The Lyme disease agent, borrelia burgdorferi, colonizing the gut of the tick lxodes scapularis,can transmit pathogens to vertebrate hosts including humans. B. burgdorferi colonization increases the expression of several tick gut genes including pixr. Abrogation of PIXR function in vivo alters the gut microbiome， metabolome and immune responses. Changes in the gut microbial members are likely to influence the metabolome of the tick gut due to differences in the metabolic functions unique to the specific bacteria genera. Changes in the composition of intestinal metabolites can be analyzed by means of untargeted metabolomics. https://www.creative-proteomics.com/services/untargeted-metabolomics.htm
The current study investigated the immunomodulatory
potential of ethyl acetate soluble supernatant of
Lactobacillus casei (LC-EAS) in vitro. The effect of
LC-EAS on nitric oxide release was analyzed in RAW
264.7 cells, wherein, an inhibition in nitric oxide production
through suppression of inducible nitric oxide synthase
mRNA expression was observed. Evaluation of LC-EAS
on LPS-induced peripheral blood mononuclear cells
showed a down-regulation in TNF-a and IL-6 genes and an
upregulation of IL-10. An inhibition in the protein
expression of NF-kB, ERK1/2 and STAT3 phosphorylation
confirms the immunomodulatory potential of LC-EAS. The
effect of LC-EAS on in vitro intestinal epithelial cells was
investigated using HT-29 human colon adenocarcinoma
cancer cells. LC-EAS exhibited an inhibition of NF-jB and
ERK1/2 phosphorylation, whereas STAT3 phosphorylation
was unregulated. To evaluate the downstream target of
STAT3 upregulation, expression of the intestinal trefoil
factor TFF3 which is a NF-jB regulator and STAT3
downstream target was studied. LC-EAS was observed to
elevate TFF3 mRNA expression. Overall the study shows
that the anti-inflammatory potential of LC-EAS is through
inhibition of NF-kB in different cell types.
Quantitative Analysis of Transporter Protein using TripleTOF® 6600 SystemSCIEX
Transport plays an important role in the absorption, distribution, and elimination of a variety of drugs.
In recent years, a large number of transporters, both efflux (ATP-binding cassette (ABC) family) and influx (solute carrier (SLC) family members) have been identified and well characterized in vitro.
However, the abundance of these transporters in the hepatocyte and cell lines as well as in the tissues such as intestine, liver, and kidney has not been accurately quantitated due to technical challenges.
This work aims to build a robust liquid chromatography-mass spectrometry (LC-MS) workflow on the SCIEX TripleTOF® 6600 platform to enable the quantitation of a variety of SLC and ABC drug transporters expressed in the hepatocyte and cell line plasma membranes.
The current study investigated the immunomodulatory
potential of ethyl acetate soluble supernatant of
Lactobacillus casei (LC-EAS) in vitro. The effect of
LC-EAS on nitric oxide release was analyzed in RAW
264.7 cells, wherein, an inhibition in nitric oxide production
through suppression of inducible nitric oxide synthase
mRNA expression was observed. Evaluation of LC-EAS
on LPS-induced peripheral blood mononuclear cells
showed a down-regulation in TNF-a and IL-6 genes and an
upregulation of IL-10. An inhibition in the protein
expression of NF-kB, ERK1/2 and STAT3 phosphorylation
confirms the immunomodulatory potential of LC-EAS. The
effect of LC-EAS on in vitro intestinal epithelial cells was
investigated using HT-29 human colon adenocarcinoma
cancer cells. LC-EAS exhibited an inhibition of NF-jB and
ERK1/2 phosphorylation, whereas STAT3 phosphorylation
was unregulated. To evaluate the downstream target of
STAT3 upregulation, expression of the intestinal trefoil
factor TFF3 which is a NF-jB regulator and STAT3
downstream target was studied. LC-EAS was observed to
elevate TFF3 mRNA expression. Overall the study shows
that the anti-inflammatory potential of LC-EAS is through
inhibition of NF-kB in different cell types.
Quantitative Analysis of Transporter Protein using TripleTOF® 6600 SystemSCIEX
Transport plays an important role in the absorption, distribution, and elimination of a variety of drugs.
In recent years, a large number of transporters, both efflux (ATP-binding cassette (ABC) family) and influx (solute carrier (SLC) family members) have been identified and well characterized in vitro.
However, the abundance of these transporters in the hepatocyte and cell lines as well as in the tissues such as intestine, liver, and kidney has not been accurately quantitated due to technical challenges.
This work aims to build a robust liquid chromatography-mass spectrometry (LC-MS) workflow on the SCIEX TripleTOF® 6600 platform to enable the quantitation of a variety of SLC and ABC drug transporters expressed in the hepatocyte and cell line plasma membranes.
Great advances have been made in the past five decades in understanding the molecular mechanics of the two-component signal transduction pathway in bacteria but its applications in Medicine and Food Industries are yet to be fully unravelled. We discuss the varying changes in the extracellular environment of bacteria and their possession of multiple Two-Component Systems with each being specialize to react to a specific environmental signal, such as pH, nutrient level, redox state, osmotic pressure, quorum signals, and antibiotics. The sensitivity of this response transmits information between
different Two-Component Systems to form a complex signal transduction network. Bacteria’s signal transduction system, referred to as a two-component system, are essential for adaptation to external stimuli. These systems provides a signal transduction pathways widely employed from prokaryotes to eukaryotes. Typically, each two-component system composed of a sensor protein distinctively monitors an external signal(s) and a response regulator (RR) that controls gene expression and other physiological activities which are collectively assembled in a signal transduction pathway. This annex reviews the molecular mechanics underlying the signal transduction systems in prokaryotic organisms. It is not uncommon to hear, either explicitly or implicitly, the statement that “two component regulatory systems are well understood”. Therefore, we examine the current models of the mechanisms of the regulatory systems and provide viable suggestions to further expand its applications in drug efficiency and antibiotic resistance in humans as well as enhancing the shelf-life of products in the food
industry. We also outline the challenges that might have quenched possible trials of this application to human health.
Moving into the Post-MetagenomicEra of Gut Microbiome ResearchJonathan Clarke
Julian Marchesi's presentation slides from our previous Microbiome R&D and Business Collaboration Forum. For information about this years event please visit http://www.globalengage.co.uk/microbiota.html
Application of proteomics for identification of abiotic stress tolerance in c...Vivek Zinzala
It is the study of “Proteome”.
The word "proteome" is a blend of "protein" and "genome”.
Large scale study of Proteins.
Particularly their structures and functions.
Study of full set of proteins in a cell type or tissue, and changes during various conditions
For more information, you can visit https://www.creative-proteomics.com/services/protein-post-translational-modification-analysis.htm. In this video, we introduce some commonly used methods to detect PPIs and techniques for proteome-scale interactome maps.
Explore Host Cell Protein Analysis at Creative ProteomicsCreative Proteomics
The selection of high-resolution mass spectrometry data depends on the acquisition mode, and thousands of proteins can be identified. When using SWATH acquisition technology for relative or absolute quantification, the sensitivity can reach 10μg/mL. The reproducibility is excellent, the method is simple, and the measurement throughput is high. https://www.creative-proteomics.com/services/host-cell-protein-analysis.htm
Host cell protein (HCP) is a protein produced or encoded by a host cell during the synthesis of recombinant therapeutic proteins. Recombinant therapeutic proteins are usually produced by genetically modified prokaryotic or eukaryotic host cells using cell culture or fermentation techniques. Genetic engineering enables host cells to be transformed to selectively express the target protein. https://www.creative-proteomics.com/services/host-cell-protein-analysis.htm
Abdominal Tuberculosis – How Far are Our Diagnostics Illuminating?Apollo Hospitals
Tuberculosis can involve any part of the gastrointestinal tract from mouth to anus, the peritroneum, pancreas and the hepatobiliary system. Gastrointestinal tuberculosis mimics many clinical conditions and only a high degree of suspicion can help in the diagnosis otherwise there are chances of missing it leading to high morbidity and mortality. Various methods of diagnosis are available but which one is the right test for a particular patient needs to be ascertained. Culture remains the gold standard method of diagnosis. Fast track cultures like MGIT/M Bact Alert 3 D can give faster results with in few days to few weeks. Molecular tests are fastest and can be used as a supplementary test. Nested PCR can give results with in few hours.
Untargeted and targeted lipidomics are two categories of lipidomics that are often used in combination for the discovery and quantification of differential lipid molecules. Untargeted lipidomics uses LC-MS and GC-MS technologies to unbiasedly detect the dynamic changes of all lipid molecules before and after the stimulation or disturbance in cells, tissues, organs, or organisms. Through bioinformatics analysis to screen differential lipid molecules and analyze their pathways, untargeted lipidomics can reveal the physiological mechanism of their changes. Targeted lipidomics is the research and analysis of a specific class of lipids. Obtainingtedious data from this assay is not the end goal. Bioinformatics analysis can organize, mine, and visualize data, and thus extract useful biological information from large amounts of data to help with scientific discovery. https://lipidomics.creative-proteomics.com/untargeted-lipidomics.htm
Cytokines are a class of highly active, multifunctional, soluble small-molecule proteins secreted by activated immune cells and certain stromal cells. Cytokines are widely involved in various biological functions such as immune response, cell migration, and signal transduction through paracrine, autocrine, and endocrine approaches. Cytokine assays can assist in determining the immune function of the body and help in research related to the disease mechanism, diagnosis, and treatment. There are various assays for cytokines, and you can choose the most appropriate assay according to sample size, assay needs, and budget. https://cytokine.creative-proteomics.com/luminex-cytokine-detection-service.htm
More Related Content
Similar to Assessment of the Tick Gut Metabolome Composition.pdf
Great advances have been made in the past five decades in understanding the molecular mechanics of the two-component signal transduction pathway in bacteria but its applications in Medicine and Food Industries are yet to be fully unravelled. We discuss the varying changes in the extracellular environment of bacteria and their possession of multiple Two-Component Systems with each being specialize to react to a specific environmental signal, such as pH, nutrient level, redox state, osmotic pressure, quorum signals, and antibiotics. The sensitivity of this response transmits information between
different Two-Component Systems to form a complex signal transduction network. Bacteria’s signal transduction system, referred to as a two-component system, are essential for adaptation to external stimuli. These systems provides a signal transduction pathways widely employed from prokaryotes to eukaryotes. Typically, each two-component system composed of a sensor protein distinctively monitors an external signal(s) and a response regulator (RR) that controls gene expression and other physiological activities which are collectively assembled in a signal transduction pathway. This annex reviews the molecular mechanics underlying the signal transduction systems in prokaryotic organisms. It is not uncommon to hear, either explicitly or implicitly, the statement that “two component regulatory systems are well understood”. Therefore, we examine the current models of the mechanisms of the regulatory systems and provide viable suggestions to further expand its applications in drug efficiency and antibiotic resistance in humans as well as enhancing the shelf-life of products in the food
industry. We also outline the challenges that might have quenched possible trials of this application to human health.
Moving into the Post-MetagenomicEra of Gut Microbiome ResearchJonathan Clarke
Julian Marchesi's presentation slides from our previous Microbiome R&D and Business Collaboration Forum. For information about this years event please visit http://www.globalengage.co.uk/microbiota.html
Application of proteomics for identification of abiotic stress tolerance in c...Vivek Zinzala
It is the study of “Proteome”.
The word "proteome" is a blend of "protein" and "genome”.
Large scale study of Proteins.
Particularly their structures and functions.
Study of full set of proteins in a cell type or tissue, and changes during various conditions
For more information, you can visit https://www.creative-proteomics.com/services/protein-post-translational-modification-analysis.htm. In this video, we introduce some commonly used methods to detect PPIs and techniques for proteome-scale interactome maps.
Explore Host Cell Protein Analysis at Creative ProteomicsCreative Proteomics
The selection of high-resolution mass spectrometry data depends on the acquisition mode, and thousands of proteins can be identified. When using SWATH acquisition technology for relative or absolute quantification, the sensitivity can reach 10μg/mL. The reproducibility is excellent, the method is simple, and the measurement throughput is high. https://www.creative-proteomics.com/services/host-cell-protein-analysis.htm
Host cell protein (HCP) is a protein produced or encoded by a host cell during the synthesis of recombinant therapeutic proteins. Recombinant therapeutic proteins are usually produced by genetically modified prokaryotic or eukaryotic host cells using cell culture or fermentation techniques. Genetic engineering enables host cells to be transformed to selectively express the target protein. https://www.creative-proteomics.com/services/host-cell-protein-analysis.htm
Abdominal Tuberculosis – How Far are Our Diagnostics Illuminating?Apollo Hospitals
Tuberculosis can involve any part of the gastrointestinal tract from mouth to anus, the peritroneum, pancreas and the hepatobiliary system. Gastrointestinal tuberculosis mimics many clinical conditions and only a high degree of suspicion can help in the diagnosis otherwise there are chances of missing it leading to high morbidity and mortality. Various methods of diagnosis are available but which one is the right test for a particular patient needs to be ascertained. Culture remains the gold standard method of diagnosis. Fast track cultures like MGIT/M Bact Alert 3 D can give faster results with in few days to few weeks. Molecular tests are fastest and can be used as a supplementary test. Nested PCR can give results with in few hours.
Untargeted and targeted lipidomics are two categories of lipidomics that are often used in combination for the discovery and quantification of differential lipid molecules. Untargeted lipidomics uses LC-MS and GC-MS technologies to unbiasedly detect the dynamic changes of all lipid molecules before and after the stimulation or disturbance in cells, tissues, organs, or organisms. Through bioinformatics analysis to screen differential lipid molecules and analyze their pathways, untargeted lipidomics can reveal the physiological mechanism of their changes. Targeted lipidomics is the research and analysis of a specific class of lipids. Obtainingtedious data from this assay is not the end goal. Bioinformatics analysis can organize, mine, and visualize data, and thus extract useful biological information from large amounts of data to help with scientific discovery. https://lipidomics.creative-proteomics.com/untargeted-lipidomics.htm
Cytokines are a class of highly active, multifunctional, soluble small-molecule proteins secreted by activated immune cells and certain stromal cells. Cytokines are widely involved in various biological functions such as immune response, cell migration, and signal transduction through paracrine, autocrine, and endocrine approaches. Cytokine assays can assist in determining the immune function of the body and help in research related to the disease mechanism, diagnosis, and treatment. There are various assays for cytokines, and you can choose the most appropriate assay according to sample size, assay needs, and budget. https://cytokine.creative-proteomics.com/luminex-cytokine-detection-service.htm
The basics of data processing are to convert the original data file into a representation to help easily access the characteristics of each observed ion. These characteristics include ion retention time and m/z time, as well as ion intensity measurements in each raw data file. In addition to these basic features, data processing can also extract other information, such as the isotope distribution of ions. https://www.creative-proteomics.com/services/bioinformatic-univariate-analysis-service.htm
In line with the ICH Q6B Guidance, Creative Proteomics offers protein analysis and charac-terization services, including structure analysis, physicochemical properties, biological activi-ty, immunochemical properties, as well as purity and impurity determination to ensure thequality and consistency of your products. https://www.creative-proteomics.com/pronalyse/protein-characterization.html
Cytokines are a class of highly active, multifunctional, soluble small-molecule proteins secreted by activated immune cells and specific stromal cells. Cytokines are widely involved in various biological functions such as immune response, cell migration, and signal transduction through paracrine, autocrine, and endocrine approaches. Cytokine assays can assist in determining the immune function of the body and help in research related to the disease mechanism, diagnosis, and treatment. There are various assays for cytokines, and you can choose the most appropriate assay according to sample size, assay needs, and budget. https://cytokine.creative-proteomics.com/cytokine-panel-service.htm
Typical molecular biomarkers include proteins, genetic mutations, and aberrant methylation patterns. abnormal transcripts, miRNAs, and other biological molecules. Protein biomarkers are considered reliable indicators of the disease state and clinical outcome as they are the endpoints of biological processes. Remarkable innovations in proteomic technologies in the last few years have greatly accelerated the process of biomarker discovery. https://www.creative-proteomics.com/services/proteomics-service.htm
Untargeted Metabolomics Strategy VS Targeted Metabolomics Strategy.pdfCreative Proteomics
Metabolomics can be divided into non-targeted and targeted metabolomics. Non-target-ed metabolomics can analyze metabolites derived from the organisms comprehensively and systematically. It is an unbiased metabolomics analysis that can discover new bio-markers. Targeted metabolomics is the study and analysis of specific metabolites.
Edman Degradation is one of the N-terminal amino acid sequence analysis methods for peptide chains/proteins sequencing. The protein is reacted with PTC under weakly basic conditions and then treated with an acid to free the amino-terminal residue of the peptide chain in the form of PTH-AA for subsequent analysis. Peptide Mapping analysis is an effective method for rapidly localizing protein sequences and is a commonly used strategy in protein identification. The method uses mass spectrometry for peptide analysis and compares the obtained spectra with a protein database to obtain amino acid information. De Novo Protein Sequencing is a method based on the enzymatically cleaved peptides that exhibit regular fragmentation in mass spectrometry to obtain amino acid information from the mass differences in regular mass spectral peaks. https://www.creative-proteomics.com/services/proteomics-service.htm
Untargeted metabolomics is mainly conducted to comprehensively understand biochemical information metabolism in organisms. Using liquid chromatography-mass spectrometry technology, almost all metabolites under certain physiological or other specific conditions can be qualitatively and quantitatively analyzed for the identification of different metabolites. https://metabolomics.creative-proteomics.com/untargeted-metabolomics-service.htm
A chiral substance can rotate its polarization plan when plane-polarized light passes through it. This phenomenon is called "optical rotation." Here is the reason for the optical rotation: when the left-handed light and the right-handed light that make up the plane polarized light propagate through a chiral material, their refractive indices are different (nR≠nL). Therefore, the propagation speed of the circularly polarized light in the two directions in the chira material is different (vR≠vL), which leads to the rotation of the polarization plane. https://www.creative-proteomics.com/pronalyse/the-principle-of-circular-dichroism.html
Edman Degradation is one of the N-terminal amino acid sequence analysis methods for peptide chains/proteins sequencing. The protein is reacted with PTC under weakly basic conditions and then treated with an acid to free the amino-terminal residue of the peptide chain in the form of PTH-AA for subsequent analysis. Peptide Mapping analysis is an effective method for rapidly localizing protein sequences and is a commonly used strategy in protein identification. The method uses mass spectrometry for peptide analysis and compares the obtained spectra with a protein database to obtain amino acid information. De Novo Protein Sequencing is a method based on the enzymatically cleaved peptides that exhibit regular fragmentation in mass spectrometry to obtain amino acid information from the mass differences in regular mass spectral peaks. https://www.creative-proteomics.com/services/proteomics-service.htm
At present, strategies for proteomics research can be divided into discovery proteomics and targeted proteomics. Discovery proteomics is more concerned with protein screening and dynamics, while targeted proteomics focuses more on detecting target proteins/peptides to achieve absolute quantification. https://www.creative-proteomics.com/ngpro/targeted-proteomics.html
Protein qualitative analysis based on mass spectrometry explores protein expression within organisms. Mass spectrometry offers highly efficient, robust, and accurate results and is one of the core technologies for proteomic research. Protein identification is a common topic for biochemistry research, and mass spectrometry is considered one of the most useful techniques that solve this issue. Two major strategies that are widely used for protein identification by mass spectrometry are MALDI-TOF-based protein fingerprinting and LC-MS/MS-based peptide sequencing. Meanwhile, LC-MS/MS reserved higher sensitivity and ability than MALDl-TOF and can accurately identify multiple protein components from a single sample. https://www.creative-proteomics.com/services/protein-identification.htm
Untargeted metabolomics is mainly conducted to comprehensively understand biochemical information of metabolism in organisms. Using liquid chromatography-mass spectrometry technology(LC-MS), almost all metabolites under certain physiological or other specific conditions can be qualitatively and quantitatively analyzed for the identification of different metabolites. To the greatest extent, untargeted metabolomics reflects the multiple dynamic responses of living organisms to external stimuli, pathophysiological changes, and gene mutations in metabolite levels in vivo, offering a new perspective for disease diagnosis, pathological research, new drug development, drug toxicology, and other studies. https://metabolomics.creative-proteomics.com/untargeted-metabolomics-service.htm
Untargeted metabolomics is mainly conducted to comprehensively understand biochemical information of metabolism in organisms. Using liquid chromatography-mass spectrometry technology, almost all metabolites under certain physiological or other specific conditions can be qualitatively and quantitatively analyzed for the identification of different metabolites. https://www.creative-proteomics.com/services/untargeted-metabolomics.htm
Untargeted metabolomics is mainly conducted to comprehensively understand biochemical information of metabolism in organisms. Using liquid chromatography-mass spectrometry technology, almost all metabolites under certain physiological or other specific conditions can be qualitatively and quantitatively analyzed for the identification of different metabolites. https://www.creative-proteomics.com/services/untargeted-metabolomics.htm
Metabolomics is a study of a complete set of metabolites in a specific cell or organism. Metabolomics analysis aims at simultaneous identification and quantitative analysis of intracellular metabolites. Since metabolomics is focused on a whole set of metabolites, it reflects the metabolomics activity of the organism, and hence, allows researchers to explore the biological system. An Accurate study on metabolomics relies on sensitive and sophisticated analytic platforms and bioinformatics analysis systems. With years of developing and refining our bioinformatics analysis system, Creative Proteomics offers comprehensive bioinformatics support to our clients’ research! https://www.creative-proteomics.com/services/bioinformatic-analysis-for-metabolomics-study.htm
Proteins play a key role in molecular recognition and are at the core of all biological processes. They can interact with other components of the cell, such as small molecular metabolites, nucleic acids, membranes and other proteins to build supramolecular components and carefully design molecular machines that perform various functions, from chemical catalysis, mechanical work to signal transmission And adjustment. So far, large-scale protein-protein interactions have been identified, and all the generated data is collected in a special database, which can create large-scale protein interaction networks. Like metabolism or genetic/epigenetic networks, the study of PPIs can help us understand the mechanisms of signal transduction, transmembrane transport, cell metabolism and other biological processes through stable or transient, covalent or non-covalent interactions. https://www.creative-proteomics.com/services/protein-protein-interaction-networks.htm
Untargeted metabolomics is mainly conducted to comprehensively understand biochemical information of metabolism in organisms. Using liquid chromatography-mass spectrometry technology, almost all metabolites under certain physiological or other specific conditions can be qualitatively and quantitatively analyzed for the identification of different metabolites. https://www.creative-proteomics.com/services/untargeted-metabolomics.htm
Proteomics is a discipline that analyzes the dynamics of protein components, including expression levels and modification states from a holistic perspective, understands the interactions and connections between proteins, reveals the function of proteins and the laws of cell life, and studies all proteins in cells and their behaviours. Creative Proteomics can provide a comprehensive range of proteomics services to help you better conduct research in the drug discovery process, which includes: protein gel and imaging analysis, protein identification, protein quantification, top-down proteomics, peptidomics, post-translational modification analysis, and protein-protein interaction. https://www.creative-proteomics.com/services/protein-gel-and-imaging-analysis.htm
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.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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 .
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.
insect taxonomy importance systematics and classification
Assessment of the Tick Gut Metabolome Composition.pdf
1. Assessment of the Tick Gut Metabolome Composition
The gut microbiome is involved in the regulation of various metabolic pathways in the host.
Some metabolites that are generated and released by the gut microbiota play a vital role in host
metabolism, signaling, and immunity. Creative Proteomics provides untargeted metabolomics
service to help you analyze the composition of intestinal microbial metabolites.
Metabolomic Profiling
Untargeted Metabolomics
The Lyme disease agent, borrelia burgdorferi, colonizing the gut of the tick Ixodes scapularis,
can transmit pathogens to vertebrate hosts including humans. B. burgdorferi colonization
increases the expression of several tick gut genes including pixr. Abrogation of PIXR function in
vivo alters the gut microbiome, metabolome and immune responses. Changes in the gut
microbial members is likely to influence the metabolome of the tick gut due to differences in the
metabolic functions unique to the specific bacteria genera. Changes in the composition of
intestinal metabolites can be analyzed by means of untargeted metabolomics
ASSAY OVERVIEW
Extract intestinal metabolites. The analysis is carried out using ultra performance liquid
chromatography and quadrupole time-of-flight mass spectrometry (UPLC-Q TOF).
2-Chloro-L-phenylalanine (Sigma) is used as an internal standard. The raw data of the MS is
processed and verified. Data obtained from the LC-Q TOF MS system are filtered for denoising
2. to remove compounds. The filtered data are standardized by peak area normalization and
processed with the SIMCA.
DATA OVERVIEW
A total of 59 metabolites were identified on Positive mode (73 hits in total), and 64 metabolites
were identified on Negative mode (85 hits in total). At least 38 and 39 differentially represented
metabolites were identified under positive and negative mode, respectively, between the guts of
ticks fed on PIXR-immunized or ovalbumin-immunized mice and is shown graphically by
hierarchical clustering to heatmap.
Features
Fully automatic, high-throughput, one-stop full-spectrum metabolomics service
UHPLC-QTOF-MS (Agilent 1290) and UHPLC + AB QTOF 5600(ACQUITY UHPLC) can be
used for analysis.
Quick turnaround time.
Applications
Development and validation of metabolite-related disease diagnostic markers.
Mechanism of metabolite related signaling pathway study.
Reference:
Narasimhan S, Schuijt T J, Abraham N M, et al. Modulation of the tick gut milieu by a secreted
tick protein favors Borrelia burgdorferi colonization. Nature communications, 2017, 8(1): 184.
