Lecture 3 (Animal Development) PDF

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Axes and symmetry N bottom the 98 S  divides animal regital to both planes 900 widesifthmmade hemis hemis suite t soesgm.int em righf Equatorial spminalpole plane By My My EBay dorsal meridional ventral mummman Nsm plane so F arm regbal pole gto divides ventral sides JofooooooaeJafaafg right dorsal  front it back (Cranial) (Caudal) left Anteroposterior axis 56 Dorsoventral axis Mediolateral axis separ anterior posterior Transverse sections 8 Frontal sections separate dorsal ventral side middle offore Sagittal section closer to left separate left right  For Appendages: – Proximal = near the body – Distal = away from the body TEST Morphogenetic Process Cells need to change shape and/or move side basal apical r Epithelium linkedtoeachother work together as a unit embryoni Polarized cells Mesenchyme scattered cells isolated bound to interact w extracell don't inter w each other Morphogenetic Process can transition to the other cell Epithelium to mesenchyme: Dispersal Mesenchyme to epithelium: Condensation  Morphogenetic Process Apical constriction 0 Epith Involution Invagination detach from epith separate form new layer but then interot layers to thicken thecell W each other mor Morphogenetic Process Epiboly Epith cells stretch out to cover the whole embryo become thinner  hey s vide Approaches to Developmental Biology Experimental Embryology Surgery transplants etc Genetic approaches modern knock out overexpress  Experimental Embryology Determined what is "normal": standard laboratory conditions Stage series: course of development over standard stages  The Fate map tracing of cell lineages during development, to see what they become... freelivigembry Techniques use transparent animals modern dye marking radioactive labeling modern genetic marking  cells big dye  Tunicate: – sea squirt  deter its was and to natural piquet I fate mope Tunicate embryo Fate map of the tunicate embryo blue ectoderm red mesoderm yellow endoderm all Fate map of the tunicate embryo neage he rep cell division originator cells become mature  used for more complicated indived Genetic markers as cell lineage tracers Chimeric embryo or mosaic embryo Thave large nucleolus Gene Expression Notes created on January 14, 2025 at 10:09 AM by Minutes AI Gene Expression Analysis (00:07 - 10:07) Use of mutant samples to study gene expression. Knockout of specific proteins can be analyzed. Process of obtaining and labeling cDNA. Messenger RNA is purified and converted to cDNA. cDNA from wild type is labeled with green dye; cDNA from mutants is labeled with Hybridization and Array Analysis Application of labeled cDNA to gene arrays. Arrays consist of spots representing different genes. Hybridization occurs when complementary cDNA binds to the corresponding Interpretation of results based on dye color. Yellow indicates equal expression in both wild type and mutant. Green indicates higher expression in wild type. Red indicates higher expression in mutants. RNA Sequencing (RNA-seq) RNA-seq as a modern method for gene expression analysis. Messenger RNA is sequenced to identify and quantify gene expression. Requires significant computing power to align sequences to the genome. Direct counting of RNA molecules for gene expression quantification. Example: Comparing reads for a specific gene like PAX6 in wild type versus These notes were taken with Minutes AI (https://myminutes.ai) Protein Quantification Mass spectrometry used for protein quantification. Allows counting of proteins and their fragments in cells. Similar methodology to RNA quantification can be applied to proteins. Gene Expression Techniques (10:07 - 19:53) Comparison of techniques for gene expression analysis. Some techniques may be easier and sufficient for certain purposes. Rich labs may have more resources for advanced methods. ChIP-Seq Technique ChIP (Chromatin Immunoprecipitation) sequencing purpose. Identifies where transcription factors bind in the genome. Helps determine which genes are activated or repressed by transcription factors. Process overview. Cells are treated with formaldehyde to create cross-links between transcription Genomic DNA is isolated and sheared into smaller fragments. Specific antibodies are used to precipitate DNA linked to the transcription factor. Sequencing of the precipitated DNA reveals binding sites. CRISPR Methodology Introduction to CRISPR as a gene editing tool. Used for generating gene deletions and creating mutants. Considered more specific, targeted, and efficient than older methods. Mechanism of CRISPR. Cas9 protein cuts double-stranded DNA. These notes were taken with Minutes AI (https://myminutes.ai)  Guide RNA (gRNA) directs Cas9 to the specific gene to be edited. Allows for mutation creation or repair through error-prone repair mechanisms. Developmental Biology: Axis and Symmetry Importance of axis and symmetry in early embryos. Polarization of eggs, with distinct animal and vegetal poles. Establishment of axes occurs prior to fertilization. Description of egg structure. Animal pole referred to as the upper region. Vegetal pole referred to as the lower region. Axis Development (19:55 - 29:53) Sperm fertilization helps establish the dorsal-ventral and left-right axis. Dorsal refers to the upper part of the body; ventral refers to the lower side. Equatorial plane divides the animal and vegetable hemispheres. Meridional plane corresponds to longitude and separates left and right sides. Anatomical Sections Transverse section goes along the anterior-posterior axis. Frontal section separates dorsal and ventral sides. Sagittal section separates left and right at the middle of the animal. Parasagittal refers to sections away from the midline. Morphogenetic Processes Morphogenetic processes involve changes in structure and shape during development. Two types of embryonic cells: These notes were taken with Minutes AI (https://myminutes.ai)  Epithelial cells form epithelium and are tightly bound together. Mesenchymal cells are distinct from epithelial cells. Epithelial cells are polarized with an apical side and a basal side. They communicate through links between cells. Cell Types in Early Embryo (29:54 - 39:52) Two general cell types: epithelial and mesenchymal cells. Epithelial cells are connected and healthy bound. Mesenchymal cells are scattered, isolated, and operate as independent units. Transition Between Cell Types Epithelial cells can transition to mesenchymal cells. This process is commonly referred to as EMT (epithelial to mesenchymal Mesenchymal cells can condense to form epithelial cells. This process is called condensation. Morphogenetic Processes Involution Involves separation of cells to form a second epithelial layer below the first. Invagination Forms a circular structure that can create a tube while maintaining an epithelial Epiboly Epithelial cells can stretch and cover the embryo. This process involves cells multiplying and becoming larger to enclose the Approaches to Developmental Biology These notes were taken with Minutes AI (https://myminutes.ai)  Experimental embryology Classical approach involving physical manipulation of embryos. Techniques include surgeries and transplants to observe effects of cell removal. Expanding Embryology (39:53 - 49:49) Focus on genetic approaches in embryology. Use of knockouts to remove gene functions. Overexpression of genes to observe effects on development. Characterizing Normal Development Importance of understanding normal embryo behavior. Standard laboratory conditions are crucial. Temperature regulation is essential for free-living organisms. Fate Mapping Concept of fate map in embryology. Identifying regions of the embryo that form specific body parts. Tracking cell lineages from original cells to their descendants. Techniques for Observation Use of transparent animals for visibility. Injection of dyes to label specific cells. Modern methods include radioactive compounds and green fluorescent protein. Example Organism: Tunicate Description of the tunicate (sea squirt). These notes were taken with Minutes AI (https://myminutes.ai)  Simple organism with a life cycle involving egg, tadpole, and adult stages. Use of natural pigments in embryos for fate mapping. Colors indicate different tissue types: blue for ectoderm, red for mesoderm, Cell Division and Development (49:49 - 56:47) Numbers refer to division number. Example: 82 results from the first cell division. Subsequent divisions lead to cells being counted (e.g., 4.1, 4.2). Originator cells become terminally differentiated. They form mature cells through a defined process. Chimeric and Mosaic Embryos Chimeric embryos can be created using different species. Example: Quail cells can be transplanted into chick embryos. Quail cells are distinguishable due to their large nucleolus. Experiments allow mapping of developmental regions. Important for understanding normal development. Alterations can be made to study effects on physiological development. Scientific Integrity and Experimentation Science can be competitive and antagonistic. No experiment is perfect; alterations can have unpredictable effects. Importance of corroborating evidence. One experiment should not be taken as absolute truth. Further data is necessary for proper assessment. These notes were taken with Minutes AI (https://myminutes.ai)