GENE4003 SEM-1 2024 GENE4003: WORKSHEET TOPICS SET 3 AND 4 1. In Drosophila melanogaster, loss of Bicoid (bcd) results in an embryo with two tails. The bcd mutation is recessive and exhibits a maternal effect. In the cross shown below, what will be the genotypes AND phenotypes of the resulting embryos, and in what ratios? Explain your answer. bcd-/bcd (female) X bcd+/bcd (male) 2. The diagram below illustrates the normal expression of three different groups of genes (A, B, and C) within four different whorls of a developing flower. Normally, whorl 1 produces sepals, whorl 2 produces petals, whorl 3 produces stamens, and whorl 4 produces carpels. Furthermore, expression of class A genes inhibits class C genes, and expression of class C inhibits class A. B A C Whorl 1 (Sepals) 2 3 4 (Petals) (Stamens) (Carpels) What kind of mutation would produce sepals in whorls 1 and 4 and petals in whorls 2 and 3? Explain your answer. 3. "Cells of multicellular organisms become increasingly specialised as they head towards their ultimate cell fate." What kinds of experiments support this statement, and how do their results support it? 4. Describe the epigenetic changes that occur in cells during development and the role they play in differentiation of cell types within a multicellular organism. 5. Fill in the blanks in the following text about early Drosophila development with appropriate words or phrases. During oogenesis, (1)_ is synthesized in the (2)_ and transported to the pole of the egg. After fertilization, _(4)_ forms a concentration gradient that is highest at the (5) pole and lowest at the _(6)_ pole. This graded distribution of (4)_ acts as a providing (8)_ to the embryo. - In the early stages of development, (10) _ is (4)_ (4)_ activates target genes that direct the formation of the (9) axis. One of the activated target genes of _(4) _ is (10)_, which is expressed in a gradient that (11) the gradient of (4) In mutants that lack _(4)_ not sufficiently (12), and the embryo develops _(14)_ the expression of _(10), which in turn embryo. (13). This suggests that helps to specify the (15) of the 1 GENE4003 SEM-1 2024 6. You are a researcher trying to understand the epigenetic mechanisms of queen bee development. Which of the following experimental manipulations would probably not lead to the development of a queen bee? a) Feeding royal jelly to a female honeybee larva b) Feeding decitabine, a DNA methyltransferase inhibitor, to a female larva c) Injecting Dnmt3 siRNA into a female honeybee larva d) Activation of a DNA cytosine deaminase enzyme in a female larva e) Feeding royal jelly to an adult worker honeybee. 7. The composite image below shows three strains of Arabidopsis thaliana. In the diploid state, A. thaliana has two homologous sets of five chromosomes (2n = 10). a) Derive the chromosome equations for the diploid, tetraploid and octaploid strains, assuming autopolyploidy. b) Using the image, describe the relationship between ploidy, leaf size (A) and cell size (B) in this species. c) What conclusions can you draw about potential for improving crop yield by increasing ploidy levels? A C The first foliage leaf 1 mm C Diploid Tetraploid Octaploid B 0.1 mm 8. Explain how DNA methylation is passed on to daughter cells. 9. Explain how bisulfite sequencing helps researchers to detect methylated cytosines. 2 GENE4003 SEM-1 2024 10. The platypus is one of the few extant monotremes, a group of egg-laying mammals that is sister to placental mammals that bear live young. Humans and mice have two genes (Hoxa 7 and Hoxb7) with close homology to the homeobox gene Ultrabithorax in Drosophila melanogaster. A researcher interested in the function of Hox genes in the platypus is comparing two hypothetical gene phylogenies of Ubx homologues from humans, mice, platypus and Drosophila. These are shown below and labelled as Phylogeny A and Phylogeny B. Phylogeny A Hoxa7 (human) Phylogeny B Hoxa7 (human) Hoxa7 (mouse) Hoxa7 (mouse) Hoxb7 (human) Hoxa7 (platypus) Hoxb7 (mouse) Hoxb7 (human) Hoxa7 (platypus) Hoxb7 (mouse) Hoxb7 (platypus) Hoxb7 (platypus) Ubx (Drosophila) Ubx (Drosophila) a) In terms of the relative timing of putative gene duplication events during the evolution of mammals, describe how these two phylogenies differ. Your answer should identify the number of gene duplications and in what lineages they are predicted to have occurred, and should refer to orthologues and paralogues. b) Which phylogeny is most parsimonious, and why? 3