Compare the use of Lonza KGM Gold Bullet kit and Rheinwald and Green complete FAD medium in primary human epidermal keratinocytes culture and its applicability cells cultured by these medium in the construction of reconstituted skin equivalent model
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
The use of genetic engineering technology in animals has been associated with ethical issues, some of which relate to animal welfare. Discuss examples of genetically engineering animals and evaluate the ethical concerns of genetic engineering.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
The use of genetic engineering technology in animals has been associated with ethical issues, some of which relate to animal welfare. Discuss examples of genetically engineering animals and evaluate the ethical concerns of genetic engineering.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
The Effects of Genetic Alteration on Reprogramming of Fibroblasts into Induc...remedypublications2
Induced Pluripotent Stem Cells (iPSCs) can be generated from somatic cells by ectopic expression of
Yamanaka factors (
Oct4
,
Sox2
,
Klf4
and
c-Myc
) or combination of other factors. Genetic alteration
of fibroblasts exhibits an effect on reprogramming efficiency through multiple signaling pathways,
including epigenetic modifications, metabolic shifts, Mesenchymal-To-Epithelial Transition
(MET) and cell proliferation. In order to better understand the underlying mechanisms in cell fate
determination, in this review we will summarize several genetic alterations involved in the regulation
of reprogramming fibroblasts into iPSCs.
Innovative Minds in Prostate Cancer Today
IMPaCT Conference
Congressionally Directed Medical Research Program of the U.S. Department of Defense
Dr. Martin H. Hager presentation
New treatment strategies
Angiogenesis, Invasion, Metastasis
Martin H. Hager
Targeted Therapy
Cancer
Angiogenesis
Metastasis
Sox2 suppresses the invasiveness of breast cancer cells via a mechanism that ...Enrique Moreno Gonzalez
Sox2, an embryonic stem cell marker, is aberrantly expressed in a subset of breast cancer (BC). While the aberrant expression of Sox2 has been shown to significantly correlate with a number of clinicopathologic parameters in BC, its biological significance in BC is incompletely understood.
Carcinogenesis refers to the process by which a normal cell is transformed into a malignant cell and repeatedly divides to become a cancer
Chemicals which initiate this process is called chemical carcinogens
Chemicals which increase the effectiveness of carcinogens is called co-carcinogens
REGULATORY BACKGROUND
ROLE OF PROTO-ONCOGENES AND TUMOR SUPPRESSOR GENES
ACTIVATION OF PROTO ONCOGENES
OXIDATIVE STRESS IN CARCINOGENESIS
OECD guidelines
451- Carcinogenecity studies
453- Combined chronic toxicity/carcinogenecity
ICH guidelines
S1A- Guideline on the need for carcinogenicity studies of
pharmaceuticals
S1B- Testing for carcinogenicity of pharmaceuticals
S1C- Dose selection for carcinogenicity studies of pharmaceuticals
Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neu...Gul Muneer
Systemic cross-talk between lung tumors and bones
Bone marrow–derived myeloid cells can accumulate within tumors and foster
cancer outgrowth. Local immune-neoplastic interactions have been intensively
investigated, but the contribution of the systemic host environment to tumor growth
remains poorly understood. Here, we show in mice and cancer patients (n = 70) that
lung adenocarcinomas increase bone stromal activity in the absence of bone
metastasis. Animal studies reveal that the cancer-induced bone phenotype involves
bone-resident osteocalcin-expressing (Ocn+) osteoblastic cells. These cells promote
cancer by remotely supplying a distinct subset of tumor-infiltrating SiglecFhigh
neutrophils, which exhibit cancer-promoting properties. Experimentally reducing
Ocn+ cell numbers suppresses the neutrophil response and lung tumor outgrowth.
These observations posit osteoblasts as remote regulators of lung cancer and
identify SiglecFhigh neutrophils as myeloid cell effectors of the osteoblast-driven
protumoral response
Proteogenomic analysis of human colon cancer reveals new therapeutic opportun...Gul Muneer
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
Assessing the clinical utility of cancer genomic and proteomic data across tu...Gul Muneer
Molecular profiling of tumors promises to advance the clinical
management of cancer, but the benefits of integrating
molecular data with traditional clinical variables have not been
systematically studied. Here we retrospectively predict patient
survival using diverse molecular data (somatic copy-number
alteration, DNA methylation and mRNA, microRNA and protein
expression) from 953 samples of four cancer types from The
Cancer Genome Atlas project. We find that incorporating
molecular data with clinical variables yields statistically
significantly improved predictions (FDR < 0.05) for three
cancers but those quantitative gains were limited (2.2–23.9%).
Additional analyses revealed little predictive power across
tumor types except for one case. In clinically relevant genes,
we identified 10,281 somatic alterations across 12 cancer types
in 2,928 of 3,277 patients (89.4%), many of which would
not be revealed in single-tumor analyses. Our study provides
a starting point and resources, including an open-access
model evaluation platform, for building reliable prognostic and
therapeutic strategies that incorporate molecular data
SCT60103 March 2017 Assignment - Group 3Yvonne Chin
Compare the use of Lonza KGM Gold Bullet kit and Rheinwald and Green complete FAD medium in primary human epidermal keratinocytes culture and the applicability of cells cultured by these medium in the construction of reconstituted skin equivalent model
The Effects of Genetic Alteration on Reprogramming of Fibroblasts into Induc...remedypublications2
Induced Pluripotent Stem Cells (iPSCs) can be generated from somatic cells by ectopic expression of
Yamanaka factors (
Oct4
,
Sox2
,
Klf4
and
c-Myc
) or combination of other factors. Genetic alteration
of fibroblasts exhibits an effect on reprogramming efficiency through multiple signaling pathways,
including epigenetic modifications, metabolic shifts, Mesenchymal-To-Epithelial Transition
(MET) and cell proliferation. In order to better understand the underlying mechanisms in cell fate
determination, in this review we will summarize several genetic alterations involved in the regulation
of reprogramming fibroblasts into iPSCs.
Innovative Minds in Prostate Cancer Today
IMPaCT Conference
Congressionally Directed Medical Research Program of the U.S. Department of Defense
Dr. Martin H. Hager presentation
New treatment strategies
Angiogenesis, Invasion, Metastasis
Martin H. Hager
Targeted Therapy
Cancer
Angiogenesis
Metastasis
Sox2 suppresses the invasiveness of breast cancer cells via a mechanism that ...Enrique Moreno Gonzalez
Sox2, an embryonic stem cell marker, is aberrantly expressed in a subset of breast cancer (BC). While the aberrant expression of Sox2 has been shown to significantly correlate with a number of clinicopathologic parameters in BC, its biological significance in BC is incompletely understood.
Carcinogenesis refers to the process by which a normal cell is transformed into a malignant cell and repeatedly divides to become a cancer
Chemicals which initiate this process is called chemical carcinogens
Chemicals which increase the effectiveness of carcinogens is called co-carcinogens
REGULATORY BACKGROUND
ROLE OF PROTO-ONCOGENES AND TUMOR SUPPRESSOR GENES
ACTIVATION OF PROTO ONCOGENES
OXIDATIVE STRESS IN CARCINOGENESIS
OECD guidelines
451- Carcinogenecity studies
453- Combined chronic toxicity/carcinogenecity
ICH guidelines
S1A- Guideline on the need for carcinogenicity studies of
pharmaceuticals
S1B- Testing for carcinogenicity of pharmaceuticals
S1C- Dose selection for carcinogenicity studies of pharmaceuticals
Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neu...Gul Muneer
Systemic cross-talk between lung tumors and bones
Bone marrow–derived myeloid cells can accumulate within tumors and foster
cancer outgrowth. Local immune-neoplastic interactions have been intensively
investigated, but the contribution of the systemic host environment to tumor growth
remains poorly understood. Here, we show in mice and cancer patients (n = 70) that
lung adenocarcinomas increase bone stromal activity in the absence of bone
metastasis. Animal studies reveal that the cancer-induced bone phenotype involves
bone-resident osteocalcin-expressing (Ocn+) osteoblastic cells. These cells promote
cancer by remotely supplying a distinct subset of tumor-infiltrating SiglecFhigh
neutrophils, which exhibit cancer-promoting properties. Experimentally reducing
Ocn+ cell numbers suppresses the neutrophil response and lung tumor outgrowth.
These observations posit osteoblasts as remote regulators of lung cancer and
identify SiglecFhigh neutrophils as myeloid cell effectors of the osteoblast-driven
protumoral response
Proteogenomic analysis of human colon cancer reveals new therapeutic opportun...Gul Muneer
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
Assessing the clinical utility of cancer genomic and proteomic data across tu...Gul Muneer
Molecular profiling of tumors promises to advance the clinical
management of cancer, but the benefits of integrating
molecular data with traditional clinical variables have not been
systematically studied. Here we retrospectively predict patient
survival using diverse molecular data (somatic copy-number
alteration, DNA methylation and mRNA, microRNA and protein
expression) from 953 samples of four cancer types from The
Cancer Genome Atlas project. We find that incorporating
molecular data with clinical variables yields statistically
significantly improved predictions (FDR < 0.05) for three
cancers but those quantitative gains were limited (2.2–23.9%).
Additional analyses revealed little predictive power across
tumor types except for one case. In clinically relevant genes,
we identified 10,281 somatic alterations across 12 cancer types
in 2,928 of 3,277 patients (89.4%), many of which would
not be revealed in single-tumor analyses. Our study provides
a starting point and resources, including an open-access
model evaluation platform, for building reliable prognostic and
therapeutic strategies that incorporate molecular data
SCT60103 March 2017 Assignment - Group 3Yvonne Chin
Compare the use of Lonza KGM Gold Bullet kit and Rheinwald and Green complete FAD medium in primary human epidermal keratinocytes culture and the applicability of cells cultured by these medium in the construction of reconstituted skin equivalent model
To investigate the effect of Lonza KGM Gold bulletkit and Rheinwald and Green...Alyaa Abdul
To investigate the effect of Lonza KGM Gold bullet kit and Rheinwald and Green complete FAD medium on the construction of reconstituting skin equivalent model.
interest in stem cells is raising in different field of medicine. The question is : is it successful in Gynecology or it is still too early to say that. The present talk may help to explore this .
This is my short presentation in one of my university classes. It's obvious that the future of the stem cell biology is tightly engaged with organoids and they will absolutely change the way science is going to.
Kind regards
Shahin Ahmadian
Biotech 2019 - Leveraging Advances in Industrial Biotechnology in the Cellula...David Welch
The utilization of animal stem cells to grow muscle and fat tissues in vitro for consumption, dubbed “cell-based meat,” offers an unprecedented opportunity to transform animal agriculture and produce meat in a humane and sustainable way. This nascent, interdisciplinary industry intersects cell biology, tissue engineering, biochemical engineering, and food science, with tangential impacts on issues relating to environmental science, human health, and regulatory policies. This talk will provide an industry snapshot and highlight the current challenges to scaling cell-based meat production, focusing on the needs and opportunities for industrial biotechnology to participate in the development of new tools, resources, or optimizations required to reach price parity with traditional animal meat. Finally, applications for industrial biotechnology in the broader "cellular agriculture" fields will be discussed.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
1. Comparing Lonza KGM-Gold™ Keratinocyte
Growth Medium & Rheinwald and Green
Complete FAD Medium
A presentation by:
Bryan Yap Jin Hang
Calvin Chan Yoong Liang
Chai Jun Yang
Julian Kee Zheng Yuan
Leong Weng Hhin
2. What We Will Be Covering:
• The Basics
• Applications
• Comparison
• Current Development
• Challenges
KGM-Gold™ Keratinocyte Growth Medium
4. Composition
KGM-Gold™ Keratinocyte Growth Medium Rheinwald and Green Complete FAD
Medium
• BPE (Bovine Pitutary Extract)
• hEGF
• Insulin
• Hydrocortisone
• GA-1000 (Gentamicin, amphotericin-B)
• Epinephrine
• Transferrin
• 3 parts Dulbecco’s Modified Eagle’s
Medium
• 1 part Ham’s F12 Medium
• Adenine
• Penicillin
• Streptomycin
• Fetal Bovine Serum
• Hydrocortisone
• Cholera enterotoxin
• Epidermal Growth Factor
• Insulin
Presence of serum
5. Applications in KGM Lonza Culture and Complete FAD Medium.
KGM LONZA Medium : Cells grow mostly as undifferentiated
adherent monolayer.
Complete FAD Medium : Cells grow and differentiate into an
organotypic culture with different cell
types
(Ambler and Lamb 2012)
Applications
• Cells grown using FAD medium display better in vivo characteristics due to similar
morphology to the human skin (Skin-equivalent model).
• Thus, cells grown using FAD medium are ideal for use in Anatomical and
Physiological studies.
6. Applications of Monolayer Adherent Cultures
• Pathogenicity and Disease Progression
• The study of pathogenicity and disease progression may lead to the discovery of new
vaccines and drugs that combat illness!
KGM Lonza Medium: The “Gold Standard”
Figure _ : Growth Rate of Cells cultured in KGM Gold vs other
brands (Lonza 2017)
Figure _ : Confluency of Cells grown in KGM Gold vs other
Brands (Lonza n.d)
Why KGM Gold?
• High Yield.
• Faster Growth
Rate.
Why CFM?
• Higher similarity to
in-vivo models.
• More suited for
functional tests
such as toxicity
tests.
7. Discussion
Figure 2: Average depth of the epithelium layer in different type of media. (Lamb and
Ambler, 2013)
Figure 1: Comparison of Normal Human Epithelial Keratinocytes growth in KGM-Gold serum-free media and in complete
FAD medium with feeders. (Lamb and Ambler, 2013)
• Test for effect of different concentration of Calcium and addition of 10% serum on the
growth of epithelium layer.
• Based on the result, it is proven that higher growth of epithelium layer depends on
high concentration of calcium and addition of 10% serum.
• A-D : Test for cell motility. The cells grown in KGM-Gold are more motile and form temporary cell
attachment because the absence of calcium prevents the formation of desmosomes and cell junctions.
• E-F: Actin staining with phalloidin. Polymerised actin was detected at the leading edge of cell grown in
KGM-Gold while it is uniform in cell grown in complete FAD.
8. Discussion
Figure 4: The effect of heat-treated serum on the average depth of epithelium layer. (Lamb and Ambler, 2013)
Figure 3: The growth of epithelial layer in EpiLife serum-free medium with variation in
presence of Calcium and Serum. (Lamb and Ambler, 2013)
• Test for effect of second serum-free medium, EpiLife on the epithelial growth under
various conditions. Based on the result, EpiLife also requires both high concentration
of calcium and addition of 10% serum for the best growth result.
• Test for effect of heat-treated serum and it was found that heated serum would
increase the epidermal thickness and organisation.
9. Challenges
• Lonza KGM Gold Bullet kit
• Inability to form 3D structure (Lamb & Ambler 2013)
• Fixed through re-additon of serum
• Rheinwald & Green complete FAD medium
• Serum (Freshney 2007)
• Contamination & immunoglobulin
• Filtration (0.1 μm)
• Heat inactivation (56oC, 30 min)
• Inconsistent batches (eg: bovine) -> lasts 6 months
• Climate, animal, storage, sterilization
10. Current Developments
• Efficient Keratinocyte Differentiation Strictly Depends on JNK-Induced
Soluble Factors in Fibroblasts (Schumacher et al. 2014)
• Alternatives to the use of fetal bovine serum: serum-free cell culture
(Gstraunthaler 2003)
• Stable chemically defined surface for the culture of human
keratinocytes (Higham et al. 2003)
• A Defined, Feeder-Free, Serum-Free System to Generate In Vitro
Hematopoietic Progenitors and Differentiated Blood Cells from hESCs
and hiPSCs (Salvagiotto et al. 2011)
11. Conclusion
• Serum contains many essential growth factors that mimics inVivo
growth conditions for animal cells
• There is presence of serum in Lonza KGM-Gold™ Keratinocyte Growth
Medium while FAD formula does not have any.
• Cells grown in FAD formula shows more differentiated structures
compared to cells grown in Lonza KGM-Gold™ Keratinocyte Growth
Medium.
• Thus, cells grown in FAD formula can be used to study cell physiology
• However, Lonza KGM-Gold™ Keratinocyte Growth Medium provides
higher yield in a shorter amount of time.
12. Reference
• Schumacher, M., Schuster, C., Rogon, Z., Bauer, T., Caushaj, N., Baars, S., Szabowski, S., Bauer, C., Schorpp-Kistner, M., Hess, J., Holland-Cunz, S., Wagner, E., Eils, R.,
Angel, P. and Hartenstein, B. (2014). Efficient Keratinocyte Differentiation Strictly Depends on JNK-Induced Soluble Factors in Fibroblasts. [online]
http://www.sciencedirect.com. Available at: http://www.sciencedirect.com/science/article/pii/S0022202X15367555 [Accessed 20 Sep. 2017].
• G, G. (2003). Alternatives to the use of fetal bovine serum: serum-free cell culture. - PubMed - NCBI. [online] Ncbi.nlm.nih.gov. Available at:
https://www.ncbi.nlm.nih.gov/pubmed/14671707/ [Accessed 20 Sep. 2017].
• Higham MC, e. (2003). Development of a stable chemically defined surface for the culture of human keratinocytes under serum-free conditions for clinical use. -
PubMed - NCBI. [online] Ncbi.nlm.nih.gov. Available at: https://www.ncbi.nlm.nih.gov/pubmed/14633376 [Accessed 20 Sep. 2017].
• Salvagiotto, G., Burton, S., Daigh, C., Rajesh, D., Slukvin, I. and Seay, N. (2011). A Defined, Feeder-Free, Serum-Free System to Generate In Vitro Hematopoietic
Progenitors and Differentiated Blood Cells from hESCs and hiPSCs. [online] https://www.ncbi.nlm.nih.gov. Available at:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060827/ [Accessed 20 Sep. 2017].
• http://bio.lonza.com. (n.d.). Clonetics™ Keratinocyte Media Products. [online] Available at:
http://bio.lonza.com/uploads/tx_mwaxmarketingmaterial/Lonza_ManualsProductInstructions_Clonetics_Keratinocyte_Media_Products.pdf [Accessed 20 Sep.
2017].http://booksc.org/book/14056580/7d6182
• Lindberg, K. and Badylak, S. (2001). Porcine small intestinal submucosa (SIS): a bioscaffold supporting in vitro primary human epidermal cell differentiation and
synthesis of basement membrane proteins. [online] http://www.sciencedirect.com. Available at:
http://www.sciencedirect.com/science/article/pii/S0305417900001133 [Accessed 20 Sep. 2017].
• Kollisch, G., Kalali, B., Voelcker, V., Wallich, R., Behrendt, H., Ring, J., Bauer, S., Jakob, T., Mempel, M. and Ollert, M. (2005). Various members of the Toll-like receptor
family contribute to the innate immune response of human epidermal keratinocytes. [online] http://onlinelibrary.wiley.com. Available at:
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2567.2005.02122.x/full [Accessed 20 Sep. 2017].
• Lamb, R. and Ambler, C. (2013). Keratinocytes Propagated in Serum-Free, Feeder-Free Culture Conditions Fail to Form Stratified Epidermis in a Reconstituted Skin
Model. [online] NCBI. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543440/ [Accessed 20 Sep. 2017].
• Lonza.com. (n.d.). KGM-Gold™ Keratinocyte Growth Medium. [online] Available at: http://www.lonza.com/products-services/bio-research/primary-cells/human-
cells-and-media/keratinocytes-and-media/kgm-gold-keratinocyte-growth-medium.aspx [Accessed 20 Sep. 2017].
• Lamb, R. and Ambler, C. (2013). Keratinocytes Propagated in Serum-Free, Feeder-Free Culture Conditions Fail to Form Stratified Epidermis in a Reconstituted Skin
Model. PLoS ONE, [online] 8(1), pp.1-8. Available at: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0052494&type=printable [Accessed 19
Sep. 2017].
Editor's Notes
Other mediums – Amino acids, salts, glucose, vitamin
he ability of SIS to support epidermal cell/fibroblast attachment, migration and/or proliferation and differentiation with deposition of basement membrane(BM) components indicates that the composite model may be useful for studying cell-matrix interactions and for investigation as a dermal substitute.
*KGM = Keratinocyte Growth Medium
*FAD = Flavin Adenine Dinucleotide
JNK = Jun N-terminal kinases
hESC = human embryonic stem cell
hiPSC = human induced pluripotent stem cell