EZO-22306 Key concepts in developmental biology


Studiepunten 6.00

Group work2
Independent study0
Course coordinator(s)dr. ir. S Kranenbarg
Lecturer(s)dr. ir. R Geurts
dr. ir. R Heidstra
dr. ir. S Kranenbarg
Examiner(s)dr. ir. R Heidstra
dr. ir. R Geurts
dr. ir. S Kranenbarg

Language of instruction:

NL and/or EN

Assumed knowledge on:

Fundamentals of genetics and molecular biology (GEN-11806); Structure and function of plants (PPH-10806), Human and animal biology I (EZO-10306); Reproduction of plants (PCB-10803); Modeling biological systems (EZO-23306); Mechanisms of development (MOB-20803); Practical biological chemistry (BIC-10306).

Continuation courses:

Developmental biology of animals (EZO-30306); Regulation of plant development (MOB-30806); Molecular development (MOB-31303).


This course elaborates on the basic mechanisms of development that were introduced in ‘Mechanisms of development’ (MOB-20803). Although plants and animals have developed separately for about 1.6 billion years, an ‘overall logic of development’ can be found when plant and animals are compared. In the present course we will try to deepen our understanding of the mechanisms that underly plant and animal development. We will use several of the mathematical tools that were introduced in ‘Modeling biological systems’ (EZO-23306) to derive a more quantitative description of several developmental mechanisms. Such a quantitative description is required to properly interpret the possibilities and impossibilities of the mechanisms underlying plant and animal development.

The course is designed around six major themes. The first theme is from polarization to gradient formation. In early development, axes are determined in an initially mostly symmetrical embryo. This polarization (or symmetry-breaking) leads to the formation of gradients of signalling molecules. Concentration gradients of these morphogens are crucial to a proper interpretation of the signal. During this theme we will elaborate on the determination of the dorsoventral axis in Drosophila, which we first saw in ‘Mechanisms of development’. Furthermore, we will see how an auxin gradient is formed and maintained during plant root growth.

The second theme is gene network inference. Animal and plant development needs to be regulated, and genes are the producers of regulators such as transcription factors and morphogens. Genes do not function individually, but are part of networks. These networks often have a modular structure and regulate a specific part of development. In this second theme we will see how networks are formed and maintained and we will see examples of how networks regulate development.

Polar growth mechanisms comprise the third theme. We met polarity already in ‘Mechanisms of development’, when we discussed the early steps of Xenopus development. The Xenopus egg showed a clear polarity with a heavily pigmented animal pole and a clear vegetal pole. During this course we will focus on polarity later in development, and in association with cell movement in a particular direction (i.e. polar growth). Gene networks and gradients play an important role in the regulation of the cell’s actin skeleton. We will see how keratocytes are polarized and how they are able to move. In plants, we will try to understand tip growth in roots and pollen tubes.

In the fourth theme dynamic control of pattern formation, we will combine gradients, gene networks, and polarity to understand how detailed patterns are dynamically controlled. We will discover that the mechanism of lateral inhibition plays a crucial role in both the formation of somites in animals, and the formation of root hairs in plants. It will further become clear that communication between cells is essential to pattern formation. The fifth theme is self-organising multicellularity. In this theme you will be introduced to the slime molds, such as Dictyostelium discoideum. This organism provides an interesting example of multicellular organization derived from unicellular organisms in a single life cycle. Plants and animals have also made the transition from unicellular to multicellular organism, albeit over millions of years of evolution. We will see how the previous hemes integrate to explain the social reproductive cycle of Dictyostelium.

The sixth theme is regeneration. Regeneration is a process that is still poorly understood, but it integrates many of the aspects treated in the previous themes as well as many of the topics from ‘Mechanisms of development’. We will try to understand the current state of knowledge and possibly formulate hypothesis on how and why this intriguing phenomenon is so evidently working in amphibians and not in mammals.

The general setup of the course is that each theme is studied by two special topics. Where possible, one of the topics relates to plant development and the other to animal development. The general aspects of each theme and the special topics will be introduced during the lectures. We will end each week with the reading and discussion of a (recent) paper that summarizes the major points of that particular week.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- give examples of how a systems biology approach to developmental biology is essential to a proper understanding of the field;
- interpret and apply the quantitative approaches provided for the analysis of the five phenomena presented in the course (see contents);
- appraise the value of a scientific paper and deduce its contribution to the understanding of particular phenomenon;
- analyse a number of scientific papers on regeneration and combine their content with the content of the course into a coherent presentation;
- exemplify similarities and differences between plant and animal development from a conceptual point of view.


During a typical course week, lectures will be given on Monday and Wednesday morning. On Tuesday and Thursday morning, the students will perform computer cases (in pairs to stimulate discussion about the topic). Students are expected to prepare themselves for both the lectures and the computer cases by reading the course manual. On Friday morning the students should in-class read a paper and answer the questions that are provided. Following the reading, the paper and questions are discussed under supervision of the teacher. At the end of each week the students should write a summary of the key issues of the week.


- written exam with open questions (90%);
- presentation, including discussion (10%);
- 5 compulsory reports (individual), marks count if the average of the other marks is in between 5.0 and 5.5.


A manual is available that presents the contents of this course, and includes the exercises for the tutorials.

Verplicht voor: BBIBiologyBScB: Spec. B - Development and Adaptation5MO