Unexpected conservation and global transmission of agrobacterial virulence plasmids

Science ◽  
2020 ◽  
Vol 368 (6495) ◽  
pp. eaba5256 ◽  
Author(s):  
Alexandra J. Weisberg ◽  
Edward W. Davis ◽  
Javier Tabima ◽  
Michael S. Belcher ◽  
Marilyn Miller ◽  
...  
Keyword(s):  
Host Species ◽  
Evolutionary History ◽  
Virulence Plasmids ◽  
Ri Plasmid ◽  
Accelerated Evolution ◽  
Transfer Genes ◽  
Global Spread

The accelerated evolution and spread of pathogens are threats to host species. Agrobacteria require an oncogenic Ti or Ri plasmid to transfer genes into plants and cause disease. We developed a strategy to characterize virulence plasmids and applied it to analyze hundreds of strains collected between 1927 and 2017, on six continents and from more than 50 host species. In consideration of prior evidence for prolific recombination, it was surprising that oncogenic plasmids are descended from a few conserved lineages. Characterization of a hierarchy of features that promote or constrain plasticity allowed inference of the evolutionary history across the plasmid lineages. We uncovered epidemiological patterns that highlight the importance of plasmid transmission in pathogen diversification as well as in long-term persistence and the global spread of disease.

scholarly journals The genetic diversity of Citrus dwarfing viroid populations is mainly dependent on the infected host species

2013 ◽  
Vol 94 (3) ◽  
pp. 687-693 ◽  
Author(s):  
Matilde Tessitori ◽  
Serena Rizza ◽  
Antonella Reina ◽  
Giovanni Causarano ◽  
Francesco Di Serio
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Host Species ◽  
Sweet Orange ◽  
Trifoliate Orange ◽  
Short Term ◽  
Volkamer Lemon ◽  
Troyer Citrange

As with viruses, viroids infect their hosts as polymorphic populations of variants. Identifying possible sources of genetic variability is significant in the case of the species Citrus dwarfing viroid (CDVd) which has been proposed as a dwarfing agent for high-density citrus plantings. Here, a natural CDVd isolate (CMC) was used as an inoculum source for long-term (25 years) and short-term (1 year) bioassays in different citrus host species. Characterization of progenies indicated that the genetic stability of CDVd populations was high in certain hosts (trifoliate orange, Troyer citrange, Etrog citron, Navelina sweet orange), which preserve viroid populations similar to the original CMC isolate even after 25 years. By contrast, CDVd variant populations in Interdonato lemon and Volkamer lemon were completely different to those in the inoculated sources, highlighting how influential the host is on the genetic variability of CDVd populations. Implications for risk assessment of CDVd as a dwarfing agent are discussed.

scholarly journals Characterization of Highly Irradiated ALPIDE Silicon Sensors

Universe ◽  
2019 ◽  
Vol 5 (4) ◽  
pp. 91
Author(s):  
Valentina Raskina ◽  
Filip Křížek
Keyword(s):  
Nuclear Physics ◽  
Detection Efficiency ◽  
Tracking System ◽  
Physics Institute ◽  
Total Ionization ◽  
Silicon Sensors ◽  
Active Pixel ◽  
Academy Of Sciences

The ALICE (A Large Ion Collider Experiment) experiment at CERN will upgrade its Inner Tracking System (ITS) detector. The new ITS will consist of seven coaxial cylindrical layers of ALPIDE silicon sensors which are based on Monolithic Active Pixel Sensor (MAPS) technology. We have studied the radiation hardness of ALPIDE sensors using a 30 MeV proton beam provided by the cyclotron U-120M of the Nuclear Physics Institute of the Czech Academy of Sciences in Řež. In this paper, these long-term measurements will be described. After being irradiated up to the total ionization dose 2.7 Mrad and non-ionizing energy loss 2.7 × 10 13 1 MeV n eq · cm - 2 , ALPIDE sensors fulfill ITS upgrade project technical design requirements in terms of detection efficiency and fake-hit rate.

Post-Operative Dysphagia in Anterior Cervical Discectomy and Fusion

2021 ◽  
pp. 000348942110155
Author(s):  
Leonard Haller ◽  
Khush Mehul Kharidia ◽  
Caitlin Bertelsen ◽  
Jeffrey Wang ◽  
Karla O’Dell
Keyword(s):  
Risk Factors ◽  
Medical Records ◽  
Assessment Tool ◽  
Demographic Data ◽  
Anterior Cervical Discectomy ◽  
Cervical Discectomy ◽  
Long Term Follow Up

Objective: We sought to identify risk factors associated with long-term dysphagia, characterize changes in dysphagia over time, and evaluate the incidence of otolaryngology referrals for patients with long-term dysphagia following anterior cervical discectomy with fusion (ACDF). Methods: About 56 patients who underwent ACDF between May 2017 to February 2019 were included in the study. All patients were assessed for dysphagia using the Eating Assessment Tool (EAT-10) survey preoperatively and late postoperatively (≥1 year). Additionally, 28 patients were assessed for dysphagia early postoperatively (2 weeks—3 months). Demographic data, medical comorbidities, intraoperative details, and post-operative otolaryngology referral rates were collected from electronic medical records. Results: Of the 56 patients enrolled, 21 patients (38%) had EAT-10 scores of 3 or more at long-term follow-up. None of the demographics, comorbidities, or surgical factors assessed were associated with long-term dysphagia. Patients who reported no long-term dysphagia had a mean EAT-10 score of 6.9 early postoperatively, while patients with long-term symptoms had a mean score of 18.1 ( P = .006). Of the 21 patients who reported persistent dysphagia symptoms, 3 (14%) received dysphagia testing or otolaryngology referrals post-operatively. Conclusion: Dysphagia is a notable side effect of ACDF surgery, but there are no significant demographics, comorbidities, or surgical risk factors that predict long-term dysphagia. Early postoperative characterization of dysphagia using the EAT-10 questionnaire can help predict long-term symptoms. There is inadequate screening and otolaryngology follow-up for patients with post-ACDF dysphagia.

scholarly journals Clinical characterization of 266 patients and family members with cleft lip and/or palate with associated malformations and syndromes

2021 ◽  
Author(s):  
Theodosia Bartzela ◽  
Björn Theuerkauf ◽  
Elisabeth Reichardt ◽  
Malte Spielmann ◽  
Charlotte Opitz
Keyword(s):  
Early Identification ◽  
Congenital Malformations ◽  
Cleft Lip ◽  
Phenotypic Variability ◽  
Family Members ◽  
Pierre Robin Sequence ◽  
Associated Malformations ◽  
Pierre Robin

Abstract Objectives To clinically characterize patients and family members with cleft lip and/or palate (CL/P) and associated congenital malformations or syndromes and propose possible inheritance patterns. Materials and methods An observational study of patients with CL/P, including medical and family history and intra- and extra-oral examination of their family members, was performed. Results Two hundred sixty-six patients, 1257 family members, and 42 pedigrees were included in the study. The distribution of patients according to the cleft type was 57.9% with CLP, 25.2% with cleft palate (CPO), and 12.8% with cleft lip with/without alveolus (CL/A). Seventy-four (27.8%) patients had associated malformations, and 24 (9.2%) a syndrome. The skeletal (27.7%), cardiovascular (19.3%) systems, and eyes (22.9%) were most commonly affected. Pierre Robin Sequence (7 patients) and van der Woude (4) were the most common syndromes. The majority of patients with CPO (19/24) had an associate syndrome. The families had an average of 2.45 affected members. Conclusion Individual and interfamilial phenotypic variability in patients with CL/P makes the understanding of etiopathogenesis challenging. Clinical relevance The overall prevalence of individuals with CL/P and their pedigrees with associated malformations and syndromes emphasize the need for early identification, interdisciplinary, and long-term planning.

scholarly journals Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well‐Represented Collections

2021 ◽  
Vol 1 (5) ◽  
Author(s):  
Azalea Guerra‐García ◽  
Tania Gioia ◽  
Eric Wettberg ◽  
Giuseppina Logozzo ◽  
Roberto Papa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Evolutionary History

scholarly journals Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments

2020 ◽  
Vol 11 ◽  
Author(s):  
Zhen-Hao Luo ◽  
Qi Li ◽  
Yan Lai ◽  
Hao Chen ◽  
Bin Liao ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Evolutionary History ◽  
Mine Drainage ◽  
Iron Cycling ◽  
Acid Mine ◽  
History Analysis ◽  
Genomic Characterization ◽  
Family Based ◽  
Phylogenomic Analyses

Recent genome-resolved metagenomic analyses of microbial communities from diverse environments have led to the discovery of many novel lineages that significantly expand the phylogenetic breadth of Archaea. Here, we report the genomic characterization of a new archaeal family based on five metagenome-assembled genomes retrieved from acid mine drainage sediments. Phylogenomic analyses placed these uncultivated archaea at the root of the candidate phylum Parvarchaeota, which expand this lesser-known phylum into two family levels. Genes involved in environmental adaptation and carbohydrate and protein utilization were identified in the ultra-small genomes (estimated size 0.53–0.76 Mb), indicating a survival strategy in this harsh environment (low pH and high heavy metal content). The detection of genes with homology to sulfocyanin suggested a potential involvement in iron cycling. Nevertheless, the absence of the ability to synthesize amino acids and nucleotides implies that these archaea may acquire these biomolecules from the environment or other community members. Applying evolutionary history analysis to Parvarchaeota suggested that members of the two families could broaden their niches by acquiring the potentials of utilizing different substrates. This study expands our knowledge of the diversity, metabolic capacity, and evolutionary history of the Parvarchaeota.

scholarly journals Characterization of Postharvest Fungicide-Resistant Botrytis cinerea Isolates From Commercially Stored Apple Fruit

2017 ◽  
Vol 107 (3) ◽  
pp. 362-368 ◽  
Author(s):  
Wayne M. Jurick ◽  
Otilia Macarisin ◽  
Verneta L. Gaskins ◽  
Eunhee Park ◽  
Jiujiang Yu ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Gray Mold ◽  
Apple Fruit ◽  
Sublethal Dose ◽  
Long Term Storage ◽  
Pose Control ◽  
First Time

Botrytis cinerea causes gray mold and is an economically important postharvest pathogen of fruit, vegetables, and ornamentals. Fludioxonil-sensitive B. cinerea isolates were collected in 2011 and 2013 from commercial storage in Pennsylvania. Eight isolates had values for effective concentrations for inhibiting 50% of mycelial growth of 0.0004 to 0.0038 μg/ml for fludioxonil and were dual resistant to pyrimethanil and thiabendazole. Resistance was generated in vitro, following exposure to a sublethal dose of fludioxonil, in seven of eight dual-resistant B. cinerea isolates. Three vigorously growing B. cinerea isolates with multiresistance to postharvest fungicides were further characterized and found to be osmosensitive and retained resistance in the absence of selection pressure. A representative multiresistant B. cinerea strain caused decay on apple fruit treated with postharvest fungicides, which confirmed the in vitro results. The R632I mutation in the Mrr1 gene, associated with fludioxonil resistance in B. cinerea, was not detected in multipostharvest fungicide-resistant B. cinerea isolates, suggesting that the fungus may be using additional mechanisms to mediate resistance. Results from this study show for the first time that B. cinerea with dual resistance to pyrimethanil and thiabendazole can also rapidly develop resistance to fludioxonil, which may pose control challenges in the packinghouse environment and during long-term storage.

Long term characterization of the vehicle stock in Turkey

2021 ◽  
Vol 99 ◽  
pp. 102988
Author(s):  
Merih Aydınalp Köksal ◽  
Ş. Elçin Tekeli ◽  
Shihomi Ara Aksoy ◽  
Anna Kızıltan ◽  
Mustafa Kızıltan ◽  
...  
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