12/28/2018 1 Why Botany? Today's Topics What Is a Plant?
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
Eastern Deciduous Forest
Eastern Deciduous Forest Physical description Most of the terrain is rolling except for the Ozark Mountains, which can be steep. The average annual precipitation ranges from approximately 35 inches to 90 inches and is usually well-distributed throughout the year. Summers are hot; winters are cold. Dominant vegetation Deciduous trees dominate the landscape across the Eastern Deciduous Forest ecoregion where there is a lack of disturbance. Depending on location, trees such as oaks, hickories, maples, American beech, basswood, buckeye, yellow poplar, walnut, and birches are common in the overstory and can be indicators of a climax successional stage. Prevalent midstory trees include flowering dogwood, sassafras, sourwood, eastern redbud, hophornbeam, American hornbeam, and striped maple. Common shrubs include arrowwood, black huckleberry, blueberries, hawthorn, pawpaw, spicebush, viburnums, and witchhazel. A wide variety of forbs and ferns may be found in the understory. Common evergreen trees on many sites undergoing succession include eastern redcedar and shortleaf pine. Figure 2. Deciduous forest cover occurs over the Eastern Deciduous Forest ecoregion, except where areas have been cleared for agriculture and livestock. Changes in the composition, structure and function of the Eastern Deciduous Forest have already occurred during the past 100 years with the loss of American chestnut and the near total exclusion of fire. Prior to fire suppression, savannas and woodlands dominated by oak and shortleaf pine were prevalent over much of this ecoregion. Well-interspersed with forested areas in the Eastern Deciduous Forest ecoregion are agricultural fields, pastures and hayfields, and fields undergoing succession. Virtually all of these “old- fields” have been cropped in the past, and the vast majority has since been planted to nonnative grasses, especially tall fescue. -
"Lophophorates" Brachiopoda Echinodermata Asterozoa
Deuterostomes Bryozoa Phoronida "lophophorates" Brachiopoda Echinodermata Asterozoa Stelleroidea Asteroidea Ophiuroidea Echinozoa Holothuroidea Echinoidea Crinozoa Crinoidea Chaetognatha (arrow worms) Hemichordata (acorn worms) Chordata Urochordata (sea squirt) Cephalochordata (amphioxoius) Vertebrata PHYLUM CHAETOGNATHA (70 spp) Arrow worms Fossils from the Cambrium Carnivorous - link between small phytoplankton and larger zooplankton (1-15 cm long) Pharyngeal gill pores No notochord Peculiar origin for mesoderm (not strictly enterocoelous) Uncertain relationship with echinoderms PHYLUM HEMICHORDATA (120 spp) Acorn worms Pharyngeal gill pores No notochord (Stomochord cartilaginous and once thought homologous w/notochord) Tornaria larvae very similar to asteroidea Bipinnaria larvae CLASS ENTEROPNEUSTA (acorn worms) Marine, bottom dwellers CLASS PTEROBRANCHIA Colonial, sessile, filter feeding, tube dwellers Small (1-2 mm), "U" shaped gut, no gill slits PHYLUM CHORDATA Body segmented Axial notochord Dorsal hollow nerve chord Paired gill slits Post anal tail SUBPHYLUM UROCHORDATA Marine, sessile Body covered in a cellulose tunic ("Tunicates") Filter feeder (» 200 L/day) - perforated pharnx adapted for filtering & repiration Pharyngeal basket contractable - squirts water when exposed at low tide Hermaphrodites Tadpole larvae w/chordate characteristics (neoteny) CLASS ASCIDIACEA (sea squirt/tunicate - sessile) No excretory system Open circulatory system (can reverse blood flow) Endostyle - (homologous to thyroid of vertebrates) ciliated groove -
Evidence for Selection on a Chordate Histocompatibility Locus
ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2012.01787.x EVIDENCE FOR SELECTION ON A CHORDATE HISTOCOMPATIBILITY LOCUS Marie L. Nydam,1,2,3 Alyssa A. Taylor,3 and Anthony W. De Tomaso3 1Division of Science and Mathematics, Centre College, Danville, Kentucky 40422 2E-mail: [email protected] 3Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106 Received June 7, 2011 Accepted July 31, 2012 Allorecognition is the ability of an organism to differentiate self or close relatives from unrelated individuals. The best known applications of allorecognition are the prevention of inbreeding in hermaphroditic species (e.g., the self-incompatibility [SI] systems in plants), the vertebrate immune response to foreign antigens mediated by MHC loci, and somatic fusion, where two genetically independent individuals physically join to become a chimera. In the few model systems where the loci governing allorecognition outcomes have been identified, the corresponding proteins have exhibited exceptional polymorphism. But information about the evolution of this polymorphism outside MHC is limited. We address this subject in the ascidian Botryllus schlosseri,where allorecognition outcomes are determined by a single locus, called FuHC (Fusion/HistoCompatibility). Molecular variation in FuHC is distributed almost entirely within populations, with very little evidence for differentiation among different populations. Mutation plays a larger role than recombination in the creation of FuHC polymorphism. A selection statistic, neutrality tests, and distribution of variation within and among different populations all provide evidence for selection acting on FuHC, but are not in agreement as to whether the selection is balancing or directional. -
Unit 2 Cell Biology Page 1 Sub-Topics Include
Sub-Topics Include: 2.1 Cell structure 2.2 Transport across cell membranes 2.3 Producing new cells 2.4 DNA and the production of proteins 2.5 Proteins and enzymes 2.6 Genetic Engineering 2.7 Respiration 2.8 Photosynthesis Unit 2 Cell Biology Page 1 UNIT 2 TOPIC 1 1. Cell Structure 1. Types of organism Animals and plants are made up of many cells and so are described as multicellular organisms. Similar cells doing the same job are grouped together to form tissues. Animals and plants have systems made up of a number of organs, each doing a particular job. For example, the circulatory system is made up of the heart, blood and vessels such as arteries, veins and capillaries. Some fungi such as yeast are single celled while others such as mushrooms and moulds are larger. Cells of animals plants and fungi have contain a number of specialised structures inside their cells. These specialised structures are called organelles. Bacteria are unicellular (exist as single cells) and do not have organelles in the same way as other cells. 2. Looking at Organelles Some organelles can be observed by staining cells and viewing them using a light microscope. Other organelles are so small that they cannot be seen using a light microscope. Instead, they are viewed using an electron microscope, which provides a far higher magnification than a light microscope. Most organelles inside cells are surrounded by a membrane which is similar in composition (make-up) to the cell membrane. Unit 2 Cell Biology Page 2 3. A Typical Cell ribosome 4. -
The Origins of Chordate Larvae Donald I Williamson* Marine Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
lopmen ve ta e l B Williamson, Cell Dev Biol 2012, 1:1 D io & l l o l g DOI: 10.4172/2168-9296.1000101 e y C Cell & Developmental Biology ISSN: 2168-9296 Research Article Open Access The Origins of Chordate Larvae Donald I Williamson* Marine Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom Abstract The larval transfer hypothesis states that larvae originated as adults in other taxa and their genomes were transferred by hybridization. It contests the view that larvae and corresponding adults evolved from common ancestors. The present paper reviews the life histories of chordates, and it interprets them in terms of the larval transfer hypothesis. It is the first paper to apply the hypothesis to craniates. I claim that the larvae of tunicates were acquired from adult larvaceans, the larvae of lampreys from adult cephalochordates, the larvae of lungfishes from adult craniate tadpoles, and the larvae of ray-finned fishes from other ray-finned fishes in different families. The occurrence of larvae in some fishes and their absence in others is correlated with reproductive behavior. Adult amphibians evolved from adult fishes, but larval amphibians did not evolve from either adult or larval fishes. I submit that [1] early amphibians had no larvae and that several families of urodeles and one subfamily of anurans have retained direct development, [2] the tadpole larvae of anurans and urodeles were acquired separately from different Mesozoic adult tadpoles, and [3] the post-tadpole larvae of salamanders were acquired from adults of other urodeles. Reptiles, birds and mammals probably evolved from amphibians that never acquired larvae. -
Chapter 13 Protein Structure Learning Objectives
Chapter 13 Protein structure Learning objectives Upon completing this material you should be able to: ■ understand the principles of protein primary, secondary, tertiary, and quaternary structure; ■use the NCBI tool CN3D to view a protein structure; ■use the NCBI tool VAST to align two structures; ■explain the role of PDB including its purpose, contents, and tools; ■explain the role of structure annotation databases such as SCOP and CATH; and ■describe approaches to modeling the three-dimensional structure of proteins. Outline Overview of protein structure Principles of protein structure Protein Data Bank Protein structure prediction Intrinsically disordered proteins Protein structure and disease Overview: protein structure The three-dimensional structure of a protein determines its capacity to function. Christian Anfinsen and others denatured ribonuclease, observed rapid refolding, and demonstrated that the primary amino acid sequence determines its three-dimensional structure. We can study protein structure to understand problems such as the consequence of disease-causing mutations; the properties of ligand-binding sites; and the functions of homologs. Outline Overview of protein structure Principles of protein structure Protein Data Bank Protein structure prediction Intrinsically disordered proteins Protein structure and disease Protein primary and secondary structure Results from three secondary structure programs are shown, with their consensus. h: alpha helix; c: random coil; e: extended strand Protein tertiary and quaternary structure Quarternary structure: the four subunits of hemoglobin are shown (with an α 2β2 composition and one beta globin chain high- lighted) as well as four noncovalently attached heme groups. The peptide bond; phi and psi angles The peptide bond; phi and psi angles in DeepView Protein secondary structure Protein secondary structure is determined by the amino acid side chains. -
Course Outline for Biology Department Adeyemi College of Education
COURSE CODE: BIO 111 COURSE TITLE: Basic Principles of Biology COURSE OUTLINE Definition, brief history and importance of science Scientific method:- Identifying and defining problem. Raising question, formulating Hypotheses. Designing experiments to test hypothesis, collecting data, analyzing data, drawing interference and conclusion. Science processes/intellectual skills: (a) Basic processes: observation, Classification, measurement etc (b) Integrated processes: Science of Biology and its subdivisions: Botany, Zoology, Biochemistry, Microbiology, Ecology, Entomology, Genetics, etc. The Relevance of Biology to man: Application in conservation, agriculture, Public Health, Medical Sciences etc Relation of Biology to other science subjects Principles of classification Brief history of classification nomenclature and systematic The 5 kingdom system of classification Living and non-living things: General characteristics of living things. Differences between plants and animals. COURSE OUTLINE FOR BIOLOGY DEPARTMENT ADEYEMI COLLEGE OF EDUCATION COURSE CODE: BIO 112 COURSE TITLE: Cell Biology COURSE OUTLINE (a) A brief history of the concept of cell and cell theory. The structure of a generalized plant cell and generalized animal cell, and their comparison Protoplasm and its properties. Cytoplasmic Organelles: Definition and functions of nucleus, endoplasmic reticulum, cell membrane, mitochondria, ribosomes, Golgi, complex, plastids, lysosomes and other cell organelles. (b) Chemical constituents of cell - salts, carbohydrates, proteins, fats -
Fall Color Is a Byproduct of the Physiological Response of Temperate-Zone Plants to Shortening Days
Printed in: Southwest Horticulture (2001) 18(6):6 The Colors of Fall Ursula Schuch, Plant Sciences Department, University of Arizona, Tucson Cool nights and warm, sunny days signal the onset of fall, and perfect weather for the development of brilliant crimson, gold, copper or yellow foliage. Fall color is a byproduct of the physiological response of temperate-zone plants to shortening days. Best fall colors are generally seen in deciduous, broadleaf woody plants that originate in USDA zones 3 to 9. In Arizona, fall color is scarce in the low desert, but is displayed more generously at higher elevations. Chlorophyll is responsible for the green color of leaves or stems and enables plants to produce sugars through the process of photosynthesis. In green leaves, chlorophyll is the dominant pigment. Visible light is absorbed by pigments, and leaves appear green because chlorophyll absorbs red and blue light while transmitting and reflecting green light. Carotenoids are accessory pigments in the photosynthesis process with colors in shades of yellow to orange; however, they are much less abundant than chlorophyll. Starting in spring, when plant growth begins for temperate-zone plants, and throughout summer, chlorophyll is continuously produced in the growing leaves to enable maximum food production. This is the time of greatest stem elongation, new leaf production, and growth in girth. As summer transitions into fall, plants respond to shorter days with reduced stem elongation, initiation of leaf abscission, reduced chlorophyll production, and increased production of other pigments. This marks the onset of dormancy and the beginning of frost hardiness. The splendor of fall color begins when chlorophyll production declines in the leaves and when the less abundant carotenoids unveil yellow to orange hues, or anthocyanins flaunt colors of red and purple. -
Development of the Annelid Axochord: Insights Into Notochord Evolution Antonella Lauri Et Al
RESEARCH | REPORTS ORIGIN OF NOTOCHORD by double WMISH (Fig. 2, F to L). Although none of the genes were exclusively expressed in the annelid mesodermal midline, their combined Development of the annelid coexpression was unique to these cells (implying that mesodermal midline in annelids and chor- damesoderm in vertebrates are more similar to axochord: Insights into each other than to any other tissue). It is unlikely that the molecular similarity between annelid notochord evolution and vertebrate mesodermal midline is due to in- dependent co-option of a conserved gene cas- Antonella Lauri,1*† Thibaut Brunet,1* Mette Handberg-Thorsager,1,2‡ sette, because this would require either that this Antje H.L. Fischer,1§ Oleg Simakov,1 Patrick R. H. Steinmetz,1‖ Raju Tomer,1,2¶ cassette was active elsewhere in the body (which Philipp J. Keller,2 Detlev Arendt1,3# is not the case) or that multiple identical inde- pendent events of co-option occurred (which is The origin of chordates has been debated for more than a century, with one key issue being unparsimonious). As in vertebrates, the meso- the emergence of the notochord. In vertebrates, the notochord develops by convergence dermal midline resembles the neuroectodermal and extension of the chordamesoderm, a population of midline cells of unique molecular midline, which expresses foxD, foxA, netrin, slit, identity. We identify a population of mesodermal cells in a developing invertebrate, the marine and noggin (figs. S6 and S7) but not brachyury or annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a twist. However, unlike in chicken (10), the an- notochord-specific combination of genes. -
Origin of Chordates Part-I
ORIGIN OF CHORDATES Evolution of chordate was one of the most important event in the history of chordate as it was the beginning of evolution of more advanced chordates like bird and mammals. It is the story of origin from a primitive invertebrate like creatures to early chordates. Though first fossil of the first vertebrate the ostrachoderm was discovered from the Ordovician period but it might have originated in late Cambrian period. As early chordates were soft bodied, their fossil records are not preserved. Hence, to trace their ancestry, we have to find out the similarity among different deuterostomes to trace the origin of chordates. Some structural features shared by them such as bilateral symmetry, antero-posterior body axis, triploblastic coelomate condition, etc., may he because of their common ancestry. TIME OF ORIGIN: Late Cambrian period PLACE OF ORIGIN: Fresh water THEORIES OF INVERTEBRATE ANCESTRY OF CHORDATES Several theories have been put forwarded to explain the origin of chordates either directly from some invertebrate group or through the intervention of some protochordate. Almost every invertebrate phylum—Coelenterata, Nemertean, Phoronida, Annelids, Arthropods and Echinodermatashas been suggested. But these theories are far from being satisfactory and convincing and have only a historical value. Only the echinoderm theory has received some acceptance. DIVISION OF BILATERIA The Bilateria is divided into two major divisions (1) Protostomia and (2) Deuterostornia. This division is based on the differences in embryonic and larval developments. Protostomia includes from Annelida to Arthropoda while deuterostomia includes Echinodermata, Pogonophora and Chordate. DEUTEROSTOME LINE OF CHORDATE EVOLUTION Following common features of all Deuterostomes suggests strong evidence of a closer evolutionary relationship between the three principal deuterostome phyla – Echinodermata, Hemichordata and Chordata. -
Multidisciplinary Design Project Engineering Dictionary Version 0.0.2
Multidisciplinary Design Project Engineering Dictionary Version 0.0.2 February 15, 2006 . DRAFT Cambridge-MIT Institute Multidisciplinary Design Project This Dictionary/Glossary of Engineering terms has been compiled to compliment the work developed as part of the Multi-disciplinary Design Project (MDP), which is a programme to develop teaching material and kits to aid the running of mechtronics projects in Universities and Schools. The project is being carried out with support from the Cambridge-MIT Institute undergraduate teaching programe. For more information about the project please visit the MDP website at http://www-mdp.eng.cam.ac.uk or contact Dr. Peter Long Prof. Alex Slocum Cambridge University Engineering Department Massachusetts Institute of Technology Trumpington Street, 77 Massachusetts Ave. Cambridge. Cambridge MA 02139-4307 CB2 1PZ. USA e-mail: [email protected] e-mail: [email protected] tel: +44 (0) 1223 332779 tel: +1 617 253 0012 For information about the CMI initiative please see Cambridge-MIT Institute website :- http://www.cambridge-mit.org CMI CMI, University of Cambridge Massachusetts Institute of Technology 10 Miller’s Yard, 77 Massachusetts Ave. Mill Lane, Cambridge MA 02139-4307 Cambridge. CB2 1RQ. USA tel: +44 (0) 1223 327207 tel. +1 617 253 7732 fax: +44 (0) 1223 765891 fax. +1 617 258 8539 . DRAFT 2 CMI-MDP Programme 1 Introduction This dictionary/glossary has not been developed as a definative work but as a useful reference book for engi- neering students to search when looking for the meaning of a word/phrase. It has been compiled from a number of existing glossaries together with a number of local additions.