Identification and Detection of Microorganism esraa alaa
Molecular detection of pathogens (molecular microbiology)
is a new, dynamic and progressive spinoff of classic microbiology. It plays an important role in those clinical situations when standard microbiology (relying on the successful cultivation of potential pathogens) produces suboptimal results or completely fails.
OR
Modern approach for identification and quantification of microorganisms (pathogens) in the diagnostics of infections or foodborne illness using molecular microbiology. Broadest range of available tests and tailor-made packages.
Molecular pathology in microbiology and metagenomicsCharithRanatunga
INTRODUCTION
HISTORY
Steps
Analysis
Metagenomic Process
Sequence-based analysis
Function-based analysis
Application of metagenomics
Future Directions of metagenomics
Examples for metagenomics projects
Microbiome Identification to Characterization: Pathogen Detection Webinar Ser...QIAGEN
The research community has begun correlating the makeup of individual microbiomes with disorders and diseases such as autism, atherosclerosis, obesity and cancer. To accomplish this, researchers must first identify and characterize these microbial communities. This slidedeck will begin with a general introduction of metagenomics and an overview of experimental strategies. Following this, a comprehensive microbiome assay pipeline will be introduced. We conclude with application-based examples that demonstrate how to identify and characterize microbiome profiles.
Diagnostic Medical Microbiology - Traditional and Modern approachChhaya Sawant
Updated version of Diagnostic Microbiology - Traditional and Modern approach. The presentation is an overview of conventional techniques still used in many laboratories and new technologies such as Molecular- and Protein-based testing
Identification and Detection of Microorganism esraa alaa
Molecular detection of pathogens (molecular microbiology)
is a new, dynamic and progressive spinoff of classic microbiology. It plays an important role in those clinical situations when standard microbiology (relying on the successful cultivation of potential pathogens) produces suboptimal results or completely fails.
OR
Modern approach for identification and quantification of microorganisms (pathogens) in the diagnostics of infections or foodborne illness using molecular microbiology. Broadest range of available tests and tailor-made packages.
Molecular pathology in microbiology and metagenomicsCharithRanatunga
INTRODUCTION
HISTORY
Steps
Analysis
Metagenomic Process
Sequence-based analysis
Function-based analysis
Application of metagenomics
Future Directions of metagenomics
Examples for metagenomics projects
Microbiome Identification to Characterization: Pathogen Detection Webinar Ser...QIAGEN
The research community has begun correlating the makeup of individual microbiomes with disorders and diseases such as autism, atherosclerosis, obesity and cancer. To accomplish this, researchers must first identify and characterize these microbial communities. This slidedeck will begin with a general introduction of metagenomics and an overview of experimental strategies. Following this, a comprehensive microbiome assay pipeline will be introduced. We conclude with application-based examples that demonstrate how to identify and characterize microbiome profiles.
Diagnostic Medical Microbiology - Traditional and Modern approachChhaya Sawant
Updated version of Diagnostic Microbiology - Traditional and Modern approach. The presentation is an overview of conventional techniques still used in many laboratories and new technologies such as Molecular- and Protein-based testing
This presentation contains information about Bacterial Taxonomy, techniques of bacterial classification (Classical and Molecular characteristics) and Bergey's Manual
The Main Advantage
The main advantages of flow cytometry over histology and IHC is the possibility to precisely measure the quantities of antigens and the possibility to stain each cell with multiple antibodies-fluorophores, in current laboratories around 10 antibodies can be bound to each cell. This is much less than mass cytometer where up to 40 can be currently measured, but at a higher and slower pace.
Aquatic research
In aquatic systems, flow cytometry is used for the analysis of autofluorescing cells or cells that are fluorescently-labeled with added stains.
This research started in 1981 when Clarice Yentsch used flow cytometry to measure the fluorescence in a red tide producing dinoflagellates
Marine scientists use the sorting ability of flow cytometers to make discrete measurements of cellular activity and diversity, to conduct investigations into the mutualistic relationships between microorganisms that live in close proximity,and to measure biogeochemical rates of multiple processes in the ocean
Cell Proliferation assay
Cell proliferation is the major function in the immune system. Often it is required to analyse the proliferative nature of the cells in order to make some conclusions. One such assay to determine the cell proliferation is the tracking dye carboxyfluorescein diacetate succinimidyl ester (CFSE). It helps to monitor proliferative cells. This assay gives quantitative as well as qualitative data during time-series experiments
Cell counting
Cell sorting
Determining cell characteristics and function
Detecting microorganisms
Biomarker detection
Protein engineering detection
Diagnosis of health disorders such as blood cancers
Flow cytometry can be used for cell cycle analysis to estimate the percentages of a cell population in the different phases of the cell cycle, or it can be used with other reagents to analyze just the S phase.
Why flow cytometry is ideal for cell cycle analysis
Live-cell cycle analysis stains—Vybrant DyeCycle stains
Classic DNA cell cycle stains such as Hoechst 33342 and DRAQ5 for cell cycle analysis, but most of these have limitations that have to be considered when using them in an experiment which is why the Invitrogen Vybrant DyeCycle stains for live-cell cycle analysis were developed.
Fixed-cell cycle analysis stains FxCycle reagents
We offer classic DNA cell cycle stains such as DAPI, PI, and 7-AAD for fixed cell cycle analysis, but these reagents do not cover the full spectrum of laser excitation available.
The FxCycle reagents offer options for the 405 nm (violet) and 633 nm (red) laser thereby increasing the ability to multiplex by freeing up the 488 nm and 633 nm lasers for other cellular analyses such as immunophenotyping, apoptosis analysis, and dead cell discrimination.
Precise—Accurate cell cycle analysis in living cells
Safe—Low cytotoxicity for combining with additional live cell experiments
Cell sort compatible—Easily sort cells based on phase of the cell cycle
This presentation covers:
• Definition of life sciences
• The stages of a therapeutic drugs or vaccines R&D project
• The state of the art
• Regulatory nuances
• Pre-clinical and in the clinic issues
• Future trends
• Challenges and opportunities
• Case studies and examples
Use of DNA barcoding and its role in the plant species/varietal Identifica...Senthil Natesan
Plant DNA barcoding research is shifting beyond performance comparisons of different DNA regions towards practical applications. The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1(CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. The studies on cucumis sp for the application of DNA barcode shows the possibility of discrimination at species level not the varietal level using the matK gene barcode. The phylogenetic tree constructed by using matK gene sequences clearly differentiated the species C. sativus and C. melo which will help for the future application in cucumis taxonomy and phylogeny studies
This presentation contains information about Bacterial Taxonomy, techniques of bacterial classification (Classical and Molecular characteristics) and Bergey's Manual
The Main Advantage
The main advantages of flow cytometry over histology and IHC is the possibility to precisely measure the quantities of antigens and the possibility to stain each cell with multiple antibodies-fluorophores, in current laboratories around 10 antibodies can be bound to each cell. This is much less than mass cytometer where up to 40 can be currently measured, but at a higher and slower pace.
Aquatic research
In aquatic systems, flow cytometry is used for the analysis of autofluorescing cells or cells that are fluorescently-labeled with added stains.
This research started in 1981 when Clarice Yentsch used flow cytometry to measure the fluorescence in a red tide producing dinoflagellates
Marine scientists use the sorting ability of flow cytometers to make discrete measurements of cellular activity and diversity, to conduct investigations into the mutualistic relationships between microorganisms that live in close proximity,and to measure biogeochemical rates of multiple processes in the ocean
Cell Proliferation assay
Cell proliferation is the major function in the immune system. Often it is required to analyse the proliferative nature of the cells in order to make some conclusions. One such assay to determine the cell proliferation is the tracking dye carboxyfluorescein diacetate succinimidyl ester (CFSE). It helps to monitor proliferative cells. This assay gives quantitative as well as qualitative data during time-series experiments
Cell counting
Cell sorting
Determining cell characteristics and function
Detecting microorganisms
Biomarker detection
Protein engineering detection
Diagnosis of health disorders such as blood cancers
Flow cytometry can be used for cell cycle analysis to estimate the percentages of a cell population in the different phases of the cell cycle, or it can be used with other reagents to analyze just the S phase.
Why flow cytometry is ideal for cell cycle analysis
Live-cell cycle analysis stains—Vybrant DyeCycle stains
Classic DNA cell cycle stains such as Hoechst 33342 and DRAQ5 for cell cycle analysis, but most of these have limitations that have to be considered when using them in an experiment which is why the Invitrogen Vybrant DyeCycle stains for live-cell cycle analysis were developed.
Fixed-cell cycle analysis stains FxCycle reagents
We offer classic DNA cell cycle stains such as DAPI, PI, and 7-AAD for fixed cell cycle analysis, but these reagents do not cover the full spectrum of laser excitation available.
The FxCycle reagents offer options for the 405 nm (violet) and 633 nm (red) laser thereby increasing the ability to multiplex by freeing up the 488 nm and 633 nm lasers for other cellular analyses such as immunophenotyping, apoptosis analysis, and dead cell discrimination.
Precise—Accurate cell cycle analysis in living cells
Safe—Low cytotoxicity for combining with additional live cell experiments
Cell sort compatible—Easily sort cells based on phase of the cell cycle
This presentation covers:
• Definition of life sciences
• The stages of a therapeutic drugs or vaccines R&D project
• The state of the art
• Regulatory nuances
• Pre-clinical and in the clinic issues
• Future trends
• Challenges and opportunities
• Case studies and examples
Use of DNA barcoding and its role in the plant species/varietal Identifica...Senthil Natesan
Plant DNA barcoding research is shifting beyond performance comparisons of different DNA regions towards practical applications. The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1(CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. The studies on cucumis sp for the application of DNA barcode shows the possibility of discrimination at species level not the varietal level using the matK gene barcode. The phylogenetic tree constructed by using matK gene sequences clearly differentiated the species C. sativus and C. melo which will help for the future application in cucumis taxonomy and phylogeny studies
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Instructions for Submissions thorugh G- Classroom.pptxJheel Barad
This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
2. • TAXANOMY
• It is likened to a skilful blend in which it is
not easy to discern the ingredients (Cowan
& Steele).
• Ingredients: Classification,
Nomenclature and Identification.
3. Classification: Orderly arrangement of units
into groups based on acceptable set of
criteria.
Nomenclature: Naming or labeling of the
groups or units and individuals within the
group.
Identification: Entails the assignation of an
unknown organism to a group within a
scheme of classification.
4. Classification of Bacteria
There is no official classification of bacteria.
Taxanomy remains a matter of scientific
judgment and a generally accepted standard.
The commonly accepted classification is as
listed in 2nd edition of Bergey’s Manual of
Systematic Bacteriology.
5. Types of classification
1. Phylogenic classification
Based on evolutionary (ancestry) origins. The
ancestors of present day bacteria existed for 3
billion years. This system was used to
recognise two domains of Bacteria and
Archaea.
It is the basis of naming (nomenclature) of
bacteria.
7. Morphology: Microscopic and macroscopic
morphologies of bacteria were the first
characteristics used to identify bacteria.
• Still the cornerstone for most identification
algorithms used today, e.g.
i) The Gram’s stain is used to classify bacteria
based on their shape and staining reaction.
ii) Macroscopic appearance of colonies on
culture plates such as haemolysis on blood
agar plates, pigmentation on culture media.
8. • Biochemical typing is the most used
method for definitive identification.
Biotyping is also used for dividing group
of organisms beyond species level.
• Serological typing is useful to identify
organisms that are inert in biochemical
testing e.g. Treponema pallidum, for rapid
identification of some species e.g. Strep.
pyogenes etc.
9. • Antimicrobial pattern: pattern of
susceptibility to antibiotics.
• Pyocin typing: Pyocins are a group of low
molecular weight bactericidal proteins. Their
bactericidal activity pattern can be used to
classify bacteria.
• Phage typing: Susceptibility to phages (or
bacterial viruses) is used to identify bacteria.
11. • Cell wall content of mycolic acid has been
used to identify species of mycobacteria
(ZN stain).
• Analysis of lipid content of the whole cell
is used to characterise some bacteria.
• Commercial systems are available for
performing this analysis.
12. • Whole cell protein typing are handy tools
in characterising bacteria especially at
species level for epidemiological
purposes.
• This is done in reference laboratories.
• Cellular enzyme typing is a handy tool in
characterising bacteria especially at
species level for epidemiological
purposes.
13. 4.Numerical classification:
This a mathematical approach whereby all
features are assigned equal values. This is
the original Adansonian concept.
• The advent of computers has made this
approach to taxanomy easier to apply.
• Used mainly for research
14. 5. Genetic classification aka Molecular
genetics:
This is most precise and accurate.
Includes systems such as:
a) Guanine:Cytosine ratio:
This is now obsolete and the method has been
discarded.
15. • b) DNA hybridization: Involves comparison
of base sequence compatibility between two
strains: to determine if two isolates were in
the same genus or species.
• DNA probe: A probe from a marker strain is
annealed with DNA from test strain. If the
marker is bound to the DNA of test strain, the
identity is confirmed.
16. • Put in another way, DNA from the organism to
be identified is extracted and exposed to the
species specific probes. If the probes bind to
the DNA, then the organism’s identity is
confirmed.
• Can be applied directly to clinical specimens.
• It is definitive but tedious and requires
expertise to handle.
17. c) Nuleic acid sequencing aka DNA
amplification
Extension of the hybridization method is
Nucleic Acid sequencing or DNA amplification.
Most recent and modern, probes are used to
localise sequences that are unique to genus,
species, sub-species.
18. Various methods are used but the
commonest are PCR and LCR.
This method is changing the face of
laboratory diagnosis of infections.
It requires expertise and it is pretty
expensive.
Very wide application.
19. • d) Other genetic typing include
• i)Ribotyping and
• Ii) Plasmid analysis and
• Iii) Chromosomal DNA fragments.
• These are highly sophisticated systems
and are not in routine use.
• .
20. • Other approaches to classification
• Specific features: Based on specific ,
distinguishable features shared by all in
the group. This classification is according
to Bergey’s Manual of Determinative
Bacteriology.
• The features that require difficult process
or special apparatus are not listed.
21. NOMENCLATURE
• The term species is most commonly used
in the pragmatic classifying system. It is
the basic unit in the hierarchy of microbial
world.
• The basis of this category is that members
of the same species are able to produce
others of their kind.
• The next higher category is genus.
22. • The same genus comprises several species
which may differ in some aspects.
Further up the ladder of classification,
bacteria with similar features are placed in
successive larger categories.
Thus similar genera are grouped into family;
similar families are categorised as order;
similar orders make up class and
similar classes make up the phylum
(kingdom).
23. Theoretical classification and
Identification:
• This provides the bacteriologist with a
relatively simple and pragmatic ways of
placing bacteria into categories.
• Consideration is given to:
• Colonial morphology – This requires a
measure of experience to be able to identify
an organism by colonial appearance.
24. • This is usually confirmed with a few rapid
tests.
• Most isolates are divided into commensal,
contaminants of no clinical interest,
possible pathogen or probably pathogen
based partially on this.
• Thus, it reduces the workload of a clinical
laboratory.
25. • Gram’s stain
• In 1884, a Danish scientist, Christian Gram,
introduced a staining technique that indeed
simplified and enhanced the classification of
bacteria.
• The Gram’s stain has become the foundation
on which bacterial identification is laid.
• The staining technique is cell wall dependent
and simply divides bacteria into two groups:
Gram positive and Gram negative.
26. • The “key”:
• e.g. Coagulase test divides the species of
staphylococcus into two groups: CPS and
CNS
• Note that bacterial species are polythetic
i.e. a property may vary within a species.
• Reaction pattern of an unknown isolate is
compared to the “key” and its “goodness
of fit” with each species is determined.
27. • The key is now replaced by some
identification systems such as the API
system.
• Analytical Profile Index (API)
The numerical profile of the unknown isolate
is compared with an existing numerical
pattern for a known species.
28. The highest index (best fit) as calculated for
the unknown is the identity of the unknown.
• Unusual patterns may be due to many
factors e.g. impure culture.
• Giving an isolate a species name:
• This requires careful consideration.
29. Once identified, the isolate is assumed to
possess all the implied properties including
biochemistry, pathogenicity capability etc.
• If unequivocal, state that the isolate is
unusual.
• Routine identification of bacteria
The diagnostic bacteriologist bases his
identification strategy on what is termed
Characterization tests
30. • Routine identification of bacteria
• The diagnostic bacteriologist bases
his identification strategy on what is
termed Characterization tests
• These tests include :
• Microscopic morphology:
»Cell shape e.g. coccus
31. »Size
»Arrangement .e.g. clusters, chain
»Staining e.g. Gram + or Gram -
»Capsule characteristic
»Spore morphology e.g. round, oval,
terminal
»Flagellar arrangement e.g.
monotrichous
32. • Colonial morphology
• Solid media:
• For an experienced bench bacteriologist,
data from this source is often sufficient for
identification at genus level.
• Most clinical isolates discarded as non
significant are identified usually by colonial
appearance.
33. • Further incubation may be necessary in
order to ascertain the correct colonial
morphology of a suspected pathogen.
• Action on media- Haemolysis
- Pigmentation
- Swarming
34. Biochemical tests
• Essential tool for bacterial classification
and identification.
• Examples
- Fermentation/oxidation of carbohydrates
- Waste products
- Metabolism of organic acids, lipids, proteins
and amino acids.
35. • - pH or redox range of growth
-Tolerance of chemical agents
In short, these tests collectively define
nutritional and physiological interaction of
the organism with its enviroment.
- Usually technically simple and
inexpensive
36. especially when adapted to multi point
inoculating commercial test strips or micro
titre plate formats. But they all have
hidden complexities.
- Most yield positive (+) or negative (-)
results that are easy to read.
Enzyme activity
Characterization tests also include the
action of various enyzmes or toxins
produced by organisms.
37. • Examples:
- Coagulase for Staphylococcus species
- Lecthinase for Clostridium species
- Urease for Proteus species
The above approach is pragmatic, simple
and fast enough that the bench
bacteriologist is able to play his role in the
overall management of disease.
38. »Systematic Bacteriology
The systematic approach to the
identification of an isolated bacterium is
referred to as Systematic Bacteriology.
The bench bacteriologist combines his
theoretical knowledge of bacteriology,
disease aetiology and clinical information
as contained in request form, to initiate a
systematic identification of an isolated
bacterium.