scholarly journals Detection, Diversity, and Population Dynamics of Waterborne Phytophthora ramorum Populations

2015 ◽  
Vol 105 (1) ◽  
pp. 57-68 ◽  
Author(s):  
C. A. Eyre ◽  
M. Garbelotto
Keyword(s):  
Population Dynamics ◽  
Pathogen Detection ◽  
Phytophthora Ramorum ◽  
Natural Forests ◽  
Tree Disease ◽  
The United Kingdom ◽  
Risk Areas ◽  
Study Population ◽  
Polymerase Chain ◽  
Stream Baiting

Sudden oak death, the tree disease caused by Phytophthora ramorum, has significant environmental and economic impacts on natural forests on the U.S. west coast, plantations in the United Kingdom, and in the worldwide nursery trade. Stream baiting is vital for monitoring and early detection of the pathogen in high-risk areas and is performed routinely; however, little is known about the nature of water-borne P. ramorum populations. Two drainages in an infested California forest were monitored intensively using stream-baiting for 2 years between 2009 and 2011. Pathogen presence was determined both by isolation and polymerase chain reaction (PCR) from symptomatic bait leaves. Isolates were analyzed using simple sequence repeats to study population dynamics and genetic structure through time. Isolation was successful primarily only during spring conditions, while PCR extended the period of pathogen detection to most of the year. Water populations were extremely diverse, and changed between seasons and years. A few abundant genotypes dominated the water during conditions considered optimal for aerial populations, and matched those dominant in aerial populations. Temporal patterns of genotypic diversification and evenness were identical among aerial, soil, and water populations, indicating that all three substrates are part of the same epidemiological cycle, strongly influenced by rainfall and sporulation on leaves. However, there was structuring between substrates, likely arising due to reduced selection pressure in the water. Additionally, water populations showed wholesale mixing of genotypes without the evident spatial autocorrelation present in leaf and soil populations.

scholarly journals Detection and Quantification of Phytophthora ramorum from California Forests Using a Real-Time Polymerase Chain Reaction Assay

2004 ◽  
Vol 94 (10) ◽  
pp. 1075-1083 ◽  
Author(s):  
Katherine J. Hayden ◽  
David Rizzo ◽  
Justin Tse ◽  
Matteo Garbelotto
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Pathogen Detection ◽  
Phytophthora Species ◽  
Phytophthora Ramorum ◽  
Plant Diseases ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
New Host ◽  
Polymerase Chain

The timely and accurate detection of pathogens is a critical aid in the study of the epidemiology and biology of plant diseases. In the case of regulated organisms, the availability of a sensitive and reliable assay is essential when trying to achieve early detection of the pathogen. We developed and tested a real-time, nested polymerase chain reaction (PCR) assay for the detection of Phytophthora ramorum, causal agent of sudden oak death. This technique then was implemented as part of a widespread environmental screen throughout California. The method here described is sensitive, detecting less than 12 fg of pathogen DNA, and is specific for P. ramorum when tested across 21 Phytophthora spp. Hundreds of symptomatic samples from 33 sites in 14 California counties were assayed, resulting in the discovery of 10 new host species and 23 infested areas, including 4 new counties. With the exception of a single host, PCR-based discovery of new hosts and infested areas always was confirmed by traditional pathogen isolations and inoculation studies. Nonetheless, molecular diagnostics were key in early pathogen detection, and steered the direction of further research on this newly discovered and generalist Phytophthora species.

scholarly journals Investigations, actions and learning from an outbreak of SARS-CoV-2 infection among healthcare workers in the United Kingdom

2020 ◽  
pp. 175717742097679
Author(s):  
Kordo Saeed ◽  
Emanuela Pelosi ◽  
Nitin Mahobia ◽  
Nicola White ◽  
Christopher Labdon ◽  
...  
Keyword(s):  
Real Time ◽  
Healthcare Workers ◽  
Healthcare Facility ◽  
Rt Pcr ◽  
Serum Samples ◽  
The United Kingdom ◽  
Key Issues ◽  
Current Infection ◽  
Polymerase Chain ◽  
A Current

Background: We report an outbreak of SARS coronavirus-2 (SARS-CoV-2) infection among healthcare workers (HCW) in an NHS elective healthcare facility. Methodology: A narrative chronological account of events after declaring an outbreak of SARS-CoV-2 among HCWs. As part of the investigations, HCWs were offered testing during the outbreak. These were: (1) screening by real-time reverse transcriptase polymerase chain reaction (RT- PCR) to detect a current infection; and (2) serum samples to determine seroprevalence. Results: Over 180 HCWs were tested by real-time RT-PCR for SARS-CoV-2 infection. The rate of infection was 15.2% (23.7% for clinical or directly patient-facing HCWs vs. 4.8% in non-clinical non-patient-facing HCWs). Of the infected HCWs, 57% were asymptomatic. Seroprevalence (SARS-CoV-2 IgG) among HCWs was 13%. It was challenging to establish an exact source for the outbreak. The importance of education, training, social distancing and infection prevention practices were emphasised. Additionally, avoidance of unnecessary transfer of patients and minimising cross-site working for staff and early escalation were highlighted. Establishing mass and regular screening for HCWs are also crucial to enabling the best care for patients while maintaining the wellbeing of staff. Conclusion: To our knowledge, this is the first UK outbreak report among HCWs and we hope to have highlighted some key issues and learnings that can be considered by other NHS staff and HCWs globally when dealing with such a task in future.

Microbiome population dynamics of cold smoked sockeye salmon during refrigerated storage and after culture enrichment

2021 ◽  
Author(s):  
Karen Jarvis ◽  
Chiun-Kang Hsu ◽  
James B. Pettengill ◽  
John Ihrie ◽  
Hiren Karathia ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Foodborne Pathogens ◽  
Sockeye Salmon ◽  
Pathogen Detection ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Smoked Salmon ◽  
Spoilage Bacteria ◽  
Culture Enrichment ◽  
Processing And Storage

Cold smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold smoked salmon. Here we investigated the microbial community through targeted 16s rRNA gene and shotgun metagenomic sequencing, as means to better understand the interactions among bacteria in cold smoked salmon. Cold smoked salmon samples were tested over 30 days of aerobic storage at 4℃ and cultured at each timepoint in buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were comprised of Firmicutes and Proteobacteria namely, Carnobacterium , Brochothrix , Pseudomonas , Serratia , and Psychrobacter . Pseudomonas species were the most diverse species with 181 taxa identified. Additionally, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment.  This may facilitate improvements to pathogen detection and quality preservation of this food.

scholarly journals Impact of Multiplex Polymerase Chain Reaction Testing for Respiratory Pathogen Detection in Pediatric Patients

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S503-S503
Author(s):  
Courtney C Sutton ◽  
Patti J Walton ◽  
Montgomery F Williams ◽  
Tracey L Bastian ◽  
Michael Wright ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Polymerase Chain Reaction ◽  
Pathogen Detection ◽  
Pediatric Patients ◽  
Respiratory Pathogen ◽  
Chain Reaction ◽  
Polymerase Chain Reaction Testing ◽  
Polymerase Chain

scholarly journals CYP27B1 Gene Polymorphism rs10877012 in Patients Diagnosed with Colorectal Cancer

Nutrients ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 998
Author(s):  
Maria Latacz ◽  
Jadwiga Snarska ◽  
Elżbieta Kostyra ◽  
Konrad Wroński ◽  
Ewa Fiedorowicz ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Vitamin D ◽  
Fragment Length Polymorphism ◽  
Intestinal Cells ◽  
Chain Reaction ◽  
The Third ◽  
Pcr Rflp ◽  
Study Population ◽  
Polymerase Chain ◽  
Peripheral Leukocytes

Colorectal cancer (CRC) is the third most commonly occurring cancer worldwide. Intestinal cells are CYP27B1 gene expression sites and, as a consequence, they are capable of converting pro-vitamin D into the active paracrine and autocrine forms. It was demonstrated that rs10877012 polymorphism in the CYP27B1 gene influenced the circulating vitamin D level. This provided a rationale for determining the role that this polymorphism plays in the risk of developing colon cancer. In this study, we investigated the association of rs10877012 (T/G) polymorphism in the CYP27B1 gene with CRC susceptibility. The study population (n = 325) included CRC patients (n = 106) and healthy controls (n = 219). DNA was extracted from peripheral leukocytes and analyzed for the CYP27B1 polymorphism using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We found an association between the presence of the T allele at the polymorphic site (odds ratio (OR) = 2.94; 95% CI 1.77–4.86; p < 0.0001) and a decreased CRC incidence.

scholarly journals Prevalence of congenital non syndromic hearing loss among offspring of consanguineous marriage: a pilot study

2020 ◽  
Vol 6 (5) ◽  
pp. 874
Author(s):  
Gangadhar K. S. ◽  
Geetha Bhaktha ◽  
Manjula B. ◽  
Nageshwari P.
Keyword(s):  
Hearing Loss ◽  
Consanguineous Marriage ◽  
Gene Encoding ◽  
Single Nucleotide ◽  
Junction Protein ◽  
Study Population ◽  
Syndromic Hearing Loss ◽  
Gap Junction Protein ◽  
Polymerase Chain ◽  
Recessive Defect

<p class="abstract"><strong>Background:</strong> Mutations in the gene encoding the gap-junction protein connexin-26, is understood to be the most important cause of non-syndromic hearing loss (NSHL). An attempt to identify the single nucleotide polymorphism (SNP) for W24X mutation was done.  Consanguineous marriage was seen among the NSHL subjects.</p><p class="abstract"><strong>Methods:</strong> SNP was identified using restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR).  Forty-five subjects were screened for congenital hearing loss. Twenty subjects matched the inclusion criteria and were included in the study.</p><p class="abstract"><strong>Results:</strong> 5 out of 20 subjects were found to have mutation i.e., 25%. Though consanguinity is known to cause autosomal recessive defect, the same could not be depicted in this study.</p><p class="abstract"><strong>Conclusions:</strong> 25% of the study population had a mutation in their gene and the rest though had consanguineous marriage had not been affected genotypically.</p>

scholarly journals Electrocardiographic characteristics of patients with coronavirus disease 2019 (COVID-2019) related pneumonia at first presentation

EP Europace ◽  
2021 ◽  
Vol 23 (Supplement_3) ◽  
Author(s):  
U Nguyen ◽  
M Strik ◽  
S Abu-Arib ◽  
A Bruekers ◽  
T Nguyen ◽  
...  
Keyword(s):  
Clinical Presentation ◽  
Negative Group ◽  
Male Mortality ◽  
Funding Sources ◽  
Atrial Enlargement ◽  
Study Population ◽  
Polymerase Chain ◽  
Repolarization Abnormalities ◽  
Funding Acknowledgements

Abstract Funding Acknowledgements Type of funding sources: None. Purpose To evaluate electrocardiographic (ECG) characteristics at first presentation in patients with possible coronavirus disease (COVID-19) pneumonia. Methods and results 356 patients presenting at the emergency room with possible COVID-19 pneumonia based on clinical presentation and computed tomography findings were included and subdivided into a COVID-19 positive group ([COVID-19-positive], n = 231, 65%) and a COVID-19 negative group ([COVID-19-negative], n = 125, 35%) based on polymerase chain reaction tests. The study population was predominantly middle aged-elderly (67 ± 14 year; n = 235, 66% male). Mortality rate was 24% after 1-month follow-up. There were no significant (NS) differences in sex, age, and mortality between the COVID-19-positive and COVID-19-negative group.  Atrial fibrillation (AF) was common (9%), though its prevalence was NS (regression analyses adjusted for age and sex) different in the COVID-19-positive vs. the COVID-19-negative group. ECG characteristics reflecting atrial enlargement and repolarization abnormalities were frequently present (&lt;38% and 14% respectively). No significant differences were found between the COVID-19-positive vs. the COVID-19-negative group for the majority of morphological ECG characteristics (Figure 1 for more detailed data).  Conclusion AF and ECG characteristics reflecting atrial enlargement and repolarization abnormalities are commonly present in COVID-19 patients. The prevalence of these ECG characteristics however do NS differ from their COVID-19-negative counterparts. Abstract Figure.

scholarly journals Deletion pattern in the dystrophin gene in Duchenne muscular dystrophy patients in northeast India

2013 ◽  
Vol 04 (02) ◽  
pp. 227-229 ◽  
Author(s):  
Lakshya J Basumatary ◽  
Marami Das ◽  
Munindra Goswami ◽  
Ashok K Kayal
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Dna Analysis ◽  
Hot Spot ◽  
Dystrophin Gene ◽  
Northeast India ◽  
Deletion Rate ◽  
Study Population ◽  
Deletion Pattern ◽  
Polymerase Chain

ABSTRACTDuchenne muscular dystrophy (DMD) is an X‑linked recessive disorder that affects 1 in 3,500 males and is caused by mutations in the dystrophin gene. In this paper, we have reported DNA analysis of DMD patients by multiplex polymerase chain reaction (PCR) from various states of northeast India. Of the 69 clinically suspected patients of DMD, deletion was detected by multiplex PCR in 49 (71%) patients. Majority of the deletions (42/49, 85.7%) were located at distal hot spot region that encompasses exons 44-55 and 14.3% of the deletions were located at the proximal hot spot region (exons 2-19). In this study population, the deletion rate was 71% and was more frequent in the distal end exon.

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