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I. Concept 21.2 Scientists use bioinformatics to analyze genomes and their functions A. The Human Genome Project established databases and refined analytical software to make data available on the Internet 1. This has accelerated progress in DNA sequence analysis Centralized Resources for Analyzing Genome Sequences C. Bioinformatics resources are provided by a number of sources: 1. National Library of Medicine and the National Institutes of Health (NIH) created the National Center for Biotechnology Information (NCBI) 2. European Molecular Biology Laboratory 3. DNA Data Bank of Japan D. Genbank, the NCBI database of sequences, doubles its data approximately every 18 months E. Software is available that allows online visitors to search Genbank for matches to: 1. A specific DNA sequence 2. A predicted protein sequence 3. Common stretches of amino acids in a protein F. The NCBI website also provides 3-D views of all protein structures that have been determined Fig. 21-4 Identifying Protein-Coding Genes Within DNA Sequences G. Computer analysis of genome sequences helps identify sequences likely to encode proteins 1. Comparison of sequences of “new” genes with those of known genes in other species may help identify new genes Understanding Genes and Their Products at the Systems Level I. Proteomics is the systematic study of all proteins encoded by a genome 1. Proteins, not genes, carry out most of the activities of the cell How Systems Are Studied: An Example K. A systems biology approach can be applied to define gene circuits and protein interaction networks 1. Researchers working on Drosophila used powerful computers and software to predict 4,700 protein products that participated in 4,000 interactions 2. The systems biology approach is possible because of advances in bioinformatics Fig. 21-5 Proteins Application of Systems Biology to Medicine N. A systems biology approach has several medical applications: 1. The Cancer Genome Atlas project is currently monitoring 2,000 genes in cancer cells for changes due to mutations and rearrangements i. Treatment of cancers and other diseases can be individually tailored following analysis of gene expression patterns in a patient ii. In future, DNA sequencing may highlight diseases to which an individual is predisposed Fig. 21-6 II. Concept 21.5: Duplication, rearrangement, and mutation of DNA contribute to genome evolution A. The basis of change at the genomic level is mutation, which underlies much of genome evolution 1. The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction 2. The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification Duplication of Entire Chromosome Sets D. Accidents in meiosis can lead to one or more extra sets of chromosomes, a condition known as polyploidy 1. The genes in one or more of the extra sets can diverge by accumulating mutations; these variations may persist if the organism carrying them survives and reproduces Alterations of Chromosome Structure F. Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs 1. Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line G. Duplications and inversions result from mistakes during meiotic recombination 1. Comparative analysis between chromosomes of humans and 7 mammalian species paints a hypothetical chromosomal evolutionary history Fig. 21-11 Human chromosome 16 Blocks of DNA sequence Blocks of similar sequences in four mouse chromosomes: 7 8 16 17 J. The rate of duplications and inversions seems to have accelerated about 100 million years ago 1. This coincides with when large dinosaurs went extinct and mammals diversified K. Chromosomal rearrangements are thought to contribute to the generation of new species 1. Some of the recombination “hot spots” associated with chromosomal rearrangement are also locations that are associated with diseases Duplication and Divergence of Gene-Sized Regions of DNA N. Unequal crossing over during prophase I of meiosis can result in one chromosome with a deletion and another with a duplication of a particular region 1. Transposable elements can provide sites for crossover between nonsister chromatids Fig. 21-12 Transposable element Gene Nonsister chromatids Crossover Incorrect pairing of two homologs during meiosis and Evolution of Genes with Related Functions: The Human Globin Genes P. The genes encoding the various globin proteins evolved from one common ancestral globin gene, which duplicated and diverged about 450–500 million years ago 1. After the duplication events, differences between the genes in the globin family arose from the accumulation of mutations Fig. 21-13 Ancestral globin gene Evolutionary time Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations 2 1 2 G 1 -Globin gene family on chromosome 16 A -Globin gene family on chromosome 11 2. Subsequent duplications of these genes and random mutations gave rise to the present globin genes, which code for oxygen-binding proteins 3. The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation Table 21-2 Evolution of Genes with Novel Functions Q. The copies of some duplicated genes have diverged so much in evolution that the functions of their encoded proteins are now very different 1. For example the lysozyme gene was duplicated and evolved into the α-lactalbumin gene in mammals i. Lysozyme is an enzyme that helps protect animals against bacterial infection ii. α-lactalbumin is a nonenzymatic protein that plays a role in milk production in mammals Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling S. The duplication or repositioning of exons has contributed to genome evolution 1. Errors in meiosis can result in an exon being duplicated on one chromosome and deleted from the homologous chromosome 2. In exon shuffling, errors in meiotic recombination lead to some mixing and matching of exons, either within a gene or between two nonallelic genes Fig. 21-14 Epidermal growth factor gene with multiple EGF exons (green) Exon shuffling Exon duplication Fibronectin gene with multiple “finger” exons (orange) Plasminogen gene with a “kringle” exon (blue) Portions of ancestral genes Exon shuffling TPA gene as it exists today How Transposable Elements Contribute to Genome Evolution T. Multiple copies of similar transposable elements may facilitate recombination, or crossing over, between different chromosomes 1. Insertion of transposable elements within a proteincoding sequence may block protein production 2. Insertion of transposable elements within a regulatory sequence may increase or decrease protein production U. Transposable elements may carry a gene or groups of genes to a new location V. Transposable elements may also create new sites for alternative splicing in an RNA transcript 1. In all cases, changes are usually detrimental but may on occasion prove advantageous to an organism III. Concept 47.2-47.3 : Morphogenesis in animals involves specific changes in cell shape, position, and adhesion A. Morphogenesis is a major aspect of development in plants and animals 1. Only in animals does it involve the movement of cells The Cytoskeleton, Cell Motility, and Convergent Extension B. Changes in cell shape usually involve reorganization of the cytoskeleton 1. Microtubules and microfilaments affect formation of the neural tube Fig. 47-17-1 Ectoderm Fig. 47-17-2 Neural plate Microtubules Fig. 47-17-3 Actin filaments Fig. 47-17-4 Fig. 47-17-5 Neural tube Fig. 47-17-6 Ectoderm Neural plate Microtubules Actin filaments Neural tube C. The cytoskeleton also drives cell migration, or cell crawling, the active movement of cells D. In gastrulation, tissue invagination is caused by changes in cell shape and migration 1. Cell crawling is involved in convergent extension, a morphogenetic movement in which cells of a tissue become narrower and longer Fig. 47-18 Role of Cell Adhesion Molecules and the Extracellular Matrix E. Cell adhesion molecules located on cell surfaces contribute to cell migration and stable tissue structure 1. One class of cell-to-cell adhesion molecule is the cadherins, which are important in formation of the frog blastula Fig. 47-19 RESULTS 0.25 mm Control embryo 0.25 mm Embryo without EP cadherin F. Fibers of the extracellular matrix may function as tracks, directing migrating cells along routes 1. Several kinds of glycoproteins, including fibronectin, promote cell migration by providing molecular anchorage for moving cells Fig. 47-20 RESULTS Experiment 1 Control Matrix blocked Experiment 2 Control Matrix blocked Fig. 47-20-1 RESULTS Experiment 1 Control Matrix blocked Fig. 47-20-2 RESULTS Experiment 2 Control Matrix blocked Concept 47.3: The developmental fate of cells depends on their history and on inductive signals • Cells in a multicellular organism share the same genome • Differences in cell types is the result of differentiation, the expression of different genes • Two general principles underlie differentiation: 1. During early cleavage divisions, embryonic cells must become different from one another – If the egg’s cytoplasm is heterogenous, dividing cells vary in the cytoplasmic determinants they contain 2. After cell asymmetries are set up, interactions among embryonic cells influence their fate, usually causing changes in gene expression – This mechanism is called induction, and is mediated by diffusible chemicals or cell-cell interactions Fate Mapping • Fate maps are general territorial diagrams of embryonic development • Classic studies using frogs indicated that cell lineage in germ layers is traceable to blastula cells Fig. 47-21 Epidermis Epidermis Central nervous system 64-cell embryos Notochord Blastomeres injected with dye Mesoderm Endoderm Blastula (a) Fate map of a frog embryo Neural tube stage (transverse section) Larvae (b) Cell lineage analysis in a tunicate Fig. 47-21a Epidermis Epidermis Central nervous system Notochord Mesoderm Endoderm Blastula (a) Fate map of a frog embryo Neural tube stage (transverse section) • Techniques in later studies marked an individual blastomere during cleavage and followed it through development Fig. 47-21b 64-cell embryos Blastomeres injected with dye Larvae (b) Cell lineage analysis in a tunicate Fig. 47-22 Zygote 0 Time after fertilization (hours) First cell division Nervous system, outer skin, musculature 10 Outer skin, nervous system Musculature, gonads Germ line (future gametes) Musculature Hatching Intestine Intestine Mouth Anus Eggs Vulva ANTERIOR POSTERIOR 1.2 mm Establishing Cellular Asymmetries • To understand how embryonic cells acquire their fates, think about how basic axes of the embryo are established The Axes of the Basic Body Plan • In nonamniotic vertebrates, basic instructions for establishing the body axes are set down early during oogenesis, or fertilization • In amniotes, local environmental differences play the major role in establishing initial differences between cells and the body axes Restriction of the Developmental Potential of Cells • In many species that have cytoplasmic determinants, only the zygote is totipotent • That is, only the zygote can develop into all the cell types in the adult • Unevenly distributed cytoplasmic determinants in the egg cell help establish the body axes • These determinants set up differences in blastomeres resulting from cleavage Fig. 47-23a EXPERIMENT Control egg (dorsal view) Gray crescent Experimental egg (side view) Gray crescent Thread Fig. 47-23b EXPERIMENT Control egg (dorsal view) Experimental egg (side view) Gray crescent Gray crescent Thread RESULTS Normal Belly piece Normal • As embryonic development proceeds, potency of cells becomes more limited Cell Fate Determination and Pattern Formation by Inductive Signals • After embryonic cell division creates cells that differ from each other, the cells begin to influence each other’s fates by induction The “Organizer” of Spemann and Mangold • Based on their famous experiment, Hans Spemann and Hilde Mangold concluded that the blastopore’s dorsal lip is an organizer of the embryo • The Spemann organizer initiates inductions that result in formation of the notochord, neural tube, and other organs Fig. 47-24 EXPERIMENT RESULTS Dorsal lip of blastopore Primary embryo Secondary (induced) embryo Pigmented gastrula (donor embryo) Nonpigmented gastrula (recipient embryo) Primary structures: Neural tube Notochord Secondary structures: Notochord (pigmented cells) Neural tube (mostly nonpigmented cells) Fig. 47-24a EXPERIMENT Dorsal lip of blastopore Pigmented gastrula (donor embryo) Nonpigmented gastrula (recipient embryo) Fig. 47-24b RESULTS Primary embryo Secondary (induced) embryo Primary structures: Neural tube Notochord Secondary structures: Notochord (pigmented cells) Neural tube (mostly nonpigmented cells) Formation of the Vertebrate Limb • Inductive signals play a major role in pattern formation, development of spatial organization • The molecular cues that control pattern formation are called positional information • This information tells a cell where it is with respect to the body axes • It determines how the cell and its descendents respond to future molecular signals • The wings and legs of chicks, like all vertebrate limbs, begin as bumps of tissue called limb buds Fig. 47-25 Anterior Limb bud AER ZPA Limb buds Posterior 50 µm Apical ectodermal ridge (AER) (a) Organizer regions 2 Digits Anterior 4 3 Ventral Distal Proximal Dorsal Posterior (b) Wing of chick embryo Fig. 47-25a Anterior Limb bud AER ZPA Limb buds Posterior 50 µm Apical ectodermal ridge (AER) (a) Organizer regions • The embryonic cells in a limb bud respond to positional information indicating location along three axes – Proximal-distal axis – Anterior-posterior axis – Dorsal-ventral axis Fig. 47-25b 2 Digits Anterior 4 3 Ventral Distal Proximal Dorsal Posterior (b) Wing of chick embryo • One limb-bud organizer region is the apical ectodermal ridge (AER) • The AER is thickened ectoderm at the bud’s tip • The second region is the zone of polarizing activity (ZPA) • The ZPA is mesodermal tissue under the ectoderm where the posterior side of the bud is attached to the body • Tissue transplantation experiments support the hypothesis that the ZPA produces an inductive signal that conveys positional information indicating “posterior” Fig. 47-26 EXPERIMENT Anterior New ZPA Donor limb bud Host limb bud ZPA Posterior RESULTS 4 3 2 2 4 3 Fig. 47-26a EXPERIMENT Anterior New ZPA Donor limb bud Host limb bud ZPA Posterior Fig. 47-26b RESULTS 4 3 2 2 4 3 • Signal molecules produced by inducing cells influence gene expression in cells receiving them • Signal molecules lead to differentiation and the development of particular structures • Hox genes also play roles during limb pattern formation Fig. 47-27 Fig. 47-UN1 Sperm-egg fusion and depolarization of egg membrane (fast block to polyspermy) Cortical granule release (cortical reaction) Formation of fertilization envelope (slow block to polyspermy) Fig. 47-UN2 2-cell stage forming Animal pole 8-cell stage Vegetal pole Blastocoel Blastula Fig. 47-UN3 Fig. 47-UN4 Neural tube Neural tube Notochord Notochord Coelom Coelom Fig. 47-UN5 Species: Stage: Fig. 47-UN6 You should now be able to: 1. Describe the acrosomal reaction 2. Describe the cortical reaction 3. Distinguish among meroblastic cleavage and holoblastic cleavage 4. Compare the formation of a blastula and gastrulation in a sea urchin, a frog, and a chick 5. List and explain the functions of the extraembryonic membranes 6. Describe the process of convergent extension 7. Describe the role of the extracellular matrix in embryonic development 8. Describe two general principles that integrate our knowledge of the genetic and cellular mechanisms underlying differentiation 9. Explain the significance of Spemann’s organizer in amphibian development 10. Explain pattern formation in a developing chick limb, including the roles of the apical ectodermal ridge and the zone of polarizing activity