Tumor, Tumor immunology, cancer, hallmarks of cancer, carcinoma, lymphoma, metastasis, malignant, benign, angiogenesis, oncogenes and cancer induction, kuby detailed study quick revision, proto-oncogenes, tumor antigens, antibody, experiments for tumor antigens, methods for characterization of TSTA, Immunoediting, Current research n new approaches, monoclonal antibody
Tumor, Tumor immunology, cancer, hallmarks of cancer, carcinoma, lymphoma, metastasis, malignant, benign, angiogenesis, oncogenes and cancer induction, kuby detailed study quick revision, proto-oncogenes, tumor antigens, antibody, experiments for tumor antigens, methods for characterization of TSTA, Immunoediting, Current research n new approaches, monoclonal antibody
Fluorescence- Activated Cell Sorter is a powerful technique used in cell sorting, cell-cycle analysis etc.
The presentation gives a basic understanding of the principle of FACS, instrumentation, interpretation of results, applications, how to do cell-cycle analysis using FACS and various troubleshooting tips.
Single cell analysis is getting into the focus of many research fields as it demonstrates the individual contribution of every cell in a heterogeneous population without obscuring a biological response that may otherwise occur when cells are assessed in bulk. Although single-cell research is currently gaining momentum, yet it is challenged by the lack of affordable methods to precisely isolate a single cell from a heterogeneous cell population without causing high cellular stress.
The QIAscout system is an effective and fast method to isolate viable single cells ensuring minimal manipulation of the cellular status. The QIAscout array is ideal for various cell types like adherent cells, suspension cells, cell lines, primary cells, and fluorescent cell lines providing an environment suitable for their growth and viability similar to any standard cell culture dish. The QIAscout array consists of 12,000 microrafts that can be selectively isolated containing the single cell of interest.
This novel single cell isolation method is ideal to separate single cells for further downstream analysis or cultivation of clonal sub-populations. Single cell isolation with QIAscout is compatible with multiple downstream applications such as whole genome and transcriptome amplification methods, PCR and NGS.
3D tumor spheroid models for in vitro therapeutic screening: a systematic app...Arun kumar
The potential of a spheroid tumor model composed of cells in different proliferative and metabolic
states for the development of new anticancer strategies has been amply demonstrated. However, there
is little or no information in the literature on the problems of reproducibility of data originating from
experiments using 3D models. Our analyses, carried out using a novel open source software capable of
performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology
parameters affect the response of large spheroids to treatment. In particular, we found that both
spheroid volume and shape may be a source of variability. We also compared some commercially
available viability assays specifically designed for 3D models. In conclusion, our data indicate the need
for a pre-selection of tumor spheroids of homogeneous volume and shape to reduce data variability to
a minimum before use in a cytotoxicity test. In addition, we identified and validated a cytotoxicity test
capable of providing meaningful data on the damage induced in large tumor spheroids of up to diameter
in 650 μm by different kinds of treatments.
iPSCs are pluripotent; unlike ESC, iPSCs are not derived from the embryo, but instead created from differentiated cells in the lab through a process – cellular reprogramming.
Fluorescence- Activated Cell Sorter is a powerful technique used in cell sorting, cell-cycle analysis etc.
The presentation gives a basic understanding of the principle of FACS, instrumentation, interpretation of results, applications, how to do cell-cycle analysis using FACS and various troubleshooting tips.
Single cell analysis is getting into the focus of many research fields as it demonstrates the individual contribution of every cell in a heterogeneous population without obscuring a biological response that may otherwise occur when cells are assessed in bulk. Although single-cell research is currently gaining momentum, yet it is challenged by the lack of affordable methods to precisely isolate a single cell from a heterogeneous cell population without causing high cellular stress.
The QIAscout system is an effective and fast method to isolate viable single cells ensuring minimal manipulation of the cellular status. The QIAscout array is ideal for various cell types like adherent cells, suspension cells, cell lines, primary cells, and fluorescent cell lines providing an environment suitable for their growth and viability similar to any standard cell culture dish. The QIAscout array consists of 12,000 microrafts that can be selectively isolated containing the single cell of interest.
This novel single cell isolation method is ideal to separate single cells for further downstream analysis or cultivation of clonal sub-populations. Single cell isolation with QIAscout is compatible with multiple downstream applications such as whole genome and transcriptome amplification methods, PCR and NGS.
3D tumor spheroid models for in vitro therapeutic screening: a systematic app...Arun kumar
The potential of a spheroid tumor model composed of cells in different proliferative and metabolic
states for the development of new anticancer strategies has been amply demonstrated. However, there
is little or no information in the literature on the problems of reproducibility of data originating from
experiments using 3D models. Our analyses, carried out using a novel open source software capable of
performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology
parameters affect the response of large spheroids to treatment. In particular, we found that both
spheroid volume and shape may be a source of variability. We also compared some commercially
available viability assays specifically designed for 3D models. In conclusion, our data indicate the need
for a pre-selection of tumor spheroids of homogeneous volume and shape to reduce data variability to
a minimum before use in a cytotoxicity test. In addition, we identified and validated a cytotoxicity test
capable of providing meaningful data on the damage induced in large tumor spheroids of up to diameter
in 650 μm by different kinds of treatments.
iPSCs are pluripotent; unlike ESC, iPSCs are not derived from the embryo, but instead created from differentiated cells in the lab through a process – cellular reprogramming.
ELISA Vs ELISPOT - Principle, Procedure, Advantagesajithnandanam
The Enzyme Linked Immunospot (ELISPOT) technique was developed by Cecil Czerkinskdy in 1983. ELISPOT is used for the detection of secreted proteins, such as cytokines and growth factors. ELISPOT is primarily used in immunology research in the following areas:
This slide show forms part of the Introduction to Flow Cytometry seminar help by The Garvan MLC Flow Cytometry Facility. The Garvan MLC Flow Cytometry Facility is part of the Garvan Institute of Medical Research and is located in Sydney NSW.
How to Become a Thought Leader in Your NicheLeslie Samuel
Are bloggers thought leaders? Here are some tips on how you can become one. Provide great value, put awesome content out there on a regular basis, and help others.
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
Flow Cytometry: Guide to Understanding Applications and Benefits | The Lifesc...The Lifesciences Magazine
Flow cytometry provides unmatched insights into the properties and functions of cells, revolutionizing the fields of clinical diagnosis and biological research.
Identification of Rare and Novel Alleles in FFPE Tumor Samples | ESHG 2015 Po...Thermo Fisher Scientific
Tumors are becoming recognized as genetically heterogeneous masses of cells with different clonal histories. Identifying the mutations present in these heterogeneous masses can lead to important insights into the future behavior of the tumor and possible intervention mechanisms. However, the rarity of pathogenic mutations in small subsets of cells can make identification of such alleles difficult. In this study, we demonstrate a complete workflow that facilitates the identification of rare and novel alleles from FFPE tumor sections. We collected small regions with different cellular morphologies from lung tumor samples using laser capture microdissection, extracted both DNA and RNA from these regions, and characterized mutations present and transcript abundances by using Ion AmpliSeq™ targeted sequencing. We show that LCM facilitates the detection of alleles that are not detectable in macrodissected tissue scrapes. We also show that different regions of a tumor have very different patterns of alleles detectable and have a great deal of genetic diversity. Finally, we show that RNA expression patterns are also clearly different in the different regions. Interestingly, dissected regions with similar gross tissue morphologies display differences in alleles present and RNA expression patterns. These results suggest how we may in the future use this method to analyze mutations present in a tumor is to microdissect different subregions of the tumor, and using Ion AmpliSeq™ panels to identify the alleles present in those subregions.
Molecular characterization of a patient’s tumor to guide treatment decisions is increasingly being
applied in clinical care and can have a significant impact on disease outcome. These molecular analyses,
including mutation characterization, are typically performed on tissue acquired through a biopsy at diagnosis.
However, tumors are highly heterogeneous and sampling in its entirety is challenging. Furthermore, tumors
evolve over time and can alter their molecular genotype, making clinical decisions based on historical biopsy
data suboptimal. Personalized medicine for cancer patients aims to tailor the best treatment options for the
individual at diagnosis and during treatment. To fully enable personalized medicine it is desirable to have an
easily accessible, minimally invasive way to determine and follow the molecular makeup of a patient’s tumor
longitudinally. One such approach is through a liquid biopsy, where the genetic makeup of the tumor can be
assessed through a bio fluid sample. Liquid biopsies have the potential to help clinicians screen for disease,
stratify patients to the best treatment and monitor treatment response and resistance mechanisms in the tumor. A liquid biopsy can be used for molecular characterization of the tumor and its non-invasive nature
allows repeat sampling to monitor genetic changes over time without the need for a tissue biopsy. This review will summarize three approaches in the liquid biopsy field: circulating tumor cells (CTCs), cell free DNA (cfDNA) and exosomes. We also outline some of the analytical challenges encountered using liquid biopsy techniques to detect rare mutations in a background of wild-type sequences.
Medcrave Group - Microfluidic technologiesMedCrave
Exosomes are cell-released small membrane vesicles derived from the endolysosomal pathway with a size range of 30-150 nm. Since the first discovery in 1981, exosomes have been found to be released from various cell types and present in many biological fluids, including blood, urine, erebrospinal fluid and ascites. Significant attention has been focused on exosome molecular components (e.g. roteins, mRNA and miRNA) which have been implicated in a variety of physiological functions and pathological disease states.
For many years scientists yearned for the possibility of performing flow cytometry to analyse small bio-nanoparticles that are too small to be measured by conventional and high sensitivity instruments. These entities, extracellular vesicles, gene therapy vectors, viruses and drug delivery particles, are promised to become the next generation of therapeutics, but they have been hard to handle and characterise due to their small size and biological or chemical heterogeneity. There is therefore a strong case for bringing flow cytometry capability to the sub-200nm scale.
NanoFCM has developed the NanoAnalyzer platform that now enables true flow-cytometry measurement at the sub-micron scale, and down to particle sizes unreachable by any other flow cytometers (10-40nm depending on the nature of the substrate). Nano-flow cytometry, the technology that underpins the NanoAnalyzer, removes bias and uncertainty stemming from the use of fluorescence signal triggering by using its highly sensitive side-scatter channel to trigger particle events. The single-particle nature of the measurement prevents uncontrolled swarming events, reinforcing data integrity. High resolution of both scatter and fluorescence channels allows the assessment of subpopulations, based on size or on bio-chemical properties.
Nano-flow cytometry’s ability to measure simultaneously a (bio)-nanoparticle population for size, size distribution and bio-chemical properties on a single instrument dramatically improves data quality and throughput compared to the traditional, multiple-techniques approach involving particle characterisation and counting (DLS, NTA, RPS), combined with chemical and biological function assessment (ELISA, Western Blot, Flow Cytometry, PCR). Quantitative measurement of the active and contaminant particles in a single preparation opens up the possibility of characterisation-based nanomedicine regulatory approval, and allows the conduct of large-scale clinical studies. From the research laboratory to the quality control department, NanoFCM delivers comprehensive bio-nano analysis.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
2. What is Flow Cytometry?
‘Flow Cytometry’ as the name suggests is a technique for cell
counting and measurement of different properties of the cell
(‘cyto’= cell; ‘metry’=count/measurement).
It is a laser based technology that measures and analyses
different physical and chemical properties of the cells/particles
flowing in a stream of fluid through a beam of light.
4. Historical Perspective: Evolution of Flow
Cytometry
17th
Century
1934
1947 to
1949
1953 19651879 1968
1970s
onwards…
Development of
light microscope
by
Leeuwenhoek.
Principles of Droplet
formation by Lord
Rayleigh.
Counting of RBCs
by Moldavan by
forcing a
suspension of cells
through capillary
tube.
Development of
Coulter Principle by
Wallace Coulter and
counting of RBCs
using the first Coulter
Counter.
Optical counting of
RBCs by Crosland-
Taylor by use of
laminar flow
principles
Development of
electrostatic
inkjet droplet
deflection by
Richard Sweet
Application of
Sweet’s principle
and Coulter principle
to develop the first
cell sorter by M.
Fulwyler
Development of
fluorescence
based cell sorter
by Wolfgang
Gohde
Development of
FACS and other
advances.
5. Principles of working of Flow
Cytometer
Coulter
Principle
Principle
s of
Laminar
Flow
Electro
statics
Optics &
Light
Scatteri
ng
Flow
Cytome
try
6. Components of a Flow Cytometer
A flow cytometer is made up of three main systems: fluidics, optics, and
electronics.
The fluidics system transports particles in a stream to the laser beam for
interrogation.
The optics system consists of lasers to illuminate the particles in the
sample stream and optical filters to direct the resulting light signals to the
appropriate detectors.
The electronics system converts the detected light signals into electronic
signals that can be processed by the computer. For some instruments
equipped with a sorting feature, the electronics system is also capable of
initiating sorting decisions to charge and deflect particles.
7. Working of a Flow Cytometer
In the flow cytometer, particles are carried to the laser intercept in a fluid
stream. Any suspended particle or cell from 0.2–150 micrometers in size is
suitable for analysis.
The portion of the fluid stream where particles are located is called the sample
core.
When particles pass through the laser intercept, they scatter laser light. Any
fluorescent molecules present on the particle fluoresce.
The scattered and fluorescent light is collected by appropriately positioned
lenses.
A combination of beam splitters and filters steers the scattered and fluorescent
light to the appropriate detectors.
The detectors produce electronic signals proportional to the optical signals
striking them.
8. Applications of Flow
Cytometry
Flow cytometry is the sine qua non (without which, nothing)of the modern
researcher’s toolbox.
Flow cytometry measures multiple characteristics of individual particles
flowing in single file in a stream of fluid. Light scattering at different angles can
distinguish differences in size and internal complexity, whereas light emitted
from fluorescently labeled antibodies can identify a wide array of cell surface
and cytoplasmic antigens. This approach makes flow cytometry a powerful
tool for detailed analysis of complex populations in a short period of time.
9. Applications
Immunophenotyping
Cell subsets are measured by labeling
population-specific proteins with a fluorescent
tag on the cell surface. In clinical labs,
immunophenotyping is useful in diagnosing
hematological malignancies such as
lymphomas and leukemia.
Cell Sorting
The cell sorter is a specialized flow
cytometer with the ability to physically
isolate cells of interest into separate
collection tubes. The sorter uses
sophisticated electronics and fluidics to
identify and "kick" the cells of interest out of
the fluidic stream into a test tube.
DNA Content Analysis
The measurement of cellular DNA content by
flow cytometry uses fluorescent dyes, such as
propidium iodide, that intercalate into the DNA
helical structure. The fluorescent signal is directly
proportional to the amount of DNA in the nucleus
and can identify gross gains or losses in DNA.
Cell Cycle Analysis
Flow cytometry can analyze replication
states using fluorescent dyes to measure
the four distinct phases of the cell cycle.
Along with determining cell cycle replication
states, the assay can measure cell
aneuploidy associated with chromosomal
abnormalities.
Apoptosis
The two distinct types of cell death,
apoptosis and necrosis, can be
distinguished by flow cytometry on the basis
of differences in morphological, biochemical
and molecular changes occurring in the
dying cells.
Cell Proliferation Assays
The flow cytometer can measure proliferation by
labeling resting cells with a cell membrane
fluorescent dye, carboxyfluorescein succinimidyl
ester (CFSE). When the cells are activated, they
begin to proliferate and undergo mitosis. As the
cells divide, half of the original dye is passed on
to each daughter cell. By measuring the
reduction of the fluorescence signal, researchers
can calculate cellular activation and proliferation.
10. Fluorescence Activated Cell
Sorting (FACS)
Consider a group of lymphocytes from a mouse that have been stained with
green fluorescent antibodies specific for CD4 (e.g., fluorescein isothiocyanate,
or FITC anti-CD4) and red fluorescent antibodies specific for CD8 (e.g.,
phycoerythrin, or PE anti-CD8).
Both the labeled cells generate SSC and FSC as they pass through the laser
beam creating voltage pulses that are recorded by the computer.
However, each labeled cell will also emit light of specific wavelength as a
result of the fluorescent label. For instance, CD4 cells will emit green
fluorescent light of wavelength 525-530 nm while CD8 cells emit orange light
of wavelength 560 nm. These fluorescent signals pass through the
Photomultiplier tubes and generate voltage pulses.
The software integrates all the information for a particular cell allowing
characterization of individual cells.
11.
12. Clinical Applications: DNA
Content Analysis
Investigators are currently using techniques of DNA flow cytometry to measure ploidy status
(DNA content) and proliferative potential (S phase fraction) in a wide variety of solid tumors.
These measurements have shown relevance for diagnosis, prognosis, and treatment for
patients with cancer.
The measurement of cellular DNA content by flow cytometry uses fluorescent dyes, such as
propidium iodide, that intercalate into the DNA helical structure. The fluorescent signal is
directly proportional to the amount of DNA in the nucleus and can identify gross gains or losses
in DNA.
Abnormal DNA content, also known as “DNA content aneuploidy”, can be determined in a tumor
cell population. DNA aneuploidy generally is associated with malignancy; however, certain
benign conditions may appear aneuploid.
Cell Cycle Analysis: This technique is based on the premise that cells in G0 or G1 phases of
the cell cycle possess a normal diploid chromosomal, and hence DNA content (2n) whereas
cells in G2 and just prior to mitosis (M) contain exactly twice this amount (4n). As DNA is
synthesized during S-phase, cells are found with a DNA content ranging between 2n and 4n. A
histogram plot of DNA content against cell numbers gives the classical DNA profile for a
proliferating cell culture.
13. Flow Cytometry and Ecology
Assessments of diversity, abundance, and activity of water column
microorganisms are fundamental to studies in aquatic microbiology.
Currently, most applications of flow cytometry to environmental samples make
use of various morphological and physiological characteristics of the cells (e.g.,
size and pigment content of photosynthetic organisms).
These criteria generally are not sufficient for identification at the genus or
species level. Staining with DNA-specific fluorochromes offers information
about numbers of bacterial cells but not about their identity.
The combined use of dyes that bind preferentially to G- C or A. T base pairs
has been used to distinguish organisms of different G+C content
14. Flow Cytometry and Cancer
Research
The prognosis of patients with cancer is largely determined by the specific histological diagnosis,
tumor mass stage, and host performance status.
Quantitative cytology in the form of flow cytometry has greatly advanced the objective elucidation of
tumor cell heterogeneity by using probes that discriminate tumor and normal cells and assess
differentiate as well as proliferative tumor cell properties.
Both DNA content analysis and FACS can be utilised in cancer research.
Abnormal nuclear DMA content is a conclusive marker of malignancy and is found with increasing
frequency in leukemia (23% among 793 patients), in lymphoma (53% among 360 patients), and in
myeloma (76% among 177 patients), as well as in solid tumors (75% among 3611 patients), for an
overall incidence of 67% in 4941 patients.
Flow cytometric immunophenotyping (FCI) aids in the differentiation of chronic lymphocytic leukemia
(CLL) from mantle cell lymphoma (MCL); however, overlapping phenotypes may occur. CD11c
expression has been reported in up to 90% of CLL cases but has rarely been reported in MCL.
Whether CD11c can be used to exclude MCL has not been directly addressed. FCI reports were
reviewed for 90 MCL cases (44 patients) and 355 CLL/small lymphocytic lymphoma (SLL) cases (158
patients).