BIOL227 Discussion 1 - Introduction to Biodiversity and Microscopy PDF

BIOL227 Discussion 1: Introduction to the Course Laboratory Studies in Biodiversity Lab reports: Complete the lab report in the lab and hand to TA and sign the sheet BEFORE leaving If you are sick, email me ASAP and I will try to adjust you in another lab section (NOT always possible) If you...

BIOL227 Discussion 1: Introduction to the Course Laboratory Studies in Biodiversity Lab reports: Complete the lab report in the lab and hand to TA and sign the sheet BEFORE leaving If you are sick, email me ASAP and I will try to adjust you in another lab section (NOT always possible) If you miss a lab (with short term absence form): The remainder of the labs will count towards your lab grade. The same applies for the lab quiz. However students are STILL responsible for the content of that lab for examinations and quizzes. No make up labs Lab reports: Plagiarism Plagiarisms will not be tolerated DO NOT COPY, PARAPHRASE OR TRANSLATE ANYTHING FROM ANYWHERE WITHOUT SAYING FROM WHERE YOU OBTAINED IT!” Plagiarism cases will be handled by Code of conduct office Do not copy figures, answers, etc from other students No electronic devices during the labs! Laptops, netbooks, ipads etc only allowed in class No phones allowed in lab and class Before coming to the Labs ► Read lab manual ► Watch any videos posted ► There will be a quiz in the beginning of every lab (5 minutes). If you miss the quiz, you will receive a grade of 0 so COME EARLY. ► Bring signed copy of safety sheet in the first lab.  Course objectives 1. List unique features (at the organismal, cellular and subcellular level) of a particulartaxon 2. Identify/label these features (e.g. cell morphology, cell walls, food/contractile vacuoles, vasculature in plants, etc.) 3. Describe these features and explain why they are important. What advantage do they confer to the organism? What information does it give you in terms of the organism's environment and evolutionary history? 4. Recognize the diversity of organisms and their unique features across various levels of the taxonomic hierarchy. 5. Compare taxa within a taxon (e.g. various classes within a phylum). Courtesy of Dr. Catherine Calogeropoulos Biodiversity  BIOL227 Discussion 1: Introduction to Biodiversity Biodiversity: What is it? Bio = Life Diversity= variety 3 main types of Biodiversity: Species diversity Ecosystem diversity Genetic diversity Biodiversity is vital to sustaining life on earth. Why? Biodiversity: Types Genetic diversity Variations among the genetic resources of the organisms. Every individual of a particular species differs from each other in their genetic constitution. Example: different varieties in the same species of rice, wheat, maize, barley, etc. Species diversity different types of species found in a particular area. biodiversity at the most basic level. Ecosystem diversity variations in the microbes, plant and animal species living together and connected by food chains and food webs. diversity observed among the different ecosystems in a region. https://byjus.com/biology/biodiversity/ Biodiversity: Types https://ehealth.eletsonline.com/2015/10/worldss-largest- https://naturemanchester.wordpress.com/2021/01/20/the-cain- catalogue-of-human-genetic-diversity-created/ and-stelfox-shell-collections-in-the-manchester-museum/ https://qph.cf2.quoracdn.net/main-qimg-d730d02d0e9af1c290feb82461eae4c7-pjlq Biodiversity: Types Examples of biological diversity in the Congo River region https://www.ck12.org/book/human-biology-ecology/section/12.1/ Biodiversity: Microbes, animals, Plants Biodiversity: Taxonomy The discipline of systematics classifies organisms and determines their evolutionary relationships Taxonomy is the scientific discipline concerned with classifying and naming organisms Domain Eukarya shares more recent common ancestor with Archaea or Bacteria? Biodiversity: Common vs Scientific names Classification Using common names can be misleading Common names make poor labels Bears Robins Corn 18 Biodiversity: Binomial Nomenclature In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances Two key features of his system remain useful today -two-part names for species -hierarchical classification The two-part scientific name of a species is called a binomial The first part of the name is the genus Second part, called specific epithet, is unique for each species within a genus First letter of the genus is capitalized, and the entire species name is italicized: E.g. Homo sapiens Both parts together name the species (not the specific epithet alone) Biodiversity: Taxonomic Classification Taxonomists use a hierarchical system to classify organisms Linnaean classification groups species in increasingly broad categories. From broad to narrow: domain, kingdom, phylum, class, order, family, genus, and species Figure 26.4 Linnaean classification. Biodiversity: Taxonomic Classification Classification Taxonomists use a hierarchical system to classify organisms Species soup Genus good Information Family for gets more and more Order over general Class came Phylum Philip Kingdom King Domain Dear 21 Biodiversity: Taxonomic Classification (General) Domain Broader categories Kingdom Phylum Dumb Kings Play Class CChess On Fine Order Grain Sand Family Genus (Specific) Species Biodiversity: Taxonomic Classification Classification groups species using similar key character, combinations Groups are a taxonomic hierarchy, the boundaries of which are decided by consensus & authority, defining the limits of character similarity in a TAXA. Species Genus Family Order Class Phylum Kingdom Domain Ursus ameri- canus (American blackbear) Ursus Ursidae Carnivora Mammalia Taxonomy, Chordata Linnaean Classification Animalia Eukarya Biodiversity: Key contributors to taxonomy Classification by taxonomist –Up to the early 1970’s - all organisms were classified into a Plant / Animal But where do Fungi, Bacteria (and Archaea) etc. fit –low morphological character, variation, but inhabiting every known habitat, some with both animal & plant characters? Plant- Animal Dichotomy was inconvenient, wrong. It needed more useful major Divisions - Kingdoms There were several proposed systems for classifying organisms……one of several was widely adopted by textbooks Whittaker (1969) proposed 5 Kingdoms dividing eukaryotic organisms on Functional-Nutritional bases: 3 nutritional modes of multicellular eukaryotes: 1) absorptive- Fungi; 2) photosynthetic - Plants, and 3) heterotrophic-Animals. Unicellular - eukaryotic (Protists – with some multicellular lineages) - prokaryote (Monera) Biodiversity: 3 Domains, 4 Kingdoms in Eukarya Biol 227 CLASSIFICATIONUSES 3 DOMAINS Eukaryote - 4 Eukaryote KINGDOMS Biodiversity: 3 Domains, 4 Kingdoms in Eukarya - incudes 4 subgroups: Biodiversity: Domains of Life Tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria The tree of life is based largely on rRNA genes, as these have evolved slowly Figure 26.19 Biodiversity: Horizontal Gene Transfer There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Disparities between gene trees can be explained by the occurrence of horizontal gene transfer Horizontal gene transfer has played a key role in the evolution of both prokaryotes and eukaryotes Figure 26.20 Biodiversity: Horizontal Gene Transfer Some biologists argue that horizontal gene transfer was so common that the early history of life should be represented as a tangled network of connected branches Figure 26.21 A recipient of transferred genes Erasend with Mass extinctions – link between Geology and Biology Ancestor-descendent diversification implies a time frame on Earth, measured by Geological EONS, ERAS and PERIODS, some of which mark key changes in geology and often organism diversity. Beginning with the Hadean eon ends with the origin of life, initiating the Archaean Era on the lower left. We are now in the upper-most Epoch on the right, the Holocene https://geologyscience.com/geology- branches/paleontology/geologic-time-scale/  BIOL227 Discussion 1: Introduction to Microscopy Microscopy: Learning Outcomes 1.Describe the parts of the compound microscope (see lab document) 2.Describe the bending of light as it moves through the condenser, objective lenses and ocular lenses and media (air, water and oil). 3.Explain how an increase in resolution is achieved as we move from scanning to high- power objective lenses. 4.Practice the Köhler illumination step, oil immersion and dark- field illumination  one ten-millionth of a millimetre or 1 angstrom Figure 2.2 Comparative sizes of different objects. Credit: Jeremy Seto and derived from works by IgniX, Gringer, Jiver, Ninjatacoshell, Ali Zifan (CC-BY-SA) (CUNY Lab: Microscope) Microscopy: Branches https://byjus.com/physics/difference-between-light-microscope-and-electron- microscope/ Magnification vs Resolution? What is the relationship between them? Microscopy: Parts The light compound microscope Microscopy: Lenses Three lenses: 1. Condenser lens 2. Objective lens (Source: Willey, Joanne M., Sherwood, Linda., Woolverton, https://upload.wikimedia.org/wikipedia/commons/2/27/ Christopher J., Prescott, Lansing M. (2008). Prescott, Harley, Condenser_diagram.svg 3. Ocular lens and Klein's microbiology (7th). McGraw Hill.) The condenser lens (a collection of prisms) converges rays of light to a focal point (F). Microscopy: Refractive Index When light passes from one medium to another, refraction occurs. The medium can be air, glass or oil. When light crosses through a medium with a different density, its speed changes, which causes path of light to change. This change in direction is called refraction. The refraction index is a measure of how much a medium slows the velocity of light Refractive index of air=1 Refractive index of glass=1.52 Refractive index of immersion oil=1.52 (Source: Willey, Joanne M., Sherwood, Linda., Woolverton, Christopher J., Prescott, Lansing M. (2008). Prescott, Harley, and Klein's microbiology (7th). McGraw Hill.) Microscopy: Resolution Resolution is the ability of a lens to separate or distinguish between small objects that are close together. Ernst Abbé (1870s) a physicist worked out the resolution of lenses mathematically. Abbé equation: d =0.5l or, d = 0.5 1 n sin8 NA Where, No need to remember the equation. d= The minimal distance between two points that can be resolved. The resolving power of the objectivelens. l= the wavelength of light n= refractive index of the medium in which theobjective lens is working. Sinq= 1/2 the angle of the cone of light entering theobjective lens Numerical aperture (N.A) =n sinq Microscopy: Köhler illumination To maximize the resolution of a microscope, the Kohler illumination protocol is performed. The Köhler illumination ensures that the cone of light emerging from the condenser lens is centered in your field of view. This enables a more uniform illumination across the specimen. Consequently, both the contrast and resolution improve. The opening and closing of the aperture iris diaphragm controls the size of the cone of light emerging from the condenser lens. Inverted cone of light entering the objective lens Cone of light emerging from condenser lens and striking the specimen on slide Aperture iris diaphragm (or condenser diaphragm) Circle of light crossing up and through the aperture iris diaphragm Microscopy: Köhler illumination