Tuesday, 26 August 2008

botany - How do trees manage to grow equally in all directions?

There are some other good answers which provide part of the picture, but I think there is a fundamental organising principle which has been missed. Konrad has touched on it in his answer.



The reason trees, and most plants, tend to grow equally in all directions is that they have iteratively generated branching and radial symmetry which is controlled in a feedback loop of the growth promoting hormone auxin and auxin-sensitive auxin transporters. This is an elegant biological algorithm which explains all branching growth.



The things Konrad identifies (phototropism, gravitropism, etc.) serve as orientation cues which help the plant determine which axes to grow along, but fundamentally the process is about auxin gradients. There are exceptions, as others have pointed out in their answers, and they usually result from severe imbalances in the orientation cues.



I'll try to explain the growth process clearly (and it gives me an opportunity to try my hand at diagramming again ^_^)...




Auxin is a plant hormone (actually a class of hormones, but mostly when people say auxin, they mean indole-3-acetic acid) which promotes cell elongation and division. The basic principle which allows auxin to act in the organising way it does is that auxin is produced inside cells, and proteins which export auxin from a cell develop on the side of the cell which has the highest auxin concentration (see figure below).



cells export auxin more on the side which has the highest auxin concentration



So auxin gets transported up the concentration gradient of auxin! Thus if you get an area of high auxin concentration developing somehow, more auxin is then transported towards that area. An area of high auxin concentration relative to the surrounding tissue is called an auxin maximum (plural 'maxima').



For most of the life of the plant, auxin is produced pretty much equally in most cells. However, at the very early stages of embryo development, it gets produced preferentially along the embryonic axis (see figure below, part 1). That creates a meristem - a group of cells where cell division is taking place - at the auxin maximum at each end of the embryo. Since this particular meristem is at the apex of the plant, it is called the apical meristem, and it is usually the strongest one in the plant.



auxin patterning of plant growth



So by having a meristem at each end, the embryo then elongates as cell division is only taking place at those points. This leads to part 2 of the image above, where the two meristems get so far apart that the auxin gradient is so weak as to no longer have its organising effect (area in the red square). When that happens, the auxin produced in cells in that area concentrates in a chaotic way for a short time until another center of transport is created. This happens, as the first one did, when a particular area of the tissue has a slightly higher concentration of auxin, and so auxin in the surrounding tissue is transported towards it. This leads to part 3 of the figure, in which two new meristems are created on the sides of the plant (called lateral meristems).



Lateral meristems are where branches occur on plants. If you then imagine this process continuing to iterate over and over, you will see that the branches, as they elongate, will develop meristems at the tips and along the sides. The main stem will also continue elongating, and develop more lateral stems. The root will begin to branch, and those branches will branch, etc. If you can understand how this elegant system works, you understand how plants grow, and why they grow in repeating units as opposed to in a body plan like animals.



It also explains why, if you cut off the tip of a stem, it promotes branching. By removing the apical meristem, you get rid of the auxin gradient and enable the creating of multiple smaller meristems which each develop into branches.



So far I've explained regular branching, but the same system causes the radial symmetry which makes trees (usually) grow in all directions equally...



enter image description here



Imagine taking a cross section through a stem and looking down all the way through it (as depicted crudely above). Just as auxin gradients act to coordinate growth along the length of the plant, they also coordinate it radially, as the maxima will tend to space themselves out as far from one another as possible. That leads to branches growing in all directions equally (on average).



I welcome comments on this answer, as I think its so important to understanding plant growth that I'd like to hone my answer to make it as good as possible.

Friday, 22 August 2008

homework - What is the main general difference between Mitosis and Meiosis?

I found such a clause:




The general principle is that mitosis creates somatic cells and
meiosis creates germ cells.




However, I cannot agree. Each gametogonium needs to go through mitosis before it can enter meiosis I. So in that case mitosis is happening with germ cells so the clause is false.



I would rephrase the sentence to be




The general principle is that meiosis creates only germ cells with the possibility of a decrease in chromosome number, while mitosis can create both somatic and germ cells while the ploidy stays constant.




Ok, not perfect.



How would you say the main general difference between mitosis and meiosis?

Sunday, 17 August 2008

Pipetting damage on cells - Biology

Shear stress $tau$ in this small sizes is usually measured in dyne/cm2 or N/m2 = Pa. The equations betweeen them: $1dyn/cm^2 = 10^{-5}N/cm^2 = 0.1N/m^2 = 0.1Pa$.



What kind of damages zygotes can suffer by pipetting?




Using scanning electron microscopy, we found open holes on the surface
of lysed eggs, indicating failure of the plasma membrane to reseal
after microinjection. No holes were seen in unlysed eggs, but many of
them had membrane alterations suggestive of healed punctures.




Even a small 1.2 dyn/cm2 shear stress induces apoptosis by pipetting zygotes. So zygotes have their critical shear stress level by 1.2 dyn/cm2 and pipetting involves greater forces than 1.2 dyn/cm2.




Shear stress at 1.2 dynes/cm2 induces stress-activated protein
kinase/jun kinase phosphorylation that precedes and causes apoptosis
in embryos (Xie et al., 2006b, Biol Reprod). Pipetting embryos is
necessary for many protocols, from in vitro fertilization to
collecting embryos prior to analyzing gene expression by microarrays.
We sought to determine if pipetting upregulates phosphorylated MAPK8/9
(formerly known as stress-activated protein kinase/jun
kinase/SAPK/JNK1, 2). We found that phosphorylated MAPK8/9, a marker
of MAPK8/9 activation, is upregulated in a dose-dependent manner by
pipetting.




The critical shear stress level is somewhere between 0.01 and 1000 dyn/cm2 by animal cells depending on the cell type and species. (I think the average is somewhere about 50 dyn/cm2, but it is very hard to differentiate between articles mentioning critical shear levels and most lethal shear levels, so the range and the average might be lower.) The death constant (1/h) increases exponentially by increasing the shear stress.




An apparatus for the detailed investigation of the influence of shear
stress on adherent BHK cells was developed. Shear forces between 0.0
and 2.5 N m−2 were studied. The influence on cell viability, cell
morphology, cell lysis, and cell size was determined. Increasing shear
forces as well as increasing exposure duration caused increasing
changes in cell morphology and cell death. A “critical shear stress
level” was determined.





Shear stress related damage to a mouse hybridoma was examined by
Abu-Reesh and Kargi under laminar and turbulent conditions in a
coaxial cylinder Searle viscometer. Cells were exposed to 5 to 100
N/m2 shear stress levels for 0.5 to 3.0 h. At a given shear stress and
exposure time, turbulent shear was much more damaging than laminar
shear as also reported in the past for protozoa and plant cells. Under
turbulent conditions, damage occurred when shear stress exceeded 5
N/m2. Respiratory activity of the cells was damaged earlier than the
cell membrane, thus implying transmission of the stress signal to the
interior of the cell. Cell damage followed first-order kinetics both
in laminar and turbulent environments. For turbulent shear stress
levels of 5 to 30 N/m2, the death rate constant (kd) increased
exponentially with increasing stress level; the kd values varied over
0.1 to 1.0 1/h.





Subconfluent endothelial cultures continuously exposed to 1–5
dynes/cm2 shear proliferate at a rate comparable to that of static
cultures and reach the same saturation density (≃ 1.0–1.5 × 105
cells/cm2 ). When exposed to a laminar shear stress of 5–10 dynes/cm2
, confluent monolayers undergo a time-dependent change in cell shape
from polygonal to ellipsoidal and become uniformly oriented with flow.
Regeneration of linear “wounds” in confluent monolayer appears to be
influenced by the direction of the applied force. Preliminary studies
indicate that certain endothelial cell functions, including fluid
endocytosis, cytoskeletal assembly and nonthrombogenic surface
properties, also are sensitive to shear stress. These observations
suggest that fluid mechanical forces can directly influence
endothelial cell structure and function.





Shear stress above 0.25 dyne/cm(2) resulted in dramatic loss of
podocytes but not of proximal tubular epithelial cells (LLC-PK(1)
cells) after 20 h.





A series of careful studies has been made on blood damage in a
rotational viscometer. Specific attention has been focused on the
effects of solid surface interaction, centrifugal force, air interface
interaction, mixing of sheared and unsheared layers, cell-cell
interaction, and viscous heating. The results show that there is a
threshold shear stress, 1500 dynes/cm2, above which extensive cell
damage is directly due to shear stress, and the various secondary
effects listed above are negligible.





The shear stress threshold of some dinoflagellates (microalgae) is
even lower than that of erythrocytes (0.029 N/m2). For example, a
continuous laminar shear stress level of only 0.0044 N/m2 (equivalent
to a shear rate of 2.2 1/s) has proved lethal to the dinoflagellate
Gonyaulax polyedra.




Other cell types are not necessary as sensitive as animal cells and they don't necessary react with apoptosis (about 10 dyn/cm2) to shear stress, so you have to use necrotic (about 5000 dyn/cm2) forces to destroy them :



cell type                       size                shear sensitivity
microbial cells 1-10μm low
microbial pellets/clumps up to 1cm moderate
plant cells 100μm moderate/high
plant cell aggregates up to 1-2cm high
animal cells 20μm high
animal cells on microcarriers 80-200μm very high
fungi cells 2-10μm moderate/high



Results show that Chinese Hamster Ovaries and Human Embryonic Kidney
cells will enter the apoptotic pathway when subjected to low levels of
hydrodynamic stress (around 2.0 Pa) in oscillating, extensional flow.
In contrast, necrotic death prevails when the cells are exposed to
hydrodynamic stresses around 1.0 Pa in simple shear flow or around
500 Pa in extensional flow.




The shear sensitivity is not determined only by cell type and species, there are many other factors involved:



  • type of cell and species

  • composition and thickness of cell wall when present

  • size and morphology of cell

  • the intensity and nature of shear stress, whether turbulent or laminar, or associated with interfaces (e.g. during bubble rise and rupture)

  • growth history, both short-term (e.g. starvation) and long term adaptation

  • growth medium (trace elements, vitamins, carbon and nitrogen sources)

  • growth rate

  • growth stage

  • type and concentration of shear protective agents if present

Cells can be very sensitive to shear stress caused by turbulent flow, while not so sensitive to shear stress caused by laminar flow.




On the basis of laminar flow viscometriy measurements, a critical
shear stress level of 80-200 N/m2 has been suggested for Morindata
citrifolia cells.



... while for Daucus carota a shear stress level of 50 N/m2 has been
associated with cell damage. In other study, carrot cells in a laminar
flow Couette viscosimeter lost the ability to grow and divide in the
shear stress range of 0.5-100 N/m2. The intracellular enzyme activity
was impaired at shear stress levels above 3000N/m2, but significant
lysis did not occur until a shear stress level of 10.000 N/m2 applied
over a prolonged perioud (>1h).



In contrast to the behavior in laminar flow, the cells were quite
sensitive to turbulent impeller agitation. Impeller tip speeds of ~1.1
m/s lysed a significant proportion of the cells within 40min.




The bubble damage is severe (1000 cells by a single 3.5mm size bubble) because of the cell adherence to the interface of the bubble and the strong forces involved (>1000 dyn/cm2 by stirred bioreactors). The adhesion and so the damage can be reduced with surfactants.




It is proposed that when cells are either attached to, or very near, a
rupturing bubble, the hydrodynamic forces associated with the rupture
are sufficient to kill the cells.



All experiments were conducted with Spodoptera frugiperda (SF-9)
insect cells, in TNM-FH and SFML medium, with and without Pluronic
F-68. Experiments indicate that approximately 1050 cells are killed
per single, 3.5-mm bubble rupture in TNM-FH medium and approximately
the same number of dead cells are present in the upward jet. It was
also observed that the concentration of cells in this upward jet is
higher than the cell suspension in TNM-FH medium without Pluronic F-68
by a factor of two. It is believed that this higher concentration is
the result of cells adhering to the bubble interface. These cells are
swept up into the upward jet during the bubble rupture process.
Finally, it is suggested that a thin layer around the bubble
containing these absorbed cells is the “hypothetical killing volume”
presented by other researchers.





For a hybridoma line, reported that exposure to laminar shear stress
(208 N/m2) in unaerated flow in a cone and plate viscometer led to
substantial loss in cell count and viability within 20 min. At a
constant 180 s exposure, increasing shear stress over 100-350 N/m2
linearly enhanced cell disruption, with >90% of the cells being
destroyed at 350 N/m2 stress level. Shear stres levels associated with
bubble rupture at the surface of a bioreactor may range over 100-300
N/m2. These values are remarkably consistent with shear rates that
damaged hybridomas in unaerated laminar flow experiments.




Smaller hole pipettes cause more damage.




We also examined aspects of the gene transfer procedure that might
influence survival such as the size of injection pipettes and their
taper relative to zygote diameter, possible toxicity of the injection
medium, the timing of injection, and immediate vs. delayed pipette
withdrawal. The only factors that significantly affected cell
viability were pipette size and taper, and timing of injection in
relation to first cleavage. This suggests that zygote viability
correlates inversely with the size of the hole produced by the
injection pipette and that damage to the membrane is less successfully
repaired as the fertilized egg readies itself for division.




It is hard to find anything about the level of shear stress by pipetting. It can be certainly more than 1 dyn/cm2. It has a short duration (at most a few seconds). I think the following factors can influence the shear stress levels by pipetting:



  • pipette type

  • flow speed (faster flow can be more likely turbulent)

  • bubble formation

Probably more factors are involved but I am not a pipetting expert. ;-) I agree with the others, it surely depends on the personal skills e.g. an amateur can create huge bubbles by pipetting, which can kill a lot of cells by formation and disruption...



I agree with Artem that this is an experiment to do especially if the result is important for you. What you need to create a model about pipette damage, are the shear stress levels by pipetting and the critical shear stress levels of the cells. I think it is hard to design and experiment in which you can measure the shear stress levels in your pipettes and there is no flow model for pipetting as far as I know, so it can be a good topic for a thesis or a diploma work.

Saturday, 16 August 2008

microbiology - Are single-celled organisms capable of learning?

I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for "adaptive anticipation" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system.



In the case of E. coli, it has been shown that the bacteria can anticipate the environment it is about to enter. E. coli in the digestive tracts of mammals will typically be exposed to initially a lactose, and then later to a maltose environment as the bacteria pass down through the animal tract. This suggests that upon encountering a lactose environment, maltose operons are induced. I.e., upon encountering lactose, maltose is anticipated. This suggests a "genetic memory" of the sequence of sugar types where lactose is always encountered before maltose.



Further cultures (500 generations) of E. coli in the absence of maltose but in the presence of lactose reduced the maltose operon activity to negligible levels, suggesting that this is an adaptive prediction of environmental changes.



Mitchell, A et al., Adaptive Prediction of environmental changes by microorganisms, 2009, 460, 1038

Tuesday, 12 August 2008

Are there any examples of sudden leaps in evolution?

@kmm and @shigeta provided you with a nice observational account of sudden leaps in large organisms. However, if you want to look at where this is the norm and try to build a mathematical theory then you need to look at something much smaller; the prime candidate is affinity maturation.



In the human immune system, when exposed to an antigen B cells produce antibodies. If it is your first exposure to the antigen then the antibodies produced will probably have very low binding affinity. However, after some exposure time, your B cells will start to produce antibodies with much higher affinities for the antigen and thus you will be able to better fight off the disease. The cool part, is that the antigen produced is tune via an evolutionary process!



There is differential survival, with only antibodies with the highest affinity being able to survive. Variability is introduced by a very high mutation rate in the complementarity determing region (CDR). (Tonegawa, 1983). The length of this evolutionary process is very short, typically a local equilibrium is found after only 6-8 nucleotide changes in CDR (Crews et al., 1981; Tonegawa, 1983; Clark et al., 1985), so you need only a few point mutations to quickly develop a drastically better tuned antibody.



The standard mathematical model for this is Kauffman's NK model. With a protein sequence on $N$ sites, we say that evolution is fast (and we have a sudden leap) if after our fitness landscape changes, we can get to a new local equilibrium in a number of generations that scales with $log N$. Kauffman & Weinberger (1989) showed how this model can be used to study affinity maturation, and showed that to achieve a sudden leap we need high epistasis and low correlations between pointwise mutants. In particular, their model suggests that typical epistasis in the CDR is on the order of 40 proteins (out of the total 112 proteins in the CDR).




References



Clark, S.H., Huppi, K., Ruezinsky, D., Staudt, L., Gerhard, W., & Weigert, M. (1985). Inter- and intraclonal diversity in the antibody response to influenza hemagglutin. J. Exp. Med. 161, 687.



Crews, S., Griffin, J., Huang, H., Calame, K., & Hood, L. (1981). A single V gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. Cell 25, 59.



Kauffman, S. and Weinberger, E. (1989) The NK Model of rugged fitness landscapes and its application to the maturation of the immune response. Journal of Theoretical Biology, 141(2): 211-245



Tonegawa, S. (1983). Somatic generation of antibody diversity. Nature 302, 575.

Sunday, 10 August 2008

bioinorganic chemistry - What is the molecular mechanism of cystine bond formation?

If your question is with respect to a eukaryotic cell, the di-sulfide bridge/bond is formed in the rough endoplasmic reticulum which is an oxidative environment (unlike most other organelles which are reductive). This paper may be of relevance to you:



Pathways for protein disulphide bond formation - Frand et al, Trends Cell Biol. 2000 May;10(5):203-10.

human biology - What causes knuckle "popping" and the feeling of relief that comes from it?

Nobody really knows where it comes from. The currently most popular theory is that pulling the joint apart leads the gases in the joint's cartilage to accumulate and form a bubble which then pops when you let it spring back. The only thing that has been researched is whether it has an effect on the joint, but people who do it regularly don't seem to have any problems with their joints more than anyone else (I'll find the reference once I have time). Apart from that it's hard to get funding for this kind of research because it has little practical use.



Relief like feeling? That must be subjective to you, I used to do it every now and then but I don't remember getting any relief from it. In that case, it's probably the same relief as other people get from picking their nose, their ears, biting their nails, etc. It's called compensation reaction.