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23. What are the main differences between adherent and suspended cell?
Suspended: no stress fibers, actin mainly distributed as a cortex, no focal
adhesions, roundish cells
Adherent: actin stress fibers and elongated MTs can form, focal adhesion
complexes form, elongated cell form

24. Explain viscoelasticity!

The term viscoelasticity describes that a material (e.g. all biological
materials) has elastic as well as viscous contributions.
 What are stress and strain? How do they differ from force &
elongation?

 You are given a purely viscous/elastic material and apply a constant

step-stress. Sketch the strain response!
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 How can you model viscous/elastic/viscoelastic materials?

Explain the Kelvin-Voigt model, the Maxwell-element and variants of
these options.

25. Name cell probing techniques and explain their specific advantages &
disadvantages!

26. Explain the Optical Stretcher and its working principle!

 Force generation due to optical force generated by refraction on dialectic

material
 Laser has a Gaussian intensity profile with the highest photon density in
the middle, thus forces are higher towards the middle of the beam.
 Cells have a large refractive index than the surrounding, thus momentum
increases when light enters the cell -> due to momentum conservation
momentum in opposite direction arises -> the cell is stretched
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27. What is thermorheology?

Temperature plays a fundamental role in rheology. Based on the empirical
observation that material functions (e.g. creep compliance) show similar shapes
when measured at different temperatures, the concept of time–temperature
superposition (TTS) has been widely used to study the rheological behavior of
polymers for about 70 years. Material functions recorded at different temperatures
can be rescaled to overlap, resulting in a single master curve. The said curve is
frequently used to extend the experimentally accessible time or frequency range,
whereas the scaling factors provide an insight into underlying molecular dynamics.
 Why is this approach important in the Optical Stretcher?

First of all, cells are heated up by the stretch lasers and we have to be able to
account for the heating effects. If the heating is too high, components of the
cells start to denature and cells are killed, which would not be a physiological
response (which is intended to be investigated). Second, passive and active
effects can be decoupled.
 How do different cell types respond?
Some cells behave like a purely passive material and can be modelled with TTS.
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However, if cells are active, i.e. effects are clearly non-equilibrium properties,
TTS does not fit the behavior.

28. Why are cancer cells softer than healthy cells?

Healthy cells are mostly stationary and have a rather compact form. Cancerous
cells change their cytoskeletal composition to become softer in order to be able
to squeeze through densely packed tissues. Also check EMT.

29. What are integrins and cadherins? What are they good for?

 Both are transmembrane receptors

 Integrins couple the cytoskeleton to the ECM
 Cadherins couple the cytoskeletons of neighbouring cells
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30. What are focal adhesions and why are they needed to generate traction
forces?
Focal adhesion complexes facilitate the connection of the cell to the substrate or
surrounding matrix. Due to these connection points, cells are able to propel
themselves forward by generating pulling forces transmitted through these
anchorage points.

31. What are the differences between mature and developing neurons?
Developing neurons have a growth cone while mature neurons for synapsis at the
end of the axon (axonal terminal).
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 What are the differences between dendrites and the axon?

Both extend from the soma, which can have multiple dendrites to receive
information but only one axon to transmit information.

32. What is the growth cone? Explain its key elements and how it is finding its
path! What is stochastic resonance?
A growth cone is a large actin-supported extension of a developing or regenerating
neurite seeking its synaptic target. The morphology of the growth cone can be
easily described by using the hand as an analogy. The fine extensions of the
growth cone are pointed filopodia known as microspikes. The filopodia are like the
"fingers" of the growth cone; they contain bundles of actin filaments (F-actin) that
give them shape and support. Filopodia are the dominant structures in growth
cones, and they appear as narrow cylindrical extensions which can extend several
micrometres beyond the edge of the growth cone. The filopodia are bound by a
membrane which contains receptors, and cell adhesion molecules that are
important for axon growth and guidance. In between filopodia—much like the
webbing of the hands—are the "lamellipodia". These are flat regions of dense actin
meshwork instead of bundled F-actin as in filopodia. They often appear adjacent
to the leading edge of the growth cone and are positioned between two filopodia,
giving them a "veil-like" appearance. In growth cones, new filopodia usually
emerge from these inter-filopodial veils.
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It constantly probes the environment to find the right path to the target region by
growing and retraction phases. Due to this noisy movement, the growth cone can
amplify external stimuli to eventually find the right path.
Stochastic resonance is a phenomenon where a signal that is normally too weak
to be detected by a sensor, can be boosted by adding white noise to the signal,
which contains a wide spectrum of frequencies. The frequencies in the white noise
corresponding to the original signal's frequencies will resonate with each other,
amplifying the original signal while not amplifying the rest of the white noise
(thereby increasing the signal-to-noise ratio which makes the original signal more
prominent). Further, the added white noise can be enough to be detectable by the
sensor, which can then filter it out to effectively detect the original, previously
undetectable signal. This phenomenon of boosting undetectable signals by
resonating with added white noise extends to many other systems, whether
electromagnetic, physical or biological, and is an area of research.

33. What are chemotaxis and durotaxis? Give examples!

Chemotaxis: guidance by chemical cues
Durotaxis: guidance by substrate stiffness

Can a cell move easier on soft or stiff substrates?

34. What are the differences between epithelial and mesenchymal cells? What is
EMT and what are the characteristics?
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EMT: Epithelial to mesenchymal transition

35. What is meant by bifurcation during tissue development?

During development cells can differentiate into more specialized cell types. This
specialization always follows a bifurcation and these cells can never specialize into
three new cell types.

36. What is morphogenesis and embryogenesis? What are compartments?

Morphogenesis is the biological process that causes an organism to develop its
shape. It is one of three fundamental aspects of developmental biology along with
the control of cell growth and cellular differentiation, unified in evolutionary
developmental biology. The process controls the organized spatial distribution of
cells during the embryonic development of an organism. Morphogenesis can take
place also in a mature organism, in cell culture or inside tumor cell masses.
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Morphogenesis also describes the development of unicellular life forms that do not
have an embryonic stage in their life cycle, or describes the evolution of a body
structure within a taxonomic group. Morphogenetic responses may be induced in
organisms by hormones, by environmental chemicals ranging from substances
produced by other organisms to toxic chemicals or radionuclides released as
pollutants, and other plants, or by mechanical stresses induced by spatial
patterning of the cells.
Embryogenesis is the process by which the embryo forms and develops. In
mammals, the term refers chiefly to early stages of prenatal development, whereas
the terms fetus and fetal development describe later stages. Embryonic
development starts with the fertilization of the egg cell (ovum) by a sperm cell,
(spermatozoon). Once fertilized, the ovum is referred to as a zygote, a single
diploid cell. The zygote undergoes mitotic divisions with no significant growth (a
process known as cleavage) and cellular differentiation, leading to development of
a multicellular embryo.
Compartments can be simply defined as separate, different, adjacent cell
populations, which upon juxtaposition, create a lineage boundary. This boundary
prevents cell movement from cells from different lineages across this barrier,
restricting them to their compartment. Subdivisions are established by morphogen
gradients and maintained by local cell-cell interactions, providing functional units
with domains of different regulatory genes, which give rise to distinct fates.
Compartment boundaries are found across species.
37. What is the idea behind inverse morphogenesis during cancer development?
Cancer progresses in the inverse order of the specialization of the tissue during
development.

38. Explain the 2d cell motility assay! Explain random and collective motion!
Some cells move collectively, i.e. the fronts move as a whole (healthy epithelial
cells). Some cell types, however, do not move as a united front but single cells can
detach from the front and move singularly (metastatic cancer cells).
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What hinders migration in tissues?

Geometrical constrictions such as pore sizes -> e.g. nuclei get stuck; strong binding
to neighbors;…

39. How to recognize cytoskeletal structures in fluorescent images of cells:

 Actin: network structures, mostly present at cell periphery; also in bundled
form as stress fibers (finger-like structures pointing outwards and
surrounded by cell membrane)
 Microtubules: Mostly single long filaments; rather stiff (and straight), but can
be bent by large forces or intentional defects in the structure. Reach from
the interior to periphery
 Vimentin (intermediate filament): Soft and thus curvy configuration;
surrounding the nucleus to protect it
 Focal adhesions: Clusters at the end of actin filaments

40. What is jamming in classical granular materials? Name examples

Jamming is the physical process by which the viscosity of some mesoscopic
materials, such as granular materials, glasses, foams, polymers, emulsions, and
other complex fluids, increases with increasing particle density. The jamming
transition has been proposed as a new type of phase transition, with similarities to
a glass transition but very different from the formation of crystalline solids. While a
glass transition occurs when the liquid state is cooled, the jamming transition
happens when density is increased. This crowding of the constituent particles
prevents them from exploring phase space, making the aggregate material behave
as a solid. The system may be able to unjam if volume fraction is decreased, or
external stresses are applied such that they exceed the yield stress.
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What is cell jamming? What are the three parameters spanning the phase
space of jammed cellular systems?
Cells are soft materials and can occupy the entire space while hard spheres, for
instance, can max occupy about 75% of the entire volume. Thus, the packing ratio
of cells is one. Although they fill the entire volume, the system is not necessarily
jammed since other parameters are central.

41. How does cell movement looks like for densities far from and close to the
jamming transition?
Far from jamming transitions: Cells can move rather freely and even as single cells;
no collective motion.
Close to jamming transition: cells move more and more collectively due to
geometrical constraints by their neighbors.
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42. What is the shape parameter? What is the unjamming transition in cellular
systems?

T1 transition: cells can change the position with their neighbor.

Shape parameter = perimeter / (square root of area)