Mitochondria provide important cellular functions including
oxidative phosphorylation, fatty acid biosynthesis, and acting as
gatekeepers to apoptosis.
International Journal of Stem Cell Research and Transplantation (IJST) is an international, Open Access, peer-reviewed journal, which mainly focuses, on the advancements made in the field of cell biology, specifically in the field of Stem Cells.
International Journal of Stem Cell Research and Transplantation (IJST) is a peer-reviewed journal, and is dedicated to providing information with respect to the latest advancements that are being upgraded in our everyday life with respect to the application of Stem cells.
International Journal of Stem Cell Research and Transplantation (IJST) is an international, Open Access, peer-reviewed journal, which mainly focuses, on the advancements made in the field of cell biology, specifically in the field of Stem Cells.
International Journal of Stem Cell Research and Transplantation (IJST) is a peer-reviewed journal, and is dedicated to providing information with respect to the latest advancements that are being upgraded in our everyday life with respect to the application of Stem cells.
International Journal of Stem Cell Research and Transplantation (IJST) ISSN:2328-3548, is a free, Open Access, Peer-reviewed, exclusive online journal covering areas of Stem cell research, translational work and Clinical studies in the specialty of Stem Cells and Transplantation including allied specialties relevant to the core subject, which is dedicated in publishing high quality manuscripts.
Protein aggregation is the most discussed topic as it is being linked to many neurodegenerative diseases. Here, in these slides I have tried to explain about protein aggregation and its mechanism.
Alejo Rodriguez-Fraticelli, from Dr Fernando Martin-Belmonte’s laboratory in the CBMSO in Spain, has recently published with co-workers a paper in the Journal of Cell Biology in which they describe their approach to epithelial cells morphogenesis and uncover the role of cell confinement on epithelial polarity via peripheral actin contractility. The team sheds light on a phenomenon that is crucial to understand the physiology of the organs, but also the mechanisms underlying the development and progression of agressive epithelial cancers.
How different diseases originate with slightest changes in proteins. Understanding ALS , Parkinson, Alzhiemer , Taupathies development which may lead to their treatment!
A physical sciences network characterization of non-tumorigenic and metastati...Shashaanka Ashili
To investigate the transition from non-cancerous to metastatic from a physical sciences perspective, the
Physical Sciences–Oncology Centers (PS-OC) Network performed molecular and biophysical comparative studies of the non-tumorigenic MCF-10A and metastatic DA-MB-231 breast epithelial cell lines, commonly used as models of cancer metastasis. Experiments were performed in 20 laboratories from 12 PS-OCs. Each laboratory was supplied with identical aliquots and common reagents and culture protocols. Analyses of these measurements revealed dramatic differences in their mechanics, migration, adhesion, oxygen response, and proteomic profiles. Model-based multi-omics approaches identified key differences between these cells’ regulatory networks involved in morphology and survival. These results provide a multifaceted description of cellular parameters of two widely used cell lines and demonstrate the value of the PS-OC Network approach for integration of diverse experimental observations to elucidate the phenotypes associated with cancer metastasis.
International Journal of Stem Cell Research and Transplantation (IJST) ISSN:2328-3548, is a free, Open Access, Peer-reviewed, exclusive online journal covering areas of Stem cell research, translational work and Clinical studies in the specialty of Stem Cells and Transplantation including allied specialties relevant to the core subject, which is dedicated in publishing high quality manuscripts.
Protein aggregation is the most discussed topic as it is being linked to many neurodegenerative diseases. Here, in these slides I have tried to explain about protein aggregation and its mechanism.
Alejo Rodriguez-Fraticelli, from Dr Fernando Martin-Belmonte’s laboratory in the CBMSO in Spain, has recently published with co-workers a paper in the Journal of Cell Biology in which they describe their approach to epithelial cells morphogenesis and uncover the role of cell confinement on epithelial polarity via peripheral actin contractility. The team sheds light on a phenomenon that is crucial to understand the physiology of the organs, but also the mechanisms underlying the development and progression of agressive epithelial cancers.
How different diseases originate with slightest changes in proteins. Understanding ALS , Parkinson, Alzhiemer , Taupathies development which may lead to their treatment!
A physical sciences network characterization of non-tumorigenic and metastati...Shashaanka Ashili
To investigate the transition from non-cancerous to metastatic from a physical sciences perspective, the
Physical Sciences–Oncology Centers (PS-OC) Network performed molecular and biophysical comparative studies of the non-tumorigenic MCF-10A and metastatic DA-MB-231 breast epithelial cell lines, commonly used as models of cancer metastasis. Experiments were performed in 20 laboratories from 12 PS-OCs. Each laboratory was supplied with identical aliquots and common reagents and culture protocols. Analyses of these measurements revealed dramatic differences in their mechanics, migration, adhesion, oxygen response, and proteomic profiles. Model-based multi-omics approaches identified key differences between these cells’ regulatory networks involved in morphology and survival. These results provide a multifaceted description of cellular parameters of two widely used cell lines and demonstrate the value of the PS-OC Network approach for integration of diverse experimental observations to elucidate the phenotypes associated with cancer metastasis.
Proteomics, definatio , general concept, signficanceKAUSHAL SAHU
INTRODUCTION
GENERAL CONCEPT
WHY PROTEIOMIC NECESERY?
WHAT PROTEOMIC CAN ANSWER?
PRTEOMICS- ANALYSIS AND IDENTIFICATION OF PROTEIN
TWO-DIMENSIONAL SDS-PAGE
MASS SPECTROMETERS
SIGNIFICANCE OF STUDY AN ITS IMPORTANCE
APPLICATIONS
CHALLENGES
CONCLUSIONS
REFERENCES
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.
Apoptosis is characterized by several biochemical features including cell shrinkage, membrane blebbing, chromosome condensation, nuclear fragmentation, DNA laddering and the eventual engulfment of the cell by phagosomes.
ELISA is a well know term that is an abbreviation of Enzyme Linked Immunosorbent Assay. This microplate based technique relies on the use of an antibody that has been linked to an enzyme. In the presence of an appropriate substrate, enzymatic activity produces a color change as the ELISA readout, which can be measured and provides information about the presence and quantity of the target antigen in the sample material.
Electrophoresis is a simple, rapid, and highly sensitive analytical technique to study the properties of proteins and nucleic acids, and has become a principle tool in analytical chemistry, biochemistry, and molecular biology. Polyacrylamide gel electrophoresis (PAGE) can be used to analyze the size, amount, purity, and isoelectric point of polypeptides and proteins. Sodium dodecyl sulfate polyacrylamide discontinuous gel electrophoresis (SDS PAGE) is the most commonly used system whereby proteins become separated strictly by their size, but there are different variations of this technique.
Antibody-oligonucleotide (Ab-Oligo) conjugates have been used in
numerous applications from diagnostics to therapeutics and were
developed through an unmet need for precise and efficient detection of low-abundance proteins. Ab-Oligo conjugates have since played a significant role in enhancing an extensive range of biological techniques that include immunological and proteomic research, biomarker discovery, clinical diagnostics – including point-of-care, as well as other novel techniques. Antibodies can be readily conjugated to oligonucleotides via their amino acid residues, making them suitable for most in vitro applications, as they possess several functional groups.
His Tag Protein Production and PurificationExpedeon
The study of protein regulation, structure, and function relies heavily on the expression and purification of recombinant proteins. Many recombinant proteins are expressed as fusion proteins, meaning that they contain an affinity / epitope tag. A tag is a short sequence of DNA that codes for a specific amino acid, which is frequently inserted into a target gene at the point of coding for expression at either the N or C terminal of the protein required.
GELFrEE® 8100 Fractionation System Tech NoteExpedeon
Successful sample preparation is a key step during any analytical
procedure and begins with a defined experimental design. Important steps in sample preparation include proteolytic digestion of proteins into peptide fragments, and peptide fractionation. This is especially important prior to applications such as mass spectrometry (MS).
Antibody-oligonucleotide (Ab-Oligo) conjugates have been used in
numerous applications from diagnostics to therapeutics and were
developed through an unmet need for precise and efficient detection of low-abundance proteins.
Proteomics of small proteins from plant tissuesExpedeon
Small genes and the proteins that they encode can play important biological roles including signaling, development, and mediation of plant-microbe interactions in organisms ranging from bacteria to plants to mammals (Frith et al.; Basrai et al.; Galindo et al.; Hemm et al. 2008, 2010; Kastenmeyer et al.). However, genes that encode proteins containing <100 residues are difficult to identify reliably solely by DNA sequence analysis (Dinger et al.)
Proteomic profiling of fractionated post-myocardial infarctionExpedeon
Acute myocardial infarction remains a leading cause of morbidity and mortality worldwide.Heart failure is the result of adverse remodeling of the collagenous scar that replaces the
damaged myocardium after MI. Markers of LV remodeling can be either identified in the circulation (e.g. serum or plasma) or detected in the heart by imaging technologies or biopsy.
NVoy technology is a quantum leap in protein processing, production and analysis. It uses proprietary NV polymers to enhance protein solubility and stability through the formation of multi-point reversible complexes with proteins without altering their structure.
Circular dichroism spectroscopy is an analytical technique used to estimate the secondary and tertiary structure of proteins. This technique can be used to confirm whether structure has been retained during protein processing, but is frequently adversely affected by additives such as solubility enhancers and detergents.
NVoy technology is a quantum leap in protein processing, production and analysis. It uses proprietary NV polymers to enhance protein solubility and stability through the formation of multi-point reversible complexes with proteins without altering their structure.
Protein processing and production is often hampered by the formation of aggregates that restrict and complicate
the handling of proteins, antibodies and enzymes. NVoy is designed to minimise the sequential losses in consecutive
protein processing steps which would otherwise dramatically reduce the overall protein yield.
NVoy technology is a quantum leap in protein processing, production and analysis. It uses proprietary NV polymers to enhance protein solubility and stability through the formation of multi-point reversible complexes with proteins without altering their structure.
NVoy technology is a quantum leap in protein processing, production and analysis. It uses proprietary NV polymers to enhance protein solubility and stability through the formation of multi-point reversible complexes with proteins without altering their structure.
GELFrEE1 affords rapid mass-based protein separation over a range 10-150 kDa. Here, we demonstrate a multiplexed design enabling increased loading capacity and throughput. We
demonstrate comprehensive analysis of the yeast proteome using GELFrEE coupled to LC-MS/MS analysis.
Identification and characterization of intact proteins in complex mixturesExpedeon
The ability to fully characterize proteins in their intact forms allows thorough biological investigation of the functional importance of changes such as post-translational modifications, protein isoforms/sequence variations, and protease cleavages.
Improved coverage of the proteome using gel eluted liquidExpedeon
It has long been understood that sample fractionation is critically important to generating quality, comprehensive proteomics data. In spite of the continual improvements in speed and sensitivity of mass spectrometers, these instruments are still unable to adequately overcome the enormous challenge
of most biological samples without multiple dimensions of separation prior to mass analysis.
Optimization of experimental protocols for cellular lysisExpedeon
In this project, we have compared existing sample preparation methods for proteomics studies against newly developed FASP method and our in-house developed SDS-TCA protocol. For our
preliminary studies, we have chosen a very well characterized soil microbe Pseudomonas putida.
Characterization of intact antibodies by pre-fractionation using gel electrop...Expedeon
Antibodies represent an important class of proteins due to their central role in the immune response. Moreover, there is an increasing interest in the use of recombinant antibodies as novel drug therapies.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
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.
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.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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.
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.
Top down proteomics of soluble and integral membrane proteins
1. IDENTIFICATION OF POSTTRANSLATIONAL MODIFICATIONS
PROTEIN DETECTION AND IDENTIFICATION
GLOBAL IDENTIFICATION
INTRODUCTION
Mitochondria provide important cellular functions including
oxidative phosphorylation, fatty acid biosynthesis, and acting as
gatekeepers to apoptosis. These biological processes are highly
regulated by post-translational modification and protein cleavage
events, making them highly attractive to study at the intact protein
level. With recent advances in protein separation technology and
instrumentation it is now possible to detect, identify, and
characterize hundreds to thousands of intact proteins in an
isoform specific manner. Even with these advances, integral
membrane proteins, which play vital roles in mitochondrial
function, are often underrepresented in proteomic studies due to
their hydrophobic character and lower abundance. In this work,
we establish protocols for the enrichment, separation,
identification, and characterization of mitochondrial proteins with
particular emphasis on integral membrane proteins.
OVERVIEW
Isolation of mitochondria followed by GELFrEE and nano LC-
MS/MS allows for >100 identified intact mitochondrial proteins
from human cell lines
The developed Top Down proteomics platform is readily
amenable to the analysis of membrane proteins on an LC
timescale , capable of identifying post-translational modifications
Examination of the fragmentation of integral membrane proteins
has revealed extensive fragmentation on the transmembrane
domain helices, leading to hyperconfident identification
Top Down Proteomics of Soluble and Integral Membrane Proteins from Human Mitochondria
Adam D. Catherman1, Kenneth R. Durbin2, Mingxi Li2, Dorothy R. Ahlf2, John C. Tran3. Bryan P. Early3, Paul M. Thomas2,3, Neil L. Kelleher1,2,3
1Department of Chemistry, 2Department of Molecular Biosciences, 3Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
75
ACKNOWLEDGEMENTS
The authors would like to thank the other members of the Top Down Proteomics Development Team at Northwestern University as
well as Expedeon. Funding was provided by the National Institutes of Health (GM067193), the UIUC Center for Neuroproteomics on
Cell to Cell Signalling (DA01830), the Chicago Biomedical Consortium, and the Robert H. Lurie Comprehensive Cancer Center.
CONCLUSIONS
Subcellular fractionation coupled to GELFrEE nano-LC MS/MS
allows for effective Top Down study of the human mitochondrion
Membrane proteins, with up to eight transmembrane domain
helices, can be identified in a relatively high-throughput manner
Top Down Proteomics is well suited for the identification of
post-translational modifications on integral membrane proteins
as well as lipid modifications on peripheral membrane proteins
Collision-induced dissociation of integral membrane proteins
leads to very confident identification through extensive
fragmentation of the transmembrane domain helices
FUTURE WORK
Future work will be focused on the comparison of untreated
H1299 cells with those undergoing chemically-induced
senescence
Higher-energy collisional dissociation (HCD) and electron
transfer dissociation (ETD) will be utilized fir fragmentation.
Additional separation strategies will be applied to improve
mitochondrial purity and proteome coverage
METHODS
Intact mitochondrial were isolated from HeLa or H1299 cells by
use of differential centrifugation followed by Percoll density
gradient centrifugation
Molecular weight fractions were prepared using the GELFREE
8100 Fractionation System (Expedeon). SDS was removed from
the fractions using MeOH/CHCl3/H2O precipitation.
Nano-LC separations were performed PLRPS columns utilizing
gradients of 05% H2O, 5% ACN and 95% ACN, 5% H2O each
with 0.2% formic acid.
Mass spectra were collected on both 12 T LTQ Velos FT-ICR or
Orbitrap Elite instruments.
SAMPLE FRACTIONATION
Figure 1: Platform for the Top Down analysis of mitochondrial proteins.
CID OF INTEGRAL MEMBRANE PROTEINS
Protein
Sample
GELFrEE
SDS RemovalNano-LC MS/MS
Database Search
Cultured Cells
Subcellular
Fractionation
TMD Prediction
Figure 6: Graphical fragments maps for two proteins which demonstrate the
propensity for transmembrane helices to fragment relative to soluble regions.
Figure 7: Box-plot demonstrating that the integral membrane proteins were
on average identified with more confidence than the soluble and membrane
associated proteins.
Figure 3: Total ion chromatogram in which three protein mass spectra are
shown. Fragmentation of each species resulted in confident identification of
different modified forms Transmembrane helices are shown in red.
10
15
20
25
37
50
75
100
Figure 2: Western blot for common protein markers (left) showing the utility
of the subcellular fractionation and a slab gel visualization of the GELFrEE
separation (right) the mitochondrial membrane enriched fraction.
Figure 4: Subcellular localization of the 246 proteins identified from
enriched mitochondrial membrane fraction derived from HeLa cells. Of the
proteins identified within the mitochondrion, most were derived from the
inner mitochondrial membrane.
Figure 5: Distribution of the number of transmembrane helices for the 83
integral membrane proteins identified from HeLa. Thirty-three proteins
contained two or more transmembrane helices.