genomic Regions ◽  
Hiv Negative

Comparative genomic studies have identified severalMycobacterium tuberculosis-specific genomic regions of difference (RDs) which are absent in the vaccine strains ofMycobacterium bovisBCG and which may be useful in the specific diagnosis of tuberculosis (TB). In this study, all encoded proteins from DNA segment RD5 ofMycobacterium tuberculosis, that is, Rv3117–Rv3121, were recombined and evaluated by enzyme-linked immunosorbent assays for antibody reactivity with sera from HIV-negative pulmonary TB patients (n=60) and healthy controls (n=32). The results identified two immunodominant antigens, that is, Rv3117 and Rv3120, both of which revealed a statistically significant antigenic distinction between healthy controls and TB patients (P<0.05). In comparison with the well-known early-secreted antigen target 6 kDa (ESAT-6) (sensitivity 21.7%, specificity 90.6%), the higher detection sensitivity and higher specificity were achieved (Rv3117: sensitivity 25%, specificity 96.9%; Rv3120: sensitivity 31.7%, specificity 96.9%). Thus, the results highlight the immunosensitive and immunospecific nature of Rv3117 and Rv3120 and indicate promise for their use in the serodiagnosis of TB.

scholarly journals Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells

2019 ◽  
Author(s):  
Federico Comoglio ◽  
Marta Simonatto ◽  
Sara Polletti ◽  
Xin Liu ◽  
Stephen T. Smale ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Regulatory Elements ◽  
Micrococcal Nuclease ◽  
Nucleosome Remodeling ◽  
Nucleosome Dynamics ◽  
Nucleosome Organization ◽  
Regulatory Information ◽  
Different Types ◽  
Genomic Regions ◽  
The Impact

ABSTRACTAccessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). Whereas stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq datasets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing however different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.

scholarly journals Clinical outcomes of concomitant use of enteral and intravenous sedatives and analgesics in mechanically ventilated patients with COVID-19

2021 ◽  
Author(s):  
Nayoung Kang ◽  
Mohammed A Alrashed ◽  
Eric M Place ◽  
Phuongthao T Nguyen ◽  
Stephen J Perona ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Invasive Mechanical Ventilation ◽  
Institutional Review Board ◽  
Chain Reaction ◽  
Mechanically Ventilated ◽  
Ventilation Time ◽  
Institutional Review ◽  
Significant Difference ◽  
Polymerase Chain ◽  
The Impact

Abstract Disclaimer In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time. Purpose To evaluate potential differences in days on mechanical ventilation for patients with coronavirus disease 2019 (COVID-19) based on route of administration of analgesic and sedative medications: intravenous (IV) alone vs IV + enteral (EN). Summary This institutional review board–approved study evaluated ventilation time and fentanyl or midazolam requirements with or without concurrent EN hydromorphone and lorazepam. Patients were included in the study if they were 18 to 89 years old and were admitted to the intensive care unit with a positive severe acute respiratory syndrome coronavirus 2 reverse transcription and polymerase chain reaction or antigen test and respiratory failure requiring invasive mechanical ventilation for more than 72 hours. In total, 100 patients were evaluated, 60 in the IV-only group and 40 in the IV + EN group. There was not a significant difference in ventilation time between the groups (mean [SD], 19.6 [12.8] days for IV + EN vs 15.6 [11.2] days for IV only; P = 0.104). However, fentanyl (2,064 [847] μg vs 2,443 [779] μg; P &lt; 0.001) and midazolam (137 [72] mg vs 158 [70] mg; P = 0.004) requirements on day 3 were significantly higher in the IV-only group, and the increase in fentanyl requirements from day 1 to day 3 was greater in the IV-only group than in the IV + EN group (378 [625] μg vs 34 [971] μg; P = 0.033). Conclusion Addition of EN analgesic and sedative medications to those administered by the IV route did not change the duration of mechanical ventilation in patients with COVID-19, but the combination may reduce IV opioid requirements, decreasing the impact of IV medication shortages.

scholarly journals Association of the I/D polymorphism of angiotensinconverting enzyme gene with the development of essential hypertension

2019 ◽  
Vol 34 (3) ◽  
pp. 87-96
Author(s):  
O. S. Pavlova ◽  
S. E. Ogurtsova ◽  
M. M. Liventseva ◽  
T. H. Lakotko ◽  
I. Y. Korobko ◽  
...  
Keyword(s):  
Essential Hypertension ◽  
Molecular Genetic ◽  
Recessive Model ◽  
Control Group ◽  
Molecular Genetic Study ◽  
Ace Gene ◽  
Paternal Line ◽  
Male Patients ◽  
Polymerase Chain ◽  
The Impact

Objective. To determine the impact of the I/D polymorphism of the angiotensin-converting enzyme (ACE) gene on the development of essential hypertension, taking into account gender differences.Material and Methods. Clinical data were assessed and a molecular genetic study was performed in 602 people including 401 patients with essential hypertension and 201 individuals of the control group, representing the Belarusian ethnic group. Genotyping was performed using the method of polymerase chain reaction and restriction fragment length polymorphism.Results. The distribution of genotypes of the I/D polymorphism of the ACE gene did not differ between patients with hypertension and normotensive individuals: II, ID, and DD genotypes were detected in 100 (24.9%), 192 (47.9%), and 109 (27.2%) patients and in 52 (25.9%), 108 (53.7%), and 41 (20.4%) people of the comparison group, respectively. Differences were found between the distribution of DD genotype in men with hypertension and in the control group, where the frequencies were 28.4% and 17.3% (p  =  0.04), respectively, in contrast to no differences in women: 25.8% and 23.3% (p  =  0.64), respectively. Carrying the DD genotype in men compared with the ID and DD genotypes (recessive model) of the I/D polymorphism of the ACE gene increased the probability of developing essential hypertension by 1.9 times (OR   =   1.89; 95% CI  =  1.04-3.44). The analysis of the prevalence of risk factors depending on the I/D polymorphism of the ACE gene showed that male patients with the DD genotype more often had burdened heredity in regard to the development of premature cardiovascular diseases (23 patients (37.7%)) compared with the individuals with II and ID genotypes: 13 (21.7%) and 14 (14.9%) patients, respectively (χ2  =  1.16; p  =   0.005), and mainly through the paternal line.Conclusions. Development of essential hypertension is associated with the carriership of the mutant DD genotype of I/D polymorphism of the ACE gene in men. 

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