Lesson 9

Read the text: Mathematical Challenges in Developmental BiologyJuly 10, 2008 GeneMaths XT software

"The focus of the academic year 2008–09 program of the Mathematical Biosciences Institute at Ohio State University will be Mathematical Challenges in Developmental Biology," says MBI director Avner Friedman. "The year program will feature a broad range of themes, such as tissue movement, morphogenesis and limb growth, neural tube formation, neuroscience in early development, and pattern formation. Mathematics already plays an important role in all these areas, but new challenges abound.

Hans Othmer, one of the organizers of the year-long program, points out that much has been learned in the last two decades about the molecular components involved in signal transduction and gene expression in a number of systems. The focus is now shifting, he says, to understanding how these components are integrated into networks, and how these networks transduce the inputs they receive and produce the desired pattern of gene expression. "Theoreticians can contribute to understanding of the relationship between network topology and functionality, and to the development of mathematical and computational tools for simulating growth, cell movement, and differentiation in developing systems."

Leah Edelstein-Keshet is a co-organizer of a workshop on cell and tissue movement. "The signal transduction pathways involved in cellular polarization and movement in eukaryotic cells, and polarity and differentiation in plants, will be important themes of our workshop," she says. "Such issues are important to morphogenesis in both animals and plants. They are also central in wound healing and invasive cancer." The organizers have designed the workshop to bridge the scales between the level of subcellular molecular mechanisms and the level of tissue functionality.

Neuroscience in early development is another topic that will be considered during the year. In the mammalian nervous system, a classic example of pattern formation is the formation of "maps." "Theories of map formation generally involve an interplay between a number of elements," says Ken Miller, an organizer of the annual program; "one example is the topographic matching of molecular gradients across axons and across the target structure." In recent years, Miller explains, "great progress has been made in elucidating the molecules involved in topographic map formation."

GeneMaths XT is perhaps the most complete and professional software for microarray analysis currently available. Its advanced concept of layers and subsets makes it is possible to work with different layers for different data outputs, for example Cy3 and Cy5, standard deviations, error values, etc., as well as different subsets of genes and/or arrays. Also unique is the full error handling through all analysis, mining, and statistics functions. Further features include:

Active History concept: record and repeat all steps of the analysis through history files and templates

Reliable data normalization for all types of arrays

Interactive querying and pattern matching

Easy plot wizard for all types of plots and graphs

Unsupervised learning through transversal clustering, hierarchical k-means partitioning, PCA, Discriminant Analysis, Self-organizing maps

Supervised learning using neural networks, support-vector machines, k-nearest neighbor

After text activity

I. Reading Exercises:

Exercise 1. Read and memorize using a dictionary:

tissue, a limb, neural tube, transduction,to contribute, cellular, wound, to heal, cancer, mammal, annual

Exercise 2. Answer the questions:

What will the focus of the Mathematical Biosciences Institute at Ohio State University be in 2008-09 year?

What will the program include?

What is the main focus of this program this year?

Why are such issues important to morphogenesis?

What another topic will be considered during the year?

Exercise 3. Match the left part with the right:

1)The focus is now shifting, he says, to understanding how these components are integrated into networks, and how	a) workshop on cell and tissue movement
2) Leah Edelstein-Keshet is a co-organizer of	b)level of subcellular molecular mechanisms and the level of tissue functionality.
3) The organizers have designed the workshop to bridge the scales between	c) another topic that will be considered during the year
4) Neuroscience in early development is	d) these networks transduce the inputs they receive and produce the desired pattern of gene expression

II. Speaking Exercises:

Exercise 1. Describe mathematical challenges in developmental Biology, cell and tissue movement, the molecular components, neuroscience using the suggested words and expressions as in example:

Mathematical Challenges in Developmental Biology,

tissue movement, morphogenesis , limb growth, neural tube formation, neuroscience in early development, and pattern formation.

Example

The year program will feature a broad range of themes, such as tissue movement, morphogenesis and limb growth, neural tube formation, neuroscience in early development, and pattern formation.

cell and tissue movement

eukaryotic ,cells, differentiation , plants, polarization, important, themes ,workshop, movement, cellular

Neuroscience

nervous, example , pattern ,formation, map , an interplay, a number, elements, mammalian , system

Exercise 2. Ask questions to the given answers:

1)Question:______________________________________________________?

Answer: Mathematical Challenges in Developmental Biology 2)Question:______________________________________________________?

Answer: Topographic map formation.

3)Question______________________________________________________?

Answer: Theoreticians can contribute to understanding of the relationship between network topology and functionality

4)Question____________________________________________________?

Answer: The inputs they receive and produce.

III. Writing exercises:

Exercise 1. Complete the sentences with the suggested words: number, molecular,

shifting, integrated, learned

Hans Othmer, one of the organizers of the year-long program, points out that much has been__________ in the last two decades about the_____________components involved in signal transduction and gene expression in a ____________of systems. The focus is now___________, he says, to understanding how these components are___________ into networks

Exercise 2. Fill in the table with words and expressions from the text:

	themes	place	processes
Example They are also central in	-	-	wound healing and invasive cancer
Mathematics already plays an important role
Great progress has been made
Theories of map formation generally

Exercise 3. Compose a story on one of the topics (up to 100 words):

“Mathematical Challenges in Developmental Biology”

“Neuroscience and Maths”