The document describes a new technique called CLARITY that allows intact biological tissues to be made optically transparent while preserving native molecular structures. CLARITY transforms tissues into a hydrogel-hybridized construct that is transparent and permeable to macromolecules. This allows for high-resolution microscopic imaging of intact tissues down to the subcellular level. CLARITY has been applied to map neural circuits in intact mouse brains and analyze human brain samples at the subcellular level, providing a way to gain new insights into biological systems.
This document contains summaries of three laboratory assignments:
1) A column chromatography laboratory that taught protein isolation techniques and showed lysozyme purification.
2) A neurobiology workshop that covered the nervous system, neurons, and included a sheep brain dissection.
3) An in-silico drug design workshop where students identified benzene clusters that could bind to and inhibit the HIV protease protein.
Cuckoo Search Optimization of Blebs in Human Embryonic Stem CellsIJMERJOURNAL
ABSTRACT: The main aim of this project is to segment the bleb from human embryonic stem cells (hESC). The behavior of bleb can be used to distinguish apoptotic bleb from the healthy bleb. The health of the human embryonic stem cells can be determined using the portion of bleb formed on the surface of the stem cells. The complete bleb formation contains bleb extraction and retraction. This paper uses the active contour algorithm for the segmentation of bleb from human embryonic stem cells. The output of the segmentation, input video and area of bleb can be used as an input to the optimization process. The cuckoo search algorithm is utilized for optimization, which inspired from the brooding parasitism will enhance the segmentation result. The proposed method attains the quick and accurate analysis in the bleb extraction process
The document discusses a seminar presentation on protein modeling. It covers topics like molecular modeling techniques, protein structure prediction, and applications of molecular modeling. The main points are:
- Molecular modeling techniques like molecular mechanics and quantum mechanics are used to model protein structures and properties.
- Protein structure prediction aims to determine a protein's 3D structure from its amino acid sequence. This remains a challenging problem.
- Knowing a protein's structure provides insight into its function and allows designing mutations or drugs to modify the protein.
- Molecular modeling has wide applications in research areas like chemistry, biology and physics. It is used to simulate molecular behavior in chemical and biological systems.
This study developed an in vitro model for differentiating human pluripotent stem cells into retinal neurons. The differentiation process followed identifiable stages of retinal development:
1) Undifferentiated stem cells expressed pluripotent markers.
2) After 10 days of differentiation, eye field populations expressed neural and eye field transcription factors.
3) By day 30, retinal progenitor neurospheres analogous to the optic vesicle expressed retinal progenitor markers.
4) At day 70, the stem cells yielded retinal ganglion cells and photoreceptor cells, demonstrating the ability to derive major retinal cell types.
Revolution of 3 d organ model in pharmacological researchsyeddastagir9
3D organ models have gained interest as alternatives to animal testing in pharmacological research. This seminar discusses the revolution of 3D organ models with a focus on 3D bioprinting approaches. It describes various 3D bioprinting methods like biomimicry and autonomous self-assembly used to create tissue structures. Examples of 3D bioprinted structures for organs like liver, kidney, heart and neural tissue are provided. The seminar highlights current research using 3D bioprinting for applications like vascularization, drug development, and high-throughput screening.
Stem cells and nanotechnology in regenerative medicine and tissue engineeringDr. Sitansu Sekhar Nanda
Alexis Carrel, winner of the Nobel Prize in Physiology or Medicine in 1912 and the father of whole-organ transplant, was the first to develop a successful technique for end to end arteriovenous anastomosis in transplantation.
This document describes Micropatterns and CYTOO products. Micropatterns are glass surfaces treated with a cytophobic coating and etched geometric patterns coated with extracellular matrix proteins. This guides cell culture into consistent structures that mimic physiological conditions. CYTOO products include plates and chips with thousands of micropatterns to standardize cell shape, polarity, and organization for quantitative analysis of cell phenotypes, signaling, and toxicity. They improve assay reproducibility and enable analysis of relationships between cell structure, mechanics, and function.
Microdialysis is an integral part of preclinical research to determine extracellular fluid and blood concentrations of metabolites, hormones, drugs, etc, and is often used in quantifying the biochemistry of brain and peripheral tissues. However, it is a molecular-only technique and other imaging modalities are needed to provide the researcher with functional and anatomical information of the animal in vivo.
This document contains summaries of three laboratory assignments:
1) A column chromatography laboratory that taught protein isolation techniques and showed lysozyme purification.
2) A neurobiology workshop that covered the nervous system, neurons, and included a sheep brain dissection.
3) An in-silico drug design workshop where students identified benzene clusters that could bind to and inhibit the HIV protease protein.
Cuckoo Search Optimization of Blebs in Human Embryonic Stem CellsIJMERJOURNAL
ABSTRACT: The main aim of this project is to segment the bleb from human embryonic stem cells (hESC). The behavior of bleb can be used to distinguish apoptotic bleb from the healthy bleb. The health of the human embryonic stem cells can be determined using the portion of bleb formed on the surface of the stem cells. The complete bleb formation contains bleb extraction and retraction. This paper uses the active contour algorithm for the segmentation of bleb from human embryonic stem cells. The output of the segmentation, input video and area of bleb can be used as an input to the optimization process. The cuckoo search algorithm is utilized for optimization, which inspired from the brooding parasitism will enhance the segmentation result. The proposed method attains the quick and accurate analysis in the bleb extraction process
The document discusses a seminar presentation on protein modeling. It covers topics like molecular modeling techniques, protein structure prediction, and applications of molecular modeling. The main points are:
- Molecular modeling techniques like molecular mechanics and quantum mechanics are used to model protein structures and properties.
- Protein structure prediction aims to determine a protein's 3D structure from its amino acid sequence. This remains a challenging problem.
- Knowing a protein's structure provides insight into its function and allows designing mutations or drugs to modify the protein.
- Molecular modeling has wide applications in research areas like chemistry, biology and physics. It is used to simulate molecular behavior in chemical and biological systems.
This study developed an in vitro model for differentiating human pluripotent stem cells into retinal neurons. The differentiation process followed identifiable stages of retinal development:
1) Undifferentiated stem cells expressed pluripotent markers.
2) After 10 days of differentiation, eye field populations expressed neural and eye field transcription factors.
3) By day 30, retinal progenitor neurospheres analogous to the optic vesicle expressed retinal progenitor markers.
4) At day 70, the stem cells yielded retinal ganglion cells and photoreceptor cells, demonstrating the ability to derive major retinal cell types.
Revolution of 3 d organ model in pharmacological researchsyeddastagir9
3D organ models have gained interest as alternatives to animal testing in pharmacological research. This seminar discusses the revolution of 3D organ models with a focus on 3D bioprinting approaches. It describes various 3D bioprinting methods like biomimicry and autonomous self-assembly used to create tissue structures. Examples of 3D bioprinted structures for organs like liver, kidney, heart and neural tissue are provided. The seminar highlights current research using 3D bioprinting for applications like vascularization, drug development, and high-throughput screening.
Stem cells and nanotechnology in regenerative medicine and tissue engineeringDr. Sitansu Sekhar Nanda
Alexis Carrel, winner of the Nobel Prize in Physiology or Medicine in 1912 and the father of whole-organ transplant, was the first to develop a successful technique for end to end arteriovenous anastomosis in transplantation.
This document describes Micropatterns and CYTOO products. Micropatterns are glass surfaces treated with a cytophobic coating and etched geometric patterns coated with extracellular matrix proteins. This guides cell culture into consistent structures that mimic physiological conditions. CYTOO products include plates and chips with thousands of micropatterns to standardize cell shape, polarity, and organization for quantitative analysis of cell phenotypes, signaling, and toxicity. They improve assay reproducibility and enable analysis of relationships between cell structure, mechanics, and function.
Microdialysis is an integral part of preclinical research to determine extracellular fluid and blood concentrations of metabolites, hormones, drugs, etc, and is often used in quantifying the biochemistry of brain and peripheral tissues. However, it is a molecular-only technique and other imaging modalities are needed to provide the researcher with functional and anatomical information of the animal in vivo.
This document describes factors necessary to produce basoapical polarity in human glandular epithelium formed in three-dimensional culture models. The authors demonstrate that apical polarity, characterized by tight junction formation, is more sensitive to culture conditions than basal polarity. Using mammary epithelial cells, they show that both basal polarity-mediated signaling and the extracellular matrix component collagen IV are required for the development of apical polarity. A new high-throughput culture method is presented that can produce basoapically polarized glandular structures without embedding cells in a gel, opening possibilities for high-content screening applications.
Donna Milgram founded a national institute to foster female success in STEM fields. In an interview, she discusses the institute's mission to promote the potential of women in STEM and ensure they have a prominent place in science and technology. The institute aims to encourage and promote women in science, engineering, and technology through initiatives like promoting gender equality in Europe and collecting data on gender trends in STEM.
The document discusses engineering human skeletal muscle tissue for developing therapies for muscle injuries and evaluating medicines. It outlines several cell types and biomaterials that can be used, including satellite cells, myoblasts, stem cells, and natural or synthetic polymers. Novel techniques like 3D bioprinting, organ-on-chip models, and combining cell sources, scaffolds, and stimuli seek to better recreate muscle tissue functionality in vitro and in vivo. Current challenges include scaling up engineered tissues for transplantation, but emerging technologies may help address limitations and reduce animal testing.
20150924 smb noviocell juliette van den dolderSMBBV
1. Noviocell aims to accelerate stem cell research by developing a 3D polyisocyanopeptide hydrogel cell culture system that mimics the natural extracellular matrix.
2. The hydrogel provides a synthetic, reproducible scaffold that allows stem cells to grow in 3D, unlike traditional 2D cultures, while also enabling easy recovery of intact cells and tissues.
3. The hydrogel has been shown to support the growth and organization of various cell types in a 3D environment, and exhibits biomechanical properties similar to human collagen matrices.
This document contains abstracts from multiple research projects presented at the 2009 Creativity, Research & Innovation Exhibition.
The first abstract examines the effects of Centella asiatica, a traditional herbal medicine, on cognitive function in middle-aged adults. A study of 41 participants found that Centella asiatica enhanced short and long-term memory over time periods of 40 to 90 days.
The second abstract describes the design of a new self-retaining anal retractor for anorectal surgery that allows for self-retention and rotation. This aims to provide advantages for surgeons during procedures.
The third abstract details work to establish an optimal method for generating and characterizing mesench
3D BIOPRINTING USING ORGAN DERIVED SCAFFOLDS AND HUMAN PLURIPOTENT STEM CELLNivaasvignopathy
This document discusses 3D bioprinting of human organs using organ-derived extracellular matrix scaffolds and human pluripotent stem cells. The authors hypothesize that decellularized liver tissue can act as a suitable scaffold for stem cells to reorganize and potentially give rise to a fully functional liver organ when combined with 3D bioprinting techniques. The objectives are to decellularize liver tissue, recellularize it with stem cells, and 3D bioprint a liver graft. The methodology involves decellularizing a liver organ using perfusion, recellularizing the decellularized extracellular matrix with stem cells, and 3D bioprinting the stem cell-seeded scaffold
This document summarizes a research project on controlling and regulating stem cell differentiation using nanoparticles. Raman microspectroscopy is used to monitor stem cell differentiation processes at the subcellular level. The objectives are to demonstrate Raman microspectroscopy can monitor differentiation, understand how nanoparticle properties influence differentiation, and control stem cell triggering through nanoparticles. Methods include Raman spectroscopy, cell culture, and multivariate analysis. Achievements include analyzing different substrates and monitoring chondrogenic differentiation. Future work involves characterizing differentiation markers, publishing results, and investigating nanoparticle toxicity and effects on differentiation.
This document describes a microfluidic bioreactor system developed to provide controlled spatial and temporal concentration gradients of multiple molecular factors to 3D cultures of human pluripotent stem cells. The bioreactor contains rows of microwells connected by microchannels that generate stable concentration gradients when different factors are flowed through the lateral channels. Human embryonic and induced pluripotent stem cells were cultured as embryoid bodies in the bioreactor and exposed to gradients of mesoderm-inducing morphogens. Gene expression analysis showed the system could evaluate the initiation of mesodermal induction in a controlled manner. The bioreactor aims to provide a more in vivo-like model for studying stem cell development and differentiation.
This document summarizes cell-based assay solutions from Neuromics and its partnership with UB Systems. It describes 3D cell-based assays including blood-brain barrier models and extracellular matrix hydrogels. It also provides details on various human brain cell types such as endothelial cells, astrocytes, and pericytes that can be used to build customized 3D brain models. Additionally, it mentions services offered like media filling and various cell culture reagents including fetal bovine serum in different grades.
1. The document describes the structure and function of eukaryotic cells, focusing on their internal compartments.
2. Key organelles discussed include the nucleus, which houses DNA; the endoplasmic reticulum and Golgi apparatus, which synthesize and modify proteins; and lysosomes, which digest materials through enzymes.
3. Various microscopy techniques are needed to study cellular structures because most organelles are smaller than can be resolved with a standard light microscope. Electron microscopes provide higher resolution views of intracellular components.
This document discusses brain simulation and neuroscience. It begins by defining neuroscience as the study of the brain and nervous system, and their interactions with other physiological systems. This allows researchers to understand human behavior, improve health, and study learning and memory. The document then discusses neuron anatomy and different theoretical approaches in neuroscience like informatics, theoretical neuroscience, and computational neuroscience. It outlines principles of brain simulation like dense reconstruction from sparse data and iterative reconstruction and testing. Major brain simulation projects are summarized, including the Blue Brain Project which aims to simulate the entire human brain on a supercomputer.
This document discusses biomaterials inspired by the extracellular matrix (ECM). It defines biomimicry, bioinspiration and bioderivation as three paradigms for learning from biological systems. The document then describes three main types of ECM mimicry in biomaterials: 1) mimicking ECM functions by using ECM components, either through direct copying or partial copying, 2) mimicking ECM architecture and topography through hierarchical microstructure and topographical features, and 3) mimicking ECM protein design and assembly. The goal is to create biomaterials that interact with cells in similar ways to the native ECM environment.
This seminar presentation summarizes research on chemoarchitectonics and neural growth factors. It discusses chemoarchitectonics as the study of brain anatomy and function through staining specific chemicals to identify neurotransmitter patterns. The presentation reviews a study on lungfish brains that identified neuronal populations and tracts using calbindin and calretinin staining. It also discusses Brodmann's cytoarchitectonic mapping of the cerebral cortex and Nissl staining technique. Finally, it provides an overview of neurotrophins like NGF, their discovery, biogenesis, functions in neuron survival and differentiation, and signaling mechanisms through neurotrophin receptors.
The document discusses using collagen matrices and hydrogel scaffolds to culture neural cells in 3D environments, noting that collagen matrices have advantages over hydrogels like large pores and mechanical strength. It also references several studies that observed neural cells exhibiting closer to in vivo behavior when encapsulated in collagen matrices compared to other materials. The optimal conditions identified for culturing neural cells in 3D include using collagen matrices in rotating wall vessel bioreactors at 4°C temperature.
This document discusses the development of a bioprocess system using a rotating wall bioreactor and biomaterials to guide stem cell-derived retinal tissue maturation. The system aims to treat dry age-related macular degeneration and Retinitis Pigmentosa, which currently have no treatment and cause blindness. A three-stage approach is used involving computational modeling, experimental testing, and analytical validation to characterize transport phenomena within the bioreactor and optimize a composite biomaterial structure for 3D retinal tissue culture. The goal is to mature retinal progenitor cells into fully functional retinal tissue through dynamic culture conditions compared to static methods.
Three key points are summarized:
1. Three-dimensional cell cultures provide a more natural environment for cells compared to traditional 2D cultures, allowing cells to behave more like they do in vivo.
2. 3D cell culture technology is used for applications like tissue engineering, drug discovery, and analysis of cell biology. It involves engineering scaffolds and growth factors to direct cell differentiation.
3. Mathematical modeling is important for understanding the complex biological and physical factors influencing 3D cell cultures, but optimization of cultures remains an ongoing area of research due to the large number of tunable parameters.
Neuromics and UBC have a business partnership to provide 3D cell-based assay solutions and manufacture and fill media. Neuromics offers proven human cell types like brain astrocytes and endothelial cells for building blood brain barrier models. They also provide fetal bovine serum in different grades based on endotoxin levels as well as other animal sera. Customers have successfully used Neuromics' cells to create static 3D blood brain barrier models.
Journal club: iPSC derived myelinoids to study myelin biology of humansLeena Shingavi
This is a journal club presentation on the manuscript by Owen et al, published in May 2021 in the journal Developmental cell. It describes how the myelinoids were derived from the iPSCs and can be considered as model to study myelin biology.
Automated Analysis of Microscopy Images using Deep Convolutional Neural NetworkAdetayoOkunoye
This document summarizes research on using deep convolutional neural networks to automatically analyze microscopy images. The goals are to expedite the analysis of high-content microscopy data and automate tasks like cell counting and classification. The researchers trained and tested models using TensorFlow on microscopy images to classify cells, achieving over 75% accuracy. This level of automation could benefit biological research by reducing human errors and speeding up analysis of large image datasets.
Charging Fueling & Infrastructure (CFI) Program Resources by Cat PleinForth
Cat Plein, Development & Communications Director of Forth, gave this presentation at the Forth and Electrification Coalition CFI Grant Program - Overview and Technical Assistance webinar on June 12, 2024.
This document describes factors necessary to produce basoapical polarity in human glandular epithelium formed in three-dimensional culture models. The authors demonstrate that apical polarity, characterized by tight junction formation, is more sensitive to culture conditions than basal polarity. Using mammary epithelial cells, they show that both basal polarity-mediated signaling and the extracellular matrix component collagen IV are required for the development of apical polarity. A new high-throughput culture method is presented that can produce basoapically polarized glandular structures without embedding cells in a gel, opening possibilities for high-content screening applications.
Donna Milgram founded a national institute to foster female success in STEM fields. In an interview, she discusses the institute's mission to promote the potential of women in STEM and ensure they have a prominent place in science and technology. The institute aims to encourage and promote women in science, engineering, and technology through initiatives like promoting gender equality in Europe and collecting data on gender trends in STEM.
The document discusses engineering human skeletal muscle tissue for developing therapies for muscle injuries and evaluating medicines. It outlines several cell types and biomaterials that can be used, including satellite cells, myoblasts, stem cells, and natural or synthetic polymers. Novel techniques like 3D bioprinting, organ-on-chip models, and combining cell sources, scaffolds, and stimuli seek to better recreate muscle tissue functionality in vitro and in vivo. Current challenges include scaling up engineered tissues for transplantation, but emerging technologies may help address limitations and reduce animal testing.
20150924 smb noviocell juliette van den dolderSMBBV
1. Noviocell aims to accelerate stem cell research by developing a 3D polyisocyanopeptide hydrogel cell culture system that mimics the natural extracellular matrix.
2. The hydrogel provides a synthetic, reproducible scaffold that allows stem cells to grow in 3D, unlike traditional 2D cultures, while also enabling easy recovery of intact cells and tissues.
3. The hydrogel has been shown to support the growth and organization of various cell types in a 3D environment, and exhibits biomechanical properties similar to human collagen matrices.
This document contains abstracts from multiple research projects presented at the 2009 Creativity, Research & Innovation Exhibition.
The first abstract examines the effects of Centella asiatica, a traditional herbal medicine, on cognitive function in middle-aged adults. A study of 41 participants found that Centella asiatica enhanced short and long-term memory over time periods of 40 to 90 days.
The second abstract describes the design of a new self-retaining anal retractor for anorectal surgery that allows for self-retention and rotation. This aims to provide advantages for surgeons during procedures.
The third abstract details work to establish an optimal method for generating and characterizing mesench
3D BIOPRINTING USING ORGAN DERIVED SCAFFOLDS AND HUMAN PLURIPOTENT STEM CELLNivaasvignopathy
This document discusses 3D bioprinting of human organs using organ-derived extracellular matrix scaffolds and human pluripotent stem cells. The authors hypothesize that decellularized liver tissue can act as a suitable scaffold for stem cells to reorganize and potentially give rise to a fully functional liver organ when combined with 3D bioprinting techniques. The objectives are to decellularize liver tissue, recellularize it with stem cells, and 3D bioprint a liver graft. The methodology involves decellularizing a liver organ using perfusion, recellularizing the decellularized extracellular matrix with stem cells, and 3D bioprinting the stem cell-seeded scaffold
This document summarizes a research project on controlling and regulating stem cell differentiation using nanoparticles. Raman microspectroscopy is used to monitor stem cell differentiation processes at the subcellular level. The objectives are to demonstrate Raman microspectroscopy can monitor differentiation, understand how nanoparticle properties influence differentiation, and control stem cell triggering through nanoparticles. Methods include Raman spectroscopy, cell culture, and multivariate analysis. Achievements include analyzing different substrates and monitoring chondrogenic differentiation. Future work involves characterizing differentiation markers, publishing results, and investigating nanoparticle toxicity and effects on differentiation.
This document describes a microfluidic bioreactor system developed to provide controlled spatial and temporal concentration gradients of multiple molecular factors to 3D cultures of human pluripotent stem cells. The bioreactor contains rows of microwells connected by microchannels that generate stable concentration gradients when different factors are flowed through the lateral channels. Human embryonic and induced pluripotent stem cells were cultured as embryoid bodies in the bioreactor and exposed to gradients of mesoderm-inducing morphogens. Gene expression analysis showed the system could evaluate the initiation of mesodermal induction in a controlled manner. The bioreactor aims to provide a more in vivo-like model for studying stem cell development and differentiation.
This document summarizes cell-based assay solutions from Neuromics and its partnership with UB Systems. It describes 3D cell-based assays including blood-brain barrier models and extracellular matrix hydrogels. It also provides details on various human brain cell types such as endothelial cells, astrocytes, and pericytes that can be used to build customized 3D brain models. Additionally, it mentions services offered like media filling and various cell culture reagents including fetal bovine serum in different grades.
1. The document describes the structure and function of eukaryotic cells, focusing on their internal compartments.
2. Key organelles discussed include the nucleus, which houses DNA; the endoplasmic reticulum and Golgi apparatus, which synthesize and modify proteins; and lysosomes, which digest materials through enzymes.
3. Various microscopy techniques are needed to study cellular structures because most organelles are smaller than can be resolved with a standard light microscope. Electron microscopes provide higher resolution views of intracellular components.
This document discusses brain simulation and neuroscience. It begins by defining neuroscience as the study of the brain and nervous system, and their interactions with other physiological systems. This allows researchers to understand human behavior, improve health, and study learning and memory. The document then discusses neuron anatomy and different theoretical approaches in neuroscience like informatics, theoretical neuroscience, and computational neuroscience. It outlines principles of brain simulation like dense reconstruction from sparse data and iterative reconstruction and testing. Major brain simulation projects are summarized, including the Blue Brain Project which aims to simulate the entire human brain on a supercomputer.
This document discusses biomaterials inspired by the extracellular matrix (ECM). It defines biomimicry, bioinspiration and bioderivation as three paradigms for learning from biological systems. The document then describes three main types of ECM mimicry in biomaterials: 1) mimicking ECM functions by using ECM components, either through direct copying or partial copying, 2) mimicking ECM architecture and topography through hierarchical microstructure and topographical features, and 3) mimicking ECM protein design and assembly. The goal is to create biomaterials that interact with cells in similar ways to the native ECM environment.
This seminar presentation summarizes research on chemoarchitectonics and neural growth factors. It discusses chemoarchitectonics as the study of brain anatomy and function through staining specific chemicals to identify neurotransmitter patterns. The presentation reviews a study on lungfish brains that identified neuronal populations and tracts using calbindin and calretinin staining. It also discusses Brodmann's cytoarchitectonic mapping of the cerebral cortex and Nissl staining technique. Finally, it provides an overview of neurotrophins like NGF, their discovery, biogenesis, functions in neuron survival and differentiation, and signaling mechanisms through neurotrophin receptors.
The document discusses using collagen matrices and hydrogel scaffolds to culture neural cells in 3D environments, noting that collagen matrices have advantages over hydrogels like large pores and mechanical strength. It also references several studies that observed neural cells exhibiting closer to in vivo behavior when encapsulated in collagen matrices compared to other materials. The optimal conditions identified for culturing neural cells in 3D include using collagen matrices in rotating wall vessel bioreactors at 4°C temperature.
This document discusses the development of a bioprocess system using a rotating wall bioreactor and biomaterials to guide stem cell-derived retinal tissue maturation. The system aims to treat dry age-related macular degeneration and Retinitis Pigmentosa, which currently have no treatment and cause blindness. A three-stage approach is used involving computational modeling, experimental testing, and analytical validation to characterize transport phenomena within the bioreactor and optimize a composite biomaterial structure for 3D retinal tissue culture. The goal is to mature retinal progenitor cells into fully functional retinal tissue through dynamic culture conditions compared to static methods.
Three key points are summarized:
1. Three-dimensional cell cultures provide a more natural environment for cells compared to traditional 2D cultures, allowing cells to behave more like they do in vivo.
2. 3D cell culture technology is used for applications like tissue engineering, drug discovery, and analysis of cell biology. It involves engineering scaffolds and growth factors to direct cell differentiation.
3. Mathematical modeling is important for understanding the complex biological and physical factors influencing 3D cell cultures, but optimization of cultures remains an ongoing area of research due to the large number of tunable parameters.
Neuromics and UBC have a business partnership to provide 3D cell-based assay solutions and manufacture and fill media. Neuromics offers proven human cell types like brain astrocytes and endothelial cells for building blood brain barrier models. They also provide fetal bovine serum in different grades based on endotoxin levels as well as other animal sera. Customers have successfully used Neuromics' cells to create static 3D blood brain barrier models.
Journal club: iPSC derived myelinoids to study myelin biology of humansLeena Shingavi
This is a journal club presentation on the manuscript by Owen et al, published in May 2021 in the journal Developmental cell. It describes how the myelinoids were derived from the iPSCs and can be considered as model to study myelin biology.
Automated Analysis of Microscopy Images using Deep Convolutional Neural NetworkAdetayoOkunoye
This document summarizes research on using deep convolutional neural networks to automatically analyze microscopy images. The goals are to expedite the analysis of high-content microscopy data and automate tasks like cell counting and classification. The researchers trained and tested models using TensorFlow on microscopy images to classify cells, achieving over 75% accuracy. This level of automation could benefit biological research by reducing human errors and speeding up analysis of large image datasets.
Charging Fueling & Infrastructure (CFI) Program Resources by Cat PleinForth
Cat Plein, Development & Communications Director of Forth, gave this presentation at the Forth and Electrification Coalition CFI Grant Program - Overview and Technical Assistance webinar on June 12, 2024.
Welcome to ASP Cranes, your trusted partner for crane solutions in Raipur, Chhattisgarh! With years of experience and a commitment to excellence, we offer a comprehensive range of crane services tailored to meet your lifting and material handling needs.
At ASP Cranes, we understand the importance of reliable and efficient crane operations in various industries, from construction and manufacturing to logistics and infrastructure development. That's why we strive to deliver top-notch solutions that enhance productivity, safety, and cost-effectiveness for our clients.
Our services include:
Crane Rental: Whether you need a crawler crane for heavy lifting or a hydraulic crane for versatile operations, we have a diverse fleet of well-maintained cranes available for rent. Our rental options are flexible and can be customized to suit your project requirements.
Crane Sales: Looking to invest in a crane for your business? We offer a wide selection of new and used cranes from leading manufacturers, ensuring you find the perfect equipment to match your needs and budget.
Crane Maintenance and Repair: To ensure optimal performance and safety, regular maintenance and timely repairs are essential for cranes. Our team of skilled technicians provides comprehensive maintenance and repair services to keep your equipment running smoothly and minimize downtime.
Crane Operator Training: Proper training is crucial for safe and efficient crane operation. We offer specialized training programs conducted by certified instructors to equip operators with the skills and knowledge they need to handle cranes effectively.
Custom Solutions: We understand that every project is unique, which is why we offer custom crane solutions tailored to your specific requirements. Whether you need modifications, attachments, or specialized equipment, we can design and implement solutions that meet your needs.
At ASP Cranes, customer satisfaction is our top priority. We are dedicated to delivering reliable, cost-effective, and innovative crane solutions that exceed expectations. Contact us today to learn more about our services and how we can support your project in Raipur, Chhattisgarh, and beyond. Let ASP Cranes be your trusted partner for all your crane needs!
EV Charging at MFH Properties by Whitaker JamiesonForth
Whitaker Jamieson, Senior Specialist at Forth, gave this presentation at the Forth Addressing The Challenges of Charging at Multi-Family Housing webinar on June 11, 2024.
Charging Fueling & Infrastructure (CFI) Program by Kevin MillerForth
Kevin Miller, Senior Advisor, Business Models of the Joint Office of Energy and Transportation gave this presentation at the Forth and Electrification Coalition CFI Grant Program - Overview and Technical Assistance webinar on June 12, 2024.
Charging and Fueling Infrastructure Grant: Round 2 by Brandt HertensteinForth
Brandt Hertenstein, Program Manager of the Electrification Coalition gave this presentation at the Forth and Electrification Coalition CFI Grant Program - Overview and Technical Assistance webinar on June 12, 2024.
Implementing ELDs or Electronic Logging Devices is slowly but surely becoming the norm in fleet management. Why? Well, integrating ELDs and associated connected vehicle solutions like fleet tracking devices lets businesses and their in-house fleet managers reap several benefits. Check out the post below to learn more.
Expanding Access to Affordable At-Home EV Charging by Vanessa WarheitForth
Vanessa Warheit, Co-Founder of EV Charging for All, gave this presentation at the Forth Addressing The Challenges of Charging at Multi-Family Housing webinar on June 11, 2024.
Understanding Catalytic Converter Theft:
What is a Catalytic Converter?: Learn about the function of catalytic converters in vehicles and why they are targeted by thieves.
Why are They Stolen?: Discover the valuable metals inside catalytic converters (such as platinum, palladium, and rhodium) that make them attractive to criminals.
Steps to Prevent Catalytic Converter Theft:
Parking Strategies: Tips on where and how to park your vehicle to reduce the risk of theft, such as parking in well-lit areas or secure garages.
Protective Devices: Overview of various anti-theft devices available, including catalytic converter locks, shields, and alarms.
Etching and Marking: The benefits of etching your vehicle’s VIN on the catalytic converter or using a catalytic converter marking kit to make it traceable and less appealing to thieves.
Surveillance and Monitoring: Recommendations for using security cameras and motion-sensor lights to deter thieves.
Statistics and Insights:
Theft Rates by Borough: Analysis of data to determine which borough in NYC experiences the highest rate of catalytic converter thefts.
Recent Trends: Current trends and patterns in catalytic converter thefts to help you stay aware of emerging hotspots and tactics used by thieves.
Benefits of This Presentation:
Awareness: Increase your awareness about catalytic converter theft and its impact on vehicle owners.
Practical Tips: Gain actionable insights and tips to effectively prevent catalytic converter theft.
Local Insights: Understand the specific risks in different NYC boroughs, helping you take targeted preventive measures.
This presentation aims to equip you with the knowledge and tools needed to protect your vehicle from catalytic converter theft, ensuring you are prepared and proactive in safeguarding your property.
1. Structural and molecular interrogation
of intact biological systems
Nature. 2013 May 16; 497(7449): 332–337. doi:10.1038/nature12107
NGUYEN THI NHI
Master’s Student
Department of Physiology
3. • Automatic sectioning
• Microscopy
• Imaging methods
Map structure
NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS 3
4. 4
BigBrain
An Ultrahigh-Resolution3D
Human Brain Model
NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS
- 65-year-old male
- Cutting brain (coronally - 20µm)
- Histological stain
- 3D-reconstructed image
6. NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS 6
• Brain of 3-5-week-old mouse
• Surface of a whole mouse brain
reconstructed from 550 optical
sections
Ultramicroscopy: three-
dimensional visualization of
neuronal networks in the
whole mouse brain
8. NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS 8
Optically transparent and
macromolecule-permeable construct
& Preserving native molecular
information and structure
CLARITY
9. NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS
9
acrylamid
e
formaldehyd
e
biomolecule-conjugated
monomer
hybrid
construct
CLARITY
14. The Power of PowerPoint | thepopp.com 14
Molecular
phenotyping
Figure 4
15. 15
• Imaging of local circuit wiring cellular relationships,
subcellular structures, protein complexes, nucleic acids,
…
• CLARITY also enables intact-tissue immuno-
histochemistry with multiple rounds, and antibody
labelling throughout the intact adult mouse brain.
MOUSE
NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS
16. NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS 16
HUMAN
Figure 5
Figure 5
17. 17
• CLARITY enables fine structural analysis of
human samples at subcellular level.
• Intact and accessible form suitable for
probing structural and molecular
underpinnings of physiological function and
disease.
HUMAN
NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS
18. TAKE-HOME MESSAGE
18
Transforms intact tissue into a nanoporous hydrogel-hybridized for
Optically transparent and macromolecule-permeable
construct.
Preserves native molecular information and structure.
NUCLEIC ACID AND GENE BIOCHEMISTRY CLASS
Provides access to support integrative understanding of
large-scale intact biological systems.
CLARIT
Y
Assess, approach, means, technique
Scientist explore/ discover
How did they do that
o create the brain model, we used a large-scale microtome to cut a complete paraffin-embedded brain (65-year-old male) coronally(Fig. 1), and we then acquired 7400 sections at20-mm thickness and stained them for cell bodies(14). Histological sections were digitized, result-ing in images of maximally 13,000 by 11,000 pixels(10-by-10–mm pixel size)..(A) Photographs of the fixed brain. Lateral left(top), lateral right (middle), and dorsal (bottom) views. (B) Magnetic resonance image (coronal view)and (C) 3D-reconstructed MRI volume of the fixed brain. (D) Histological sectioning. (E) Block face image of a section (pseudo colored) resting on the mounting grid that served for alignment of theblock face images. (F) Series of blockface images. (G)Cellbody–stained histological sections with the region of interest denoted by a red box. This area is shown with higher magnification in (H). (I)Series of histological images, which were 3D-reconstructed using the blockface images (F) and the MRI (C).21 JUNE 2013 VOL 340SCIENCEwww.sciencemag.org1472REPORTS
Visualizing entire neuronal networks for analysis in the intact brain has been impossible up to now.
Techniques like computer tomography or magnetic resonance imaging (MRI) do not yield cellular resolution
, and mechanical slicing procedures are insufficient to achieve high-resolution reconstructions in three dimensions. Here we present an approach that allows imaging of whole fixed mouse brains.
The advantage of this method is that the sample is preserved and can be re-imaged, if needed. But no matter how precisely it is done, cutting the sample inevitably results in distortions that make it difficult to align the images
We modified ‘ultramicroscopy’ by combining it with a special procedure to clear tissue.
We show that this new technique allows optical sectioning of fixed mouse brains with cellular resolution
and can be used to detect single GFP-labeled neurons in excised mouse hippocampi. We obtained three-dimensional (3D) images of dendritic trees and spines of populations of CA1 neurons in isolated hippocampi. Also in fruit flies and in mouse embryos, we were able to visualize details of the anatomy by imaging autofluorescence. Our method is ideally suited for high-throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models.
Whereas an alternative technique, optical projection tomography, is inherently limited to a resolution of about 20 microm, our technique allows resolution in the sub micrometer range for small objects (<2 mm). With suitable lenses it should be possible to reach this resolution throughout whole embryos.
Não lớn tuổi, lipid nhiều ?
Our 3D reconstructions are presently limited by computer power, as our graphics processors can not handle more than 600 optical slices with high resolution. Mouse brains older than 2 weekscannot be imaged completely, as heavily myelinated structures such as thalamus and brain stem do not become transparent
A thin polar membrane made of two layers of lipid molecules.
They took note of the fact that packed lipid bilayers are implicated in making tissue poorly accessible, reconstruction—both to molecular probes and to photons—by creating diffusion-barrier properties relevant
to chemical penetration, as well as light-scattering properties at the lipid–aqueous interface
If lipid bilayers could be removed nondestructively, light and macromolecules might penetrate deep into the tissue, allowing threedimensional imaging and immunohistological analysis without disassembly
/əˈkrɪl.ə.maɪd/ + /fɔːˈmæl.də.haɪd/
In this step, formaldehyde not only crosslinks the tissue, but also covalently links the hydrogel monomers to biomolecules including proteins, nucleic acids and small molecules.
hydrogel–tissue hybridization physically supports tissue structure and chemically incorporates biomolecules into the hydrogel mesh
Electric fields applied across the sample inionic detergent actively transport micelles into, and lipids out of, the tissue, leaving finestructure and crosslinked biomolecules in place. The ETC chamber is depicted in the boxedregion
3-month-old line-H mouse
the intact brain (including heavily myelinated white matter, thalamus and brainstem)becomes uniformly transparent full CLARITY processing enabled imaging of the entire intact mouse brain at cellular resolution even using single-photon microscopy (d-f)
Single-photon microscopy
Figure 2f shows a volume of unsectioned mouse brain with visualization through the cortex, hippocampus and thalamus CLARITY processing enabled imaging of the entire intact mouse brain at cellular resolution even using single-photon microscopy CLARITY thus allows rapid high-resolution optical access to dense intact tissue and, if needed, subsequent electron microscopy analysis. Optical sections from f showing negligible resolution loss even at ~3,400-µm deep:
fluorescent proteins tested, including green, yellow and red fluorescent proteins (GFP, YFPand RFP, respectively), were robust to ionic detergent extraction To quantify molecular preservation associated with tissue–hydrogel fusion, we compared protein loss in clarified mouse brain to loss from conventional methods only ~8% protein loss was seen, indicating that chemical tethering of biomolecules into hydrogel mesh can enhance the preservation of molecular tissue components. increases tissue permeability by replacing lipid bilayers with nanoporous hydrogel, enabled rapid diffusion of molecular probes deep into intact tissue, and therefore allows access to preserved biomolecules without sectioning
a. CLARITY may preserve native antigens with unusual completeness owing to the hydrogel-hybridization process. To quantify molecular preservation associated with tissue–hydrogel fusion, we compared protein loss in clarified mouse brain to loss from conventional methods.
However, when hydrogelhybridized tissue was cleared with the stringent 4% SDS solution of CLARITY, only ~8% protein loss was seen, indicating that chemical tethering of biomolecules into hydrogel mesh can enhance the preservation of molecular tissue components
b. which increases tissue permeability by replacing lipid bilayers with nanoporous hydrogel, enabled rapid diffusion of molecular probes deep intointact tissue, and therefore allows access to preserved biomolecules without sectioning. In a 1-mm-thick clarified coronal block of mouse brain, uniformly antibody stained over 3 days
d. Mander’s overlap coefficient was used to quantify the overlap between corresponding fluorescent signals derived from Cx36 and cell organelles in co-transfected cells. Co-localization was accepted at a Mander’s coefficient > 0.5; this threshold indicated that the occurrence of true co-localization surpassed the probability of chanceQuantitative co-localization analysis revealed that eYFP fluorescence and anti-GFP staining overlapped throughout the block
enabled rapid diffusion of molecular probes deep into intact tissue, and therefore allows access to preserved
To investigate axonal projections of the tyrosine hydroxylase neurons further, we clarified, tyrosine-hydroxylase-stained and imaged 1-mm-thick coronal blocks of mouse brain using a high numerical aperture objective (0.95) - is a measure of its ability to gather light and resolve fine specimen detail at a fixed object distance
Throughout the tissue volume we could unequivocally identify individual paired preand postsynaptic puncta, molecularly defining identity and position of putative excitatorysynapses
e. Right, enlarged images of boxed regions on left. Individual synaptic puncta resolved throughout depth f.g. Average immunofluorescence cross-section of PSD-95 (Postsynaptic density protein 95) puncta. . The full-width at half-maximum of the point-spread function was uniform throughout the block, indicating that loss of resolution is negligible even near the diffraction limit of conventional light microscopy
demonstrating another feature of the technique: removal of lipid membranes ensures that tissue refractive index remains nearly constant throughout large volumes, allowing high-resolution imaging h.i. We also found that the CLARITY hydrogel-conjugation process preserves small molecules such as the neurotransmitter GABA (γ-aminobutyric acid, Fig.3h) and (for in situ hybridization) messenger RNAs (Fig. 3i), paving the way for multimodal combinatorial labelling within unsectioned tissue
CLARITY was found to enable multi-round molecular phenotyping; the stable framework allowed effective removal of antibodies without fine structural damage or degraded antigenicity.We performed three consecutive rounds of staining in 1-mm-thick coronal blocks from a Thy1–eYFP H-line mouse brain, observing effective antibody removal and preserved eYFP-positive
neuronal morphology as well as re-staining capability.
Although further quantification would be required to fully map the extent to which CLARITY secures molecular information, this result
shows that elution in clarified tissue largely preserves integrity of tissue structure, cellular architecture, fluorescence signals (Fig. 4d–f) and 4′,6-diamidino-2-phenylindole (DAPI) DNA staining (Fig. 4g).
Moreover, repeated tyrosine hydroxylase staining in the first and third rounds maintained signal pattern and intensity, confirming that antigenicity is retained throughout multiple rounds of staining and elution.a, First round. Rendering of 1-mm-thick Thy1–eYFP block immunostained for tyrosine hydroxylase in non-sectioned form.
b, Antibodies eluted from block in a (4% SDS, 60 °C for 0.5 days). Tyrosine hydroxylase signal was removed and eYFP fluorescence retained c, Second round. Three-dimensional rendering of same block now immunostained for parvalbumin (red), glial fribrillary acidic protein (GFAP) (blue) and DAPI (white) d-f. Maximum projections of 100 µm volume of yellow-boxed regions in a, b and c, respectively. eYFP-positive neurons preserved. cp, cerebral peduncle; SNR, substantia nigra. Scale bar, 100 µm.
g, Optical section of white/ dotted-box region in c showing DAPI. CA, cornu ammonis; DG, dentate gyrus. Scale bar, 100 µm. h, i, Tyrosine hydroxylase channel of white box regions in a (h) and j (i). Tyrosine hydroxylase antigenicity preserved through multiple elutions. Scale bar, 100 µm.
j, Third round. Block in a–c immunostained for tyrosine hydroxylase (red) and choline acetyltransferase (ChAT) (blue) k, Three-dimensional view of hippocampus in c showing eYFP-expressing neurons (green), parvalbumin-positive neurons (red) and GFAP (blue). Alv, alveus. Scale bar, 200 µm
Using mouse brains,
They found that CLARITY was suitable for such long-banked human brain, allowing immunohistological visualization and identification of neurons and projections over large volumes (a-g).
In 0.5-mm-thick blocks of frontal lobe from an autistic patient, stored in formalin for >6 years, we were able to stain for axons with neurofilament protein and myelin basic protein,
and trace individual fibres (e).we found that many parvalbum-inpositive interneurons in this human sample, particularly in deep layers, showed isoneuronal and heteroneuronal dendritic bridges (g-m)
. In addition, by staining for parvalbumin it was possible to visualize the distribution of parvalbumin-positive neurons in the neocortex over large volumes (6.7 × 4.7 × 0.5 mm),
and trace individual parvalbumin-labelled processes Human BA10 500-µm-thick intact blocks clarified (1 day) and immunostained (3 days) (×25water-immersion objective).
a, Optical section: myelin basic protein (MBP) and parvalbumin staining. White arrowheads indicate membrane-localized myelin basic proteinaround parvalbumin-positive projections. Scale bar, 10 µm. b, Tyrosine hydroxylase and parvalbumin staining.
c, Optical section: neurofilament (NP) and GFAP. Scale bar, 20 µm. d, Somatostatin and parvalbumin stainingRendering of neurofilament-positive axonal fibres. Red, traced axon across volume. Scale bar, 500 µm. Inset: boxed region. f, Visualization of parvalbumin-positive neurons in the neocortex of autism case; layers identified as described in ref.
g, Yellowboxed region in f showing parvalbumin-positive cell bodies and fibres in layers 4, 5 and 6. Three representative parvalbumin-positive interneurons in layer 6 with ladder-shapedhetero- or iso-neuronal connections were traced (green, purple, blue). Scale bar, 100 µm h, Three-dimensional rendering of abnormal neurons in g;yellow arrowheads (1, 2) indicate ladder-shaped structures shown below in i and k.. i, Zoomed-in maximum projection of 8 µm volume showing morphology ofladder-shaped structure formed by neurites from a single neuron.
j, Tracing of structure in
k, Maximum projection of 18 µm volume showing ladder-shaped structure formed by neurites from two different neurons.
l, Tracing of structure in k. m, Iso- and hetero-neuronal dendritic bridges per neuron. Neurons selected randomly and traced in software (Methods);
dendritic bridges were manually counted. **P<0.05; error bars denote s.e.m. n=6 neurons for both
superficial and deep layers of autism case and n=4 neurons for both superficial and deep layers of control case.
n, Threedimensional reconstruction of a neuron in layer 2 (superficial) of the autism case. Typical avoidance of iso-dendritic contact was observed