scholarly journals A new biochemistry connecting pathogen detection to induced defense in plants

2021 ◽  
Author(s):  
Jane E. Parker ◽  
Giuliana Hessler ◽  
Haitao Cui
Keyword(s):  
Pathogen Detection ◽  
Induced Defense

Inkjet Printing platforms for DNA-based pathogen detection

2018 ◽  
Vol 2018 (1) ◽  
pp. 107-112 ◽  
Author(s):  
Min Zhao ◽  
Susana Diaz Amaya ◽  
Seon-ah Jin ◽  
Li-Kai Lin ◽  
Amanda J. Deering ◽  
...  
Keyword(s):  
Inkjet Printing ◽  
Pathogen Detection

Autonomous Pathogen Detection System (APDS) NYC Spring 2005 Field Test Report May to July 2005

2005 ◽  
Author(s):  
J M Dzenitis ◽  
A J Makarewicz ◽  
D R Hadley ◽  
D M Gutierrez ◽  
T R Metz ◽  
...  
Keyword(s):  
Field Test ◽  
Pathogen Detection ◽  
Detection System ◽  
Test Report

Biomedical Devices for Pathogen Detection Using Microfluidic Chips

2014 ◽  
Vol 11 (2) ◽  
pp. 116-120 ◽  
Author(s):  
Yung-Sheng Lin ◽  
Ming-Yuan-Lee ◽  
Chih-Hui Yang ◽  
Keng-Shiang Huang
Keyword(s):  
Pathogen Detection ◽  
Biomedical Devices ◽  
Microfluidic Chips

Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Akshatha Prasanna ◽  
Vidya Niranjan
Keyword(s):  
Antimicrobial Resistance ◽  
High Performance ◽  
Pathogen Detection ◽  
Bacterial Species ◽  
Workflow Management ◽  
Metagenomic Data ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent ◽  
Automated Pipeline ◽  
User Friendly

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.

scholarly journals Ecophysiological Aspects and sxt Genes Expression Underlying Induced Chemical Defense in STX-Producing Raphidiopsis raciborskii (Cyanobacteria) against the Zooplankter Daphnia gessneri

Toxins ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 406
Author(s):  
Mauro C. P. Vilar ◽  
Thiago F. C. P. Rodrigues ◽  
Luan O. Silva ◽  
Ana Beatriz F. Pacheco ◽  
Aloysio S. Ferrão-Filho ◽  
...  
Keyword(s):  
Induced Defense ◽  
Toxin Production ◽  
Grazing Pressure ◽  
Chemical Defenses ◽  
Widespread Occurrence ◽  
Genes Expression ◽  
Freshwater Bodies ◽  
Predator Response ◽  
Aquatic Food ◽  
Shed Light

Cyanobacteria stand out among phytoplankton when they form massive blooms and produce toxins. Because cyanotoxin genes date to the origin of metazoans, the hypothesis that cyanotoxins function as a defense against herbivory is still debated. Although their primary cellular function might vary, these metabolites could have evolved as an anti-predator response. Here we evaluated the physiological and molecular responses of a saxitoxin-producing Raphidiopsis raciborskii to infochemicals released by the grazer Daphnia gessneri. Induced chemical defenses were evidenced in R. raciborskii as a significant increase in the transcription level of sxt genes, followed by an increase in saxitoxin content when exposed to predator cues. Moreover, cyanobacterial growth decreased, and no significant effects on photosynthesis or morphology were observed. Overall, the induced defense response was accompanied by a trade-off between toxin production and growth. These results shed light on the mechanisms underlying zooplankton–cyanobacteria interactions in aquatic food webs. The widespread occurrence of the cyanobacterium R. raciborskii in freshwater bodies has been attributed to its phenotypic plasticity. Assessing the potential of this species to thrive over interaction filters such as zooplankton grazing pressure can enhance our understanding of its adaptive success.

Water Deficiency and Induced Defense Against a Generalist Insect Herbivore in Desert and Mediterranean Populations of Eruca sativa

2021 ◽  
Author(s):  
Ariel Ogran ◽  
Haggai Wasserstrom ◽  
Michal Barzilai ◽  
Tomer Faraj ◽  
Nir Dai ◽  
...  
Keyword(s):  
Induced Defense ◽  
Insect Herbivore ◽  
Eruca Sativa ◽  
Water Deficiency ◽  
Mediterranean Populations ◽  
Generalist Insect

scholarly journals Bacteremic sepsis leads to higher mortality when adjusting for confounders with propensity score matching

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lisa Mellhammar ◽  
Fredrik Kahn ◽  
Caroline Whitlow ◽  
Thomas Kander ◽  
Bertil Christensson ◽  
...  
Keyword(s):  
Intensive Care ◽  
Clinical Review ◽  
Pathogen Detection ◽  
Mortality Rates ◽  
Blood Cultures ◽  
Population Heterogeneity ◽  
Sepsis Diagnosis ◽  
Culture Positive ◽  
Culture Negative ◽  
Microbial Samples

AbstractOne can falsely assume that it is well known that bacteremia is associated with higher mortality in sepsis. Only a handful of studies specifically focus on the comparison of culture-negative and culture-positive sepsis with different conclusions depending on study design. The aim of this study was to describe outcome for critically ill patients with either culture-positive or -negative sepsis in a clinical review. We also aimed to identify subphenotypes of sepsis with culture status included as candidate clinical variables. Out of 784 patients treated in intensive care with a sepsis diagnosis, blood cultures were missing in 140 excluded patients and 95 excluded patients did not fulfill a sepsis diagnosis. Of 549 included patients, 295 (54%) had bacteremia, 90 (16%) were non-bacteremic but with relevant pathogens detected and in 164 (30%) no relevant pathogen was detected. After adjusting for confounders, 90-day mortality was higher in bacteremic patients, 47%, than in non-bacteremic patients, 36%, p = 0.04. We identified 8 subphenotypes, with different mortality rates, where pathogen detection in microbial samples were important for subphenotype distinction and outcome. In conclusion, bacteremic patients had higher mortality than their non-bacteremic counter-parts and bacteremia is more common in sepsis when studied in a clinical review. For reducing population heterogeneity and improve the outcome of trials and treatment for sepsis, distinction of subphenotypes might be useful and pathogen detection an important factor.

scholarly journals A Pandemic Early Warning System Decision Analysis Concept Utilizing a Distributed Network of Air Samplers via Electrostatic Air Precipitation

2021 ◽  
Vol 11 (11) ◽  
pp. 5308
Author(s):  
Joseph J. Bango ◽  
Sophia A. Agostinelli ◽  
Makayla Maroney ◽  
Michael Dziekan ◽  
Ruba Deeb ◽  
...  
Keyword(s):  
Early Warning ◽  
Early Warning System ◽  
Pathogen Detection ◽  
Clinical Laboratory ◽  
Culture Media ◽  
Morphological Characteristics ◽  
Warning System ◽  
Ambient Air ◽  
Aerosol Sampling ◽  
Distributed Network

The COVID-19 pandemic has highlighted the need for improved airborne infectious disease monitoring capability. A key challenge is to develop a technology that captures pathogens for identification from ambient air. While pathogenic species vary significantly in size and shape, for effective airborne pathogen detection the target species must be selectively captured from aerosolized droplets. Captured pathogens must then be separated from the remaining aerosolized droplet content and characterized in real-time. While improvements have been made with clinical laboratory automated sorting in culture media based on morphological characteristics of cells, this application has not extended to aerosol samples containing bacteria, viruses, spores, or prions. This manuscript presents a strategy and a model for the development of an airborne pandemic early warning system using aerosol sampling. 

scholarly journals Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Rachelle Bester ◽  
Glynnis Cook ◽  
Johannes H. J. Breytenbach ◽  
Chanel Steyn ◽  
Rochelle De Bruyn ◽  
...  
Keyword(s):  
High Throughput ◽  
Extraction Method ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Healthy Plant ◽  
Ion Torrent ◽  
Extraction Protocol ◽  
Zymo Research

Abstract Background High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. Methods Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. Results The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. Conclusions This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.

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